Polynucleotides and polypeptides in plants

The invention relates to plant transcription factor polypeptides, polynucleotides that encode them, homologs from a variety of plant species, and methods of using the polynucleotides and polypeptides to produce transgenic plants having advantageous properties compared to a reference plant. Sequence information related to these polynucleotides and polypeptides can also be used in bioinformatic search methods and is also disclosed.

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Description
RELATIONSHIP TO COPENDING APPLICATIONS

This application claims the benefit of U.S. Non-provisional application Ser. No. 09/837,944; filed Apr. 18, 2001; U.S. Provisional Application No. 60/310,847, filed Aug. 9, 2001; U.S. Non-provisional application Ser. No. 09/934,455, filed Aug. 22, 2001; U.S. Provisional Application No. 60/336,049, filed Nov. 19, 2001; U.S. Provisional Application No. 60/338,692, filed Dec. 11, 2001; U.S. Non-provisional application Ser. No. 10/171,468, filed Jun. 14, 2002; U.S. Non-provisional application Ser. No. 10/225,066, filed Aug. 9, 2002; U.S. Non-provisional application Ser. No. 10/225,067, filed Aug. 9, 2002; and U.S. Non-provisional application Ser. No. 10/225,068, filed Aug. 9, 2002, the contents of which are hereby incorporated by reference in their entirety.

TECHNICAL FIELD

This invention relates to the field of plant biology. More particularly, the present invention pertains to compositions and methods for modifying a plant phenotypically.

BACKGROUND OF THE INVENTION

A plant's traits, such as its biochemical, developmental, or phenotypic characteristics, may be controlled through a number of cellular processes. One important way to manipulate that control is through transcription factors—proteins that influence the expression of a particular gene or sets of genes. Transformed and transgenic plants that comprise cells having altered levels of at least one selected transcription factor, for example, possess advantageous or desirable traits. Strategies for manipulating traits by altering a plant cell's transcription factor content can therefore result in plants and crops with new and/or improved commercially valuable properties.

Transcription factors can modulate gene expression, either increasing or decreasing (inducing or repressing) the rate of transcription. This modulation results in differential levels of gene expression at various developmental stages, in different tissues and cell types, and in response to different exogenous (e.g., environmental) and endogenous stimuli throughout the life cycle of the organism.

Because transcription factors are key controlling elements of biological pathways, altering the expression levels of one or more transcription factors can change entire biological pathways in an organism. For example, manipulation of the levels of selected transcription factors may result in increased expression of economically useful proteins or biomolecules in plants or improvement in other agriculturally relevant characteristics. Conversely, blocked or reduced expression of a transcription factor may reduce biosynthesis of unwanted compounds or remove an undesirable trait. Therefore, manipulating transcription factor levels in a plant offers tremendous potential in agricultural biotechnology for modifying a plant's traits. A number of the agriculturally relevant characteristics of plants, and desirable traits that may be imbued by gene expression are listed below.

Useful Plant Traits

Category: Abiotic Stress; Desired Trait: Chilling Tolerance

The term “chilling sensitivity” has been used to describe many types of physiological damage produced at low, but above freezing, temperatures. Most crops of tropical origins such as soybean, rice, maize and cotton are easily damaged by chilling. Typical chilling damage includes wilting, necrosis, chlorosis or leakage of ions from cell membranes. The underlying mechanisms of chilling sensitivity are not completely understood yet, but probably involve the level of membrane saturation and other physiological deficiencies. For example, photoinhibition of photosynthesis (disruption of photosynthesis due to high light intensities) often occurs under clear atmospheric conditions subsequent to cold late summer/autumn nights. By some estimates, chilling accounts for monetary losses in the United States (U.S.) second only to drought and flooding. For example, chilling may lead to yield losses and lower product quality through the delayed ripening of maize. Another consequence of poor growth is the rather poor ground cover of maize fields in spring, often resulting in soil erosion, increased occurrence of weeds, and reduced uptake of nutrients. A retarded uptake of mineral nitrogen could also lead to increased losses of nitrate into the ground water.

Category: Abiotic Stress; Desired Trait: Freezing Tolerance.

Freezing is a major environmental stress that limits where crops can be grown and reduces yields considerably, depending on the weather in a particular growing season. In addition to exceptionally stressful years that cause measurable losses of billions of dollars, less extreme stress almost certainly causes smaller yield reductions over larger areas to produce yield reductions of similar dollar value every year. For instance, in the U.S., the 1995 early fall frosts are estimated to have caused losses of over one billion dollars to corn and soybeans. The spring of 1998 saw an estimated $200 M of damages to Georgia alone, in the peach, blueberry and strawberry industries. The occasional freezes in Florida have shifted the citrus belt further south due to $100 M or more losses. California sustained $650 M of damage in 1998 to the citrus crop due to a winter freeze. In addition, certain crops such as Eucalyptus, which has the very favorable properties of rapid growth and good wood quality for pulping, are not able to grow in the southeastern states due to occasional freezes.

Inherent winter hardiness of the crop determines in which agricultural areas it can survive the winter. For example, for wheat, the northern central portion of the U.S. has winters that are too cold for good winter wheat crops. Approximately 20% of the U.S. wheat crop is spring wheat, with a market value of $2 billion. Areas growing spring wheat could benefit by growing winter wheat that had increased winter hardiness. Assuming a 25% yield increase when growing winter wheat, this would create $500 M of increased value. Additionally, the existing winter wheat is severely stressed by freezing conditions and should have improved yields with increased tolerance to these stresses. An estimate of the yield benefit of these traits is 10% of the $4.4 billion winter wheat crop in the U.S. or $444 M of yield increase, as well as better survival in extreme freezing conditions that occur periodically.

Thus plants more resistant to freezing, both midwinter freezing and sudden freezes, would protect a farmers' investment, improve yield and quality, and allow some geographies to grow more profitable and productive crops. Additionally, winter crops such as canola, wheat and barley have 25% to 50% yield increases relative to spring planted varieties of the same crops. This yield increase is due to the “head start” the fall planted crop has over the spring planted crop and its reaching maturity earlier while the temperatures, soil moisture and lack of pathogens provide more favorable conditions.

Category: Abiotic Stress; Desired Trait: Salt Tolerance.

One in five hectares of irrigated land is damaged by salt, an important historical factor in the decline of ancient agrarian societies. This condition is only expected to worsen, further reducing the availability of arable land and crop production, since none of the top five food crops—wheat, corn, rice, potatoes, and soybean—can tolerate excessive salt.

Detrimental effects of salt on plants are a consequence of both water deficit resulting in osmotic stress (similar to drought stress) and the effects of excess sodium ions on critical biochemical processes. As with freezing and drought, high saline causes water deficit; the presence of high salt makes it difficult for plant roots to extract water from their environment (Buchanan et al. (2000) in Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, Rockville, Md.). Soil salinity is thus one of the more important variables that determines where a plant may thrive. In many parts of the world, sizable land areas are uncultivable due to naturally high soil salinity. To compound the problem, salination of soils that are used for agricultural production is a significant and increasing problem in regions that rely heavily on agriculture. The latter is compounded by over-utilization, over-fertilization and water shortage, typically caused by climatic change and the demands of increasing population. Salt tolerance is of particular importance early in a plant's lifecycle, since evaporation from the soil surface causes upward water movement, and salt accumulates in the upper soil layer where the seeds are placed. Thus, germination normally takes place at a salt concentration much higher than the mean salt level in the whole soil profile.

Category: Abiotic Stress; Desired Trait: Drought Tolerance.

While much of the weather that we experience is brief and short-lived, drought is a more gradual phenomenon, slowly taking hold of an area and tightening its grip with time. In severe cases, drought can last for many years, and can have devastating effects on agriculture and water supplies. With burgeoning population and chronic shortage of available fresh water, drought is not only the number one weather related problem in agriculture, it also ranks as one of the major natural disasters of all time, causing not only economic damage, but also loss of human lives. For example, losses from the U.S. drought of 1988 exceeded $40 billion, exceeding the losses caused by Hurricane Andrew in 1992, the Mississippi River floods of 1993, and the San Francisco earthquake in 1989. In some areas of the world, the effects of drought can be far more severe. In the Horn of Africa the 1984-1985 drought led to a famine that killed 750,000 people.

Problems for plants caused by low water availability include mechanical stresses caused by the withdrawal of cellular water. Drought also causes plants to become more susceptible to various diseases (Simpson (1981). “The Value of Physiological Knowledge of Water Stress in Plants”, In Water Stress on Plants, (Simpson, G. M., ed.), Praeger, NY, pp. 235-265).

In addition to the many land regions of the world that are too arid for most if not all crop plants, overuse and over-utilization of available water is resulting in an increasing loss of agriculturally-usable land, a process which, in the extreme, results in desertification. The problem is further compounded by increasing salt accumulation in soils, as described above, which adds to the loss of available water in soils.

Category: Abiotic Stress; Desired Trait: Heat Tolerance.

Germination of many crops is very sensitive to temperature. A transcription factor that would enhance germination in hot conditions would be useful for crops that are planted late in the season or in hot climates.

Seedlings and mature plants that are exposed to excess heat may experience heat shock, which may arise in various organs, including leaves and particularly fruit, when transpiration is insufficient to overcome heat stress. Heat also damages cellular structures, including organelles and cytoskeleton, and impairs membrane function (Buchanan, supra).

Heat shock may result a decrease in overall protein synthesis, accompanied by expression of heat shock proteins. Heat shock proteins function as chaperones and are involved in refolding proteins denatured by heat.

Category: Abiotic Stress; Desired Trait: Tolerance to Low Nitrogen and Phosphorus.

The ability of all plants to remove nutrients from their environment is essential to survival. Thus, identification of genes that encode polypeptides with transcription factor activity may allow for the generation of transgenic plants that are better able to make use of available nutrients in nutrient-poor environments.

Among the most important macronutrients for plant growth that have the largest impact on crop yield are nitrogenous and phosphorus-containing compounds. Nitrogen- and phosphorus-containing fertilizers are used intensively in agriculture practices today. An increase in grain crop yields from 0.5 to 1.0 metric tons per hectare to 7 metric tons per hectare accompanied the use of commercial fixed nitrogen fertilizer in production farming (Vance (2001) Plant Physiol. 127: 390-397). Given current practices, in order to meet food production demands in years to come, considerable increases in the amount of nitrogen- and phosphorus-containing fertilizers will be required (Vance, supra).

Nitrogen is the most abundant element in the Earth's atmosphere yet it is one of the most limiting elements to plant growth due to its lack of availability in the soil. Plants obtain N from the soil from several sources including commercial fertilizers, manure and the mineralization of organic matter. The intensive use of N fertilizers in present agricultural practices is problematic, the energy intensive Haber-Bosch process makes N fertilizer and it is estimated that the U.S. uses annually between 3-5% of the nation's natural gas for this process. In addition to the expense of N fertilizer production and the depletion of non-renewable resources, the use of N fertilizers has led to the eutrophication of freshwater ecosystems and the contamination of drinking water due to the runoff of excess fertilizer into ground water supplies.

Phosphorus is second only to N in its importance as a macronutrient for plant growth and to its impact on crop yield. Phosphorus (P) is extremely immobile and not readily available to roots in the soil and is therefore often growth limiting to plants. Inorganic phosphate (Pi) is a constituent of several important molecules required for energy transfer, metabolic regulation and protein activation (Marschner (1995) Mineral Nutrition of Higher Plants, 2nd ed., Academic Press, San Diego, Calif.). Plants have evolved several strategies to help cope with P and N deprivation that include metabolic as well as developmental adaptations. Most, if not all, of these strategies have components that are regulated at the level of transcription and therefore are amenable to manipulation by transcription factors. Metabolic adaptations include increasing the availability of P and N by increasing uptake from the soil though the induction of high affinity and low affinity transporters, and/or increasing its mobilization in the plant. Developmental adaptations include increases in primary and secondary roots, increases in root hair number and length, and associations with mycorrhizal fungi (Bates and Lynch (1996) Plant Cell Environ. 19: 529-538; Harrison (1999) Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 361-389).

Category: Biotic Stress; Desired Trait: Disease Resistance.

Disease management is a significant expense in crop production worldwide. According to EPA reports for 1996 and 1997, U.S. farmers spend approximately $6 billion on fungicides annually. Despite this expenditure, according to a survey conducted by the food and agriculture organization, plant diseases still reduce worldwide crop productivity by 12% and in the United States alone, economic losses due to plant pathogens amounts to 9.1 billion dollars (FAO, 1993). Data from these reports and others demonstrate that despite the availability of chemical control only a small proportion of the losses due to disease can be prevented. Not only are fungicides and anti-bacterial treatments expensive to growers, but their widespread application poses both environmental and health risks. The use of plant biotechnology to engineer disease resistant crops has the potential to make a significant economic impact on agriculture and forestry industries in two ways: reducing the monetary and environmental expense of fungicide application and reducing both pre-harvest and post-harvest crop losses that occur now despite the use of costly disease management practices.

Fungal, bacterial, oomycete, viral, and nematode diseases of plants are ubiquitous and important problems, and often severely impact yield and quality of crop and other plants. A very few examples of diseases of plants include:

    • Powdery mildew, caused by the fungi Erysiphe, Sphaerotheca, Phyllactinia, Microsphaera, Podosphaera, or Uncinula, in, for example, wheat, bean, cucurbit, lettuce, pea, grape, tree fruit crops, as well as roses, phlox, lilacs, grasses, and Euonymus;
    • Fusarium-caused diseases such as Fusarium wilt in cucurbits, Fusarium head blight in barley and wheat, wilt and crown and root rot in tomatoes;
    • Sudden oak death, caused by the oomycete Phytophthora ramorum; this disease was first detected in 1995 in California tan oaks. The disease has since killed more than 100,000 tan oaks, coast live oaks, black oaks, and Shreve's oaks in coastal regions of northern California, and more recently in southwestern Oregon (Roach (2001) National Geographic News, Dec. 6, 2001);
    • Black Sigatoka, a fungal disease caused by Mycosphaerella species that attacks banana foliage, is spreading throughout the regions of the world that are responsible for producing most of the world's banana crop;
    • Eutypa dieback, caused by Eutypa lata, affects a number of crop plants, including vine grape. Eutypa dieback delays shoot emergence, and causes chlorosis, stunting, and tattering of leaves;
    • Pierce's disease, caused by the bacterium Xylella fastidiosa, precludes growth of grapes in the southeastern United States, and threatens the profitable wine grape industry in northern California. The bacterium clogs the vasculature of the grapevines, resulting in foliar scorching followed by slow death of the vines. There is no known treatment for Pierce's disease;
    • Bacterial Spot caused by the bacterium Xanthomonas campestris causes serious disease problems on tomatoes and peppers. It is a significant problem in the Florida tomato industry because it spreads rapidly, especially in warm periods where there is wind-driven rain. Under these conditions, there are no adequate control measures;
    • Diseases caused by viruses of the family Geminiviridae are a growing agricultural problem worldwide. Geminiviruses have caused severe crop losses in tomato, cassaya, and cotton. For instance, in the 1991-1992 growing season in Florida, geminiviruses caused $140 million in damages to the tomato crop (Moffat (1991) Science 286: 1835). Geminiviruses have the ability to recombine between strains to rapidly produce new virulent varieties. Therefore, there is a pressing need for broad-spectrum geminivirus control;
    • The soybean cyst nematode, Heterodera glycines, causes stunting and chlorosis of soybean plants, which results in yield losses or plant death from severe infestation. Annual losses in the United States have been estimated at $1.5 billion (University of Minnesota Extension Service).

The aforementioned pathogens represent a very small fraction of diverse species that seriously affect plant health and yield. For a more complete description of numerous plant diseases, see, for example, Vidhyasekaran (1997) Fungal Pathogenesis in Plants and Crops: Molecular Biology and Host Defense Mechanisms, Marcel Dekker, Monticello, N.Y.), or Agrios (1997) Plant Pathology, Academic Press, New York, N.Y.). Plants that are able to resist disease may produce significantly higher yields and improved food quality. It is thus of considerable importance to find genes that reduce or prevent disease.

Category: Light Response; Desired Trait: Reduced Shade Avoidance.

Shade avoidance describes the process in which plants grown in close proximity attempt to out-compete each other by increasing stem length at the expense of leaf, fruit and storage organ development. This is caused by the plant's response to far-red radiation reflected from leaves of neighboring plants, which is mediated by phytochrome photoreceptors. Close proximity to other plants, as is produced in high-density crop plantings, increases the relative proportion of far-red irradiation, and therefore induces the shade avoidance response. Shade avoidance adversely affects biomass and yield, particularly when leaves, fruits or other storage organs constitute the desired crop (see, for example, Smith (1982) Annu. Rev. Plant Physiol. 33: 481-518; Ballare et al. (1990) Science 247: 329-332; Smith (1995) Annu. Dev. Plant Physiol. Mol. Biol., 46: 289-315; and Schmitt et al. (1995), American Naturalist, 146: 937-953). Alteration of the shade avoidance response in tobacco through alteration of phytochrome levels has been shown to produce an increase in harvest index (leaf biomass/total biomass) at high planting density, which would result in higher yield (Robson et al. (1996) Nature Biotechnol. 14: 995-998).

Category: Flowering Time; Desired Trait: Altered Flowering Time and Flowering Control.

Timing of flowering has a significant impact on production of agricultural products. For example, varieties with different flowering responses to environmental cues are necessary to adapt crops to different production regions or systems. Such a range of varieties have been developed for many crops, including wheat, corn, soybean, and strawberry. Improved methods for alteration of flowering time will facilitate the development of new, geographically adapted varieties.

Breeding programs for the development of new varieties can be limited by the seed-to-seed cycle. Thus, breeding new varieties of plants with multi-year cycles (such as biennials, e.g. carrot, or fruit trees, such as citrus) can be very slow. With respect to breeding programs, there would be a significant advantage in having commercially valuable plants that exhibit controllable and modified periods to flowering (“flowering times”). For example, accelerated flowering would shorten crop and tree breeding programs.

Improved flowering control allows more than one planting and harvest of a crop to be made within a single season. Early flowering would also improve the time to harvest plants in which the flower portion of the plant constitutes the product (e.g., broccoli, cauliflower, and other edible flowers). In addition, chemical control of flowering through induction or inhibition of flowering in plants could provide a significant advantage to growers by inducing more uniform fruit production (e.g., in strawberry)

A sizable number of plants for which the vegetative portion of the plant forms the valuable crop tend to “bolt” dramatically (e.g., spinach, onions, lettuce), after which biomass production declines and product quality diminishes (e.g., through flowering-triggered senescence of vegetative parts). Delay or prevention of flowering may also reduce or preclude dissemination of pollen from transgenic plants.

Category: Growth Rate; Desired Trait: Modified Growth Rate.

For almost all commercial crops, it is desirable to use plants that establish more quickly, since seedlings and young plants are particularly susceptible to stress conditions such as salinity or disease. Since many weeds may outgrow young crops or out-compete them for nutrients, it would also be desirable to determine means for allowing young crop plants to out compete weed species. Increasing seedling growth rate (emergence) contributes to seedling vigor and allows for crops to be planted earlier in the season with less concern for losses due to environmental factors. Early planting helps add days to the critical grain-filling period and increases yield.

Providing means to speed up or slow down plant growth would also be desirable to ornamental horticulture. If such means be provided, slow growing plants may exhibit prolonged pollen-producing or fruiting period, thus improving fertilization or extending harvesting season.

Category: Growth Rate; Desired Trait: Modified Senescence and Cell Death.

Premature senescence, triggered by various plant stresses, can limit production of both leaf biomass and seed yield. Transcription factor genes that suppress premature senescence or cell death in response to stresses can provide means for increasing yield. Delay of normal developmental senescence could also enhance yield, particularly for those plants for which the vegetative part of the plant represents the commercial product (e.g., spinach, lettuce).

Although leaf senescence is thought to be an evolutionary adaptation to recycle nutrients, the ability to control senescence in an agricultural setting has significant value. For example, a delay in leaf senescence in some maize hybrids is associated with a significant increase in yields and a delay of a few days in the senescence of soybean plants can have a large impact on yield. In an experimental setting, tobacco plants engineered to inhibit leaf senescence had a longer photosynthetic lifespan, and produced a 50% increase in dry weight and seed yield (Gan and Amasino (1995) Science 270: 1986-1988). Delayed flower senescence may generate plants that retain their blossoms longer and this may be of potential interest to the ornamental horticulture industry, and delayed foliar and fruit senescence could improve post-harvest shelf-life of produce.

Further, programmed cell death plays a role in other plant responses, including the resistance response to disease, and some symptoms of diseases, for example, as caused by necrotrophic pathogens such as Botrytis cinerea and Sclerotinia sclerotiorum (Dickman et al. Proc. Natl. Acad. Sci., 98: 6957-6962). Localized senescence and/or cell death can be used by plants to contain the spread of harmful microorganisms. A specific localized cell death response, the “hypersensitive response”, is a component of race-specific disease resistance mediated by plant resistance genes. The hypersensitive response is thought to help limit pathogen growth and to initiate a signal transduction pathway that leads to the induction of systemic plant defenses.

Accelerated senescence may be a defense against obligate pathogens, such as powdery mildew, that rely on healthy plant tissue for nutrients. With regard to powdery mildew, Botrytis cinerea and Sclerotinia sclerotiorum and other pathogens, transcription factors that ameliorate cell death and/or damage may reduce the significant economic losses encountered, such as, for example, Botrytis cinerea in strawberry and grape.

Category: Growth Regulator; Desired Trait: Altered Sugar Sensing

Sugars are key regulatory molecules that affect diverse processes in higher plants including germination, growth, flowering, senescence, sugar metabolism and photosynthesis. Sucrose, for example, is the major transport form of photosynthate and its flux through cells has been shown to affect gene expression and alter storage compound accumulation in seeds (source-sink relationships). Glucose-specific hexose-sensing has also been described in plants and is implicated in cell division and repression of “famine” genes (photosynthetic or glyoxylate cycles).

Category: Morphology; Desired Trait: Altered Morphology

Trichomes are branched or unbranched epidermal outgrowths or hair structures on a plant. Trichomes produce a variety of secondary biochemicals such as diterpenes and waxes, the former being important as, for example, insect pheromones, and the latter as protectants against desiccation and herbivorous pests. Since diterpenes also have commercial value as flavors, aromas, pesticides and cosmetics, and potential value as anti-tumor agents and inflammation-mediating substances, they have been both products and the target of considerable research. In most cases where the metabolic pathways are impossible to engineer, increasing trichome density or size on leaves may be the only way to increase plant productivity. Thus, it would be advantageous to discover trichome-affecting transcription factor genes for the purpose of increasing trichome density, size, or type to produce plants that are better protected from insects or that yield higher amounts of secondary metabolites.

The ability to manipulate wax composition, amount, or distribution could modify plant tolerance to drought and low humidity or resistance to insects, as well as plant appearance. In particular, a possible application for a transcription factor gene that reduces wax production in sunflower seed coats would be to reduce fouling during seed oil processing. Antisense or co-suppression of transcription factors involved in wax biosynthesis in a tissue specific manner can be used to specifically alter wax composition, amount, or distribution in those plants and crops from which wax is either a valuable attribute or product or an undesirable constituent of plants.

Other morphological characteristics that may be desirable in plants include those of an ornamental nature. These include changes in seed color, overall color, leaf and flower shape, leaf color, leaf size, or glossiness of leaves. Plants that produce dark leaves may have benefits for human health; flavonoids, for example, have been used to inhibit tumor growth, prevent of bone loss, and prevention lipid oxidation in animals and humans. Plants in which leaf size is increased would likely provide greater biomass, which would be particularly valuable for crops in which the vegetative portion of the plant constitutes the product. Plants with glossy leaves generally produce greater epidermal wax, which, if it could be augmented, resulted in a pleasing appearance for many ornamentals, help prevent desiccation, and resist herbivorous insects and disease-causing agents. Changes in plant or plant part coloration, brought about by modifying, for example, anthocyanin levels, would provide novel morphological features.

In many instances, the seeds of a plant constitute a valuable crop. These include, for example, the seeds of many legumes, nuts and grains. The discovery of means for producing larger seed would provide significant value by bringing about an increase in crop yield.

Plants with altered inflorescence, including, for example, larger flowers or distinctive floral configurations, may have high value in the ornamental horticulture industry.

Modifications to flower structure may have advantageous or deleterious effects on fertility, and could be used, for example, to decrease fertility by the absence, reduction or screening of reproductive components. This could be a desirable trait, as it could be exploited to prevent or minimize the escape of the pollen of genetically modified organisms into the environment.

Manipulation of inflorescence branching patterns may also be used to influence yield and offer the potential for more effective harvesting techniques. For example, a “self pruning” mutation of tomato results in a determinate growth pattern and facilitates mechanical harvesting (Pnueli et al. (2001) Plant Cell 13(12): 2687-2702).

Alterations of apical dominance or plant architecture could create new plant varieties. Dwarf plants may be of potential interest to the ornamental horticulture industry.

Category: Seed Biochemistry; Desired Trait: Altered Seed Oil

The composition of seeds, particularly with respect to seed oil quantity and/or composition, is very important for the nutritional value and production of various food and feed products. Desirable improvements to oils include enhanced heat stability, improved nutritional quality through, for example, reducing the number of calories in seed, increasing the number of calories in animal feeds, or altering the ratio of saturated to unsaturated lipids comprising the oils.

Category: Seed Biochemistry; Desired Trait: Altered Seed Protein

As with seed oils, seed protein content and composition is very important for the nutritional value and production of various food and feed products. Altered protein content or concentration in seeds may be used to provide nutritional benefits, and may also prolong storage capacity, increase seed pest or disease resistance, or modify germination rates. Altered amino acid composition of seeds, through altered protein composition, is also a desired objective for nutritional improvement.

Category: Seed Biochemistry; Desired Trait: Altered Prenyl Lipids.

Prenyl lipids, including the tocopherols, play a role in anchoring proteins in membranes or membranous organelles. Tocopherols have both anti-oxidant and vitamin E activity. Modified tocopherol composition of plants may thus be useful in improving membrane integrity and function, which may mitigate abiotic stresses such as heat stress. Increasing the anti-oxidant and vitamin content of plants through increased tocopherol content can provide useful human health benefits.

Category: Leaf Biochemistry; Desired Trait: Altered Glucosinolate Levels

Increases or decreases in specific glucosinolates or total glucosinolate content can be desirable depending upon the particular application. For example: (i) glucosinolates are undesirable components of the oilseeds used in animal feed, since they produce toxic effects; low-glucosinolate varieties of canola have been developed to combat this problem; (ii) some glucosinolates have anti-cancer activity; thus, increasing the levels or composition of these compounds can be of use in production of nutraceuticals; and (iii) glucosinolates form part of a plant's natural defense against insects; modification of glucosinolate composition or quantity could therefore afford increased protection from herbivores. Furthermore, tissue specific promoters can be used in edible crops to ensure that these compounds accumulate specifically in particular tissues, such as the epidermis, which are not taken for human consumption.

Category: Leaf Biochemistry; Desired Trait: Flavonoid Production.

Expression of transcription factors that increase flavonoid production in plants, including anthocyanins and condensed tannins, may be used to alter pigment production for horticultural purposes, and possibly to increase stress resistance. Flavonoids have antimicrobial activity and could be used to engineer pathogen resistance. Several flavonoid compounds have human health promoting effects such as inhibition of tumor growth, prevention of bone loss and prevention of lipid oxidation. Increased levels of condensed tannins in forage legumes would provide agronomic benefits in ruminants by preventing pasture bloat by collapsing protein foams within the rumen. For a review on the utilities of flavonoids and their derivatives, see Dixon et al. (1999) Trends Plant Sci. 4: 394-400.

The present invention relates to methods and compositions for producing transgenic plants with modified traits, particularly traits that address the agricultural and food needs described in the above background information. These traits may provide significant value in that they allow the plant to thrive in hostile environments, where, for example, temperature, water and nutrient availability or salinity may limit or prevent growth of non-transgenic plants. The traits may also comprise desirable morphological alterations, larger or smaller size, disease and pest resistance, alterations in flowering time, light response, and others.

We have identified polynucleotides encoding transcription factors, developed numerous transgenic plants using these polynucleotides, and have analyzed the plants for a variety of important traits. In so doing, we have identified important polynucleotide and polypeptide sequences for producing commercially valuable plants and crops as well as the methods for making them and using them. Other aspects and embodiments of the invention are described below and can be derived from the teachings of this disclosure as a whole.

SUMMARY OF THE INVENTION

Transgenic plants and methods for producing transgenic plants are provided. The transgenic plants comprise a recombinant polynucleotide having a polynucleotide sequence, or a sequence that is complementary to this polynucleotide sequence, that encodes a transcription factor.

The polynucleotide sequences that encode the transcription factors are listed in the Sequence Listing and include any of any of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO: 459-466; 468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538-539; 541-557; 560-568; 570-586; 595-596; 598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834; 838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965; 968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 1134-1138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 1271-1287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 1393-1394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 1523-1527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 1647-1654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 1738-1742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 1806-1812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 1921-1928; 1931-1936; 1940-1941; 1944-1946, or SEQ ID NO: 2N-1, wherein N=974-1101.

The transcription factors are comprised of polypeptide sequences listed in the Sequence Listing and include any of SEQ ID NO: 2N, wherein N=1-229, SEQ ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537; 540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720-721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910-913; 922-923; 926; 933-934; 943; 953-960; 966-967; 987-988; 994; 1011; 1035-1042; 1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 1176-1186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 1310-1314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 1399-1418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504; 1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 1621-1624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727; 1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813; 1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920; 1929-1930; 1937-1939; 1942-1943; or SEQ ID NO: 2N, wherein N=974-1101.

The transgenic plant that comprises the recombinant polynucleotide has a polynucleotide sequence, or a sequence that is complementary to this polynucleotide sequence, selected from any of the following:

    • (a) a polynucleotide sequence that encodes one of the transcription factor polypeptide sequences of Paragraph 2 of this Summary; or
    • (b) a polynucleotide sequence that comprises one of the polynucleotide sequences of paragraph 3 of this Summary.

The transgenic plant may also comprise a polynucleotide sequence that is a variant of the sequences in (a) and (b) that encode a polypeptide and regulate transcription, including:

    • (c) a sequence variant of the polynucleotide sequences of (a) or (b);
    • (d) an allelic variant of the polynucleotide sequences of (a) or (b);
    • (e) a splice variant of the polynucleotide sequences of (a) or (b);
    • (f) an orthologous sequence of the polynucleotide sequences of (a) or (b);
    • (g) a paralogous sequence of the polynucleotide sequences of (a) or (b);
    • (h) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 70% sequence homology with the polypeptide of (a), and the polypeptide comprises a conserved domain of a transcription factor that regulates transcription; or
    • (i) a polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of one or more polynucleotides of (a) or (b), and the polynucleotide sequence encodes a polypeptide that regulates transcription.

A transcription factor sequence variant is one having at least 26% amino acid sequence similarity, or at least 40% amino acid sequence identity. A preferred transcription factor sequence variant is one having at least 50% amino acid sequence identity and a more preferred transcription factor sequence variant is one having at least 65% amino acid sequence identity to the transcription factor polypeptide sequences of paragraph 3 of this Summary, and that contains at least one functional or structural characteristic of the similar transcription factor polypeptide sequences. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents.

The transcription factor polypeptides of the present invention include at least one conserved domain, and the portions of the polynucleotide sequences encoding the conserved domain generally exhibit at least 70% sequence identity with the aforementioned preferred polynucleotide sequences. In the case of zinc finger transcription factors, the percent identity across the conserved domain may be as low as 50%.

Various types of plants may be used to generate the transgenic plants, including soybean, wheat, corn, potato, cotton, rice, oilseed rape, sunflower, alfalfa, clover, sugarcane, turf, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, watermelon, mint and other labiates, rosaceous fruits, and vegetable brassicas.

The transgenic plant may be monocotyledonous, plant, and the polynucleotide sequences used to transform the transgenic plant may be derived from either a monocot or a dicot plant. Alternatively, the transgenic plant may be a dicotyledonous plant, and the polynucleotide sequences used to transform the transgenic plant may be derived from either a monocot or a dicot plant.

These transgenic plants will generally possess traits that are altered as compared to a control plant, such as a wild-type or non-transformed plant (i.e., the non-transformed plant does not comprise the recombinant polynucleotide), thus producing an phenotype that is altered when compared to the control, wild-type or non-transformed plant. These transgenic plants may also express an altered level of one or more genes associated with a plant trait as compared to the non-transformed plant. The encoded polypeptides in these transgenic plants will generally be expressed and regulate transcription of at least one gene; this gene will generally confer at least one altered trait, phenotype or expression level.

Any of the polynucleotide sequences listed in the Sequence Listing, their complements, and functional variants used to transform the transgenic plants of the present invention may further comprise regulatory elements. The regulatory elements, may comprise, for example, constitutive, inducible, or tissue-specific promoters operably linked to a polynucleotide sequence.

Presently disclosed transcription factor sequences may be used to produce transformed plants with a variety of improved traits. An example of such an altered trait is enhanced tolerance to abiotic stress, such as salt tolerance, chilling conditions, and drought conditions. Salt and drought tolerance, both forms of osmotic stress, may be mediatedin part by increased root growth or increased root hairs relative to a non-transformed, control or wild-type plant. Tolerance to abiotic stresses such as salt, chilling and drought tolerance may confer a number of survival, quality and yield improvements, including improved seed germination and improved seedling vigor, plant survival, as well as improved yield, quality, and range.

Another example of an altered trait that may be conferred by transforming plants with the presently disclosed transcription factor sequences includes altered sugar sensing. Altered sugar sensing may also be used to confer improved seed germination and improved seedling vigor, as well as altered flowering, senescence, sugar metabolism and photosynthesis characteristics.

The invention also pertains to method to produce these transgenic plants.

The present invention also relates to a method of using transgenic plants transformed with the presently disclosed transcription factor sequences, their complements or their variants to grow a progeny plant by crossing the transgenic plant with either itself or another plant, selecting seed that develops as a result of the crossing; and then growing the progeny plant from the seed. The progeny plant will generally express mRNA that encodes a transcription factor: that is, a DNA-binding protein that binds to a DNA regulatory sequence and regulates gene expression, such as that of a plant trait gene. The mRNA will generally be expressed at a level greater than a non-transformed plant; and the progeny plant is characterized by a change in a plant trait compared to the non-transformed plant.

The present invention also pertains to an expression cassette. The expression cassette comprises at least two elements, including:

    • (1) a constitutive, inducible, or tissue-specific promoter; and
    • (2) a recombinant polynucleotide having a polynucleotide sequence, or a complementary polynucleotide sequence thereof, selected from the group consisting of a polynucleotide sequence encoding a (a) polypeptide sequence selected from the transcription factor sequences in the third paragraph of this Summary; or (b) a polynucleotide sequence selected from the transcription factor polynucleotides of second paragraph of this Summary, or (c) sequence variants such as allelic or splice variants of the polynucleotide sequences of (a) or (b), where the sequence variant encodes a polypeptide that regulates transcription. The polynucleotide sequence may also comprise an orthologous or paralogous sequence of the polynucleotide sequences of (a) or (b), with these sequences encoding a polypeptide that regulates transcription, a polynucleotide sequence that encoding a polypeptide having a conserved domain that exhibits 72% or greater sequence homology with the polypeptide of (a), where the polypeptide comprising the conserved domain regulates transcription, or a polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of one or more polynucleotides of (a) or (b), where the latter polynucleotide sequence regulates transcription. In all of these cases, the recombinant polynucleotide is operably linked to the promoter of the expression cassette.

The invention also includes a host cell that comprises the expression cassette. The host cell may be a plant cell, such as, for example, a cell of a crop plant.

The invention also concerns a method for identifying a factor that is modulated by or interacts with a polypeptide of the third paragraph of this Summary. This method is conducted by:expressing the polypeptide in a plant; and then identifying at least one factor that is modulated by or interacts with the polypeptide.

The invention also pertains to a method for identifying at least one downstream polynucleotide sequence that is subject to a regulatory effect of any of the polypeptides of the third paragraph of this Summary. This method includes expressing any of the polypeptides of the third paragraph of this Summary in a plant cell; and then identifying resultant RNA or protein. The latter identification may be carried out with, for example, such methods that include Northern analysis, RT-PCR, microarray gene expression assays, reporter gene expression systems subtractive hybridization, differential display, representational differential analysis, or two-dimensional gel electrophoresis of one or more protein products.

The invention also provides a transgenic plant comprising a polynucleotide encoding a polypeptide with a conserved domain, wherein the conserved domain comprises consecutive amino acid residues Ser-Ser-Lys/Arg-Tyr/Phe-Gly-Val-Val-Pro-Gln-Pro-Asn-Gly-Arg-Typ-Gly-Ala-Gln-Ile-Tyr-Glu-Lys/Arg-His-Gln-Arg-Val-Trp-Leu-Gly-Thr-Phe-Xaa-Glu/Asp-Glu-Glu/Asp-Glu/Asp-Ala-Ala/Val-Arg-Ala/Ser-Tyr-Asp-Val/Ile-Ala/Val-Val/Ala-Xaa-Arg-Phe/Tyr-Arg-Arg/Gly-Arg-Asp-Ala-Val-Thr/Val-Asn-Phe-Lys/Arg of SEQ ID NO: 170, wherein Xaa is any amino acid residue. The invention still further provides a transgenic plant comprising a polynucleotide wherein the polynucleotide sequence is selected from the group consisting of SEQ ID NO: 169, 369, 1159 through 1175, 1949, and 2071. In another embodiment, the invention also provides a transgenic plant comprising a polynucleotide encoding a polypeptide, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 170, 370, 1176 through 1186, 1950, and 2072.

The invention also provides an expression cassette comprising a polynucleotide encoding a polypeptide with a conserved domain, wherein the conserved domain comprises consecutive amino acid residues Ser-Ser-Lys/Arg-Tyr/Phe-Gly-Val-Val-Pro-Gln-Pro-Asn-Gly-Arg-Typ-Gly-Ala-Gln-Ile-Tyr-Glu-Lys/Arg-His-Gln-Arg-Val-Trp-Leu-Gly-Thr-Phe-Xaa-Glu/Asp-Glu-Glu/Asp-Glu/Asp-Ala-Ala/Val-Arg-Ala/Ser-Tyr-Asp-Val/Ile-Ala/Val-Val/Ala-Xaa-Arg-Phe/Tyr-Arg-Arg/Gly-Arg-Asp-Ala-Val-Thr/Val-Asn-Phe-Lys/Arg of SEQ ID NO: 170, wherein Xaa is any amino acid residue. The invention still further provides an expression cassette comprising a polynucleotide sequence is selected from the group consisting of SEQ ID NO: 169, 369, 1159 through 1175, 1949, and 2071. In another embodiment, the invention also provides an expression cassette comprising a polynucleotide encoding a polypeptide, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 170, 370, 1176 through 1186, 1950, and 2072.

The invention also provides a method for producing a modified plant having a polynucleotide encoding a polypeptide with a conserved domain, wherein the conserved domain comprises consecutive amino acid residues Ser-Ser-Lys/Arg-Tyr/Phe-Gly-Val-Val-Pro-Gln-Pro-Asn-Gly-Arg-Typ-Gly-Ala-Gln-Ile-Tyr-Glu-Lys/Arg-His-Gln-Arg-Val-Trp-Leu-Gly-Thr-Phe-Xaa-Glu/Asp-Glu-Glu/Asp-Glu/Asp-Ala-Ala/Val-Arg-Ala/Ser-Tyr-Asp-Val/Ile-Ala/Val-Val/Ala-Xaa-Arg-Phe/Tyr-Arg-Arg/Gly-Arg-Asp-Ala-Val-Thr/Val-Asn-Phe-Lys/Arg of SEQ ID NO: 170, wherein Xaa is any amino acid residue. The invention still further provides a method for producing a modified plant having a polynucleotide, wherein the polynucleotide sequence is selected from the group consisting of SEQ ID NO: 169, 369, 1159 through 1175, 1949, and 2071. In another embodiment, the invention also provides a method for producing a modified plant having a polynucleotide encoding a polypeptide, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 170, 370, 1176 through 1186, 1950, and 2072.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING AND DRAWINGS

The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the invention. The traits associated with the use of the sequences are included in the Examples.

CD-ROM 1 (Copy 1) is a read-only memory computer-readable compact disc and contains a copy of the Sequence Listing in ASCII text format. The Sequence Listing is named “MBI0047.ST25.txt” and is 6,233 kilobytes in size. The copies of the Sequence Listing on the CD-ROM disc are hereby incorporated by reference in their entirety.

CD-ROM2 (Copy 2) is an exact copy of CD-R1 (Copy 1).

CD-ROM3 contains a computer-readable format (CRF) copy of the Sequence Listing as a text (.txt) file.

FIG. 1 shows a conservative estimate of phylogenetic relationships among the orders of flowering plants (modified from Angiosperm Phylogeny Group (1998) Ann. Missouri Bot. Gard. 84: 1-49). Those plants with a single cotyledon (monocots) are a monophyletic clade nested within at least two major lineages of dicots; the eudicots are further divided into rosids and asterids. Arabidopsis is a rosid eudicot classified within the order Brassicales; rice is a member of the monocot order Poales. FIG. 1 was adapted from Daly et al. (2001) Plant Physiol. 127: 1328-1333.

FIG. 2 shows a phylogenic dendogram depicting phylogenetic relationships of higher plant taxa, including clades containing tomato and Arabidopsis; adapted from Ku et al. (2000) Proc. Natl. Acad. Sci. 97: 9121-9126; and Chase et al. (1993) Ann. Missouri Bot. Gard. 80: 528-580.

FIGS. 3A, and 3B show an alignment of G682 (SEQ ID NO: 148) and polynucleotide sequences that are paralogous and orthologous to G682. The alignment was produced using MACVECTOR software (Acceirys, Inc., San Diego, Calif.).

FIGS. 4A, 4B, 4C and 4D show an alignment of G867 (SEQ ID NO: 170) and polynucleotide sequences that are paralogous and orthologous to G867. The alignment was produced using MACVECTOR software (Accelrys, Inc.).

FIGS. 5A, 5B, 5C, 5D, 5E and 5F show an alignment of G912 (SEQ ID NO: 186) and polynucleotide sequences that are paralogous and orthologous to G912. The alignment was produced using MACVECTOR software (Accelrys, Inc.).

DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS

In an important aspect, the present invention relates to polynucleotides and polypeptides, for example, for modifying phenotypes of plants. Throughout this disclosure, various information sources are referred to and/or are specifically incorporated. The information sources include scientific journal articles, patent documents, textbooks, and World Wide Web browser-inactive page addresses, for example. While the reference to these information sources clearly indicates that they can be used by one of skill in the art, each and every one of the information sources cited herein are specifically incorporated in their entirety, whether or not a specific mention of “incorporation by reference” is noted. The contents and teachings of each and every one of the information sources can be relied on and used to make and use embodiments of the invention.

It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a plant” includes a plurality of such plants, and a reference to “a “stress” is a reference to one or more stresses and equivalents thereof known to those skilled in the art, and so forth.

The polynucleotide sequences of the invention encode polypeptides that are members of well-known transcription factor families, including plant transcription factor families, as disclosed in Tables 4-5. Generally, the transcription factors encoded by the present sequences are involved in cellular metabolism, cell differentiation and proliferation and the regulation of growth. Accordingly, one skilled in the art would recognize that by expressing the present sequences in a plant, one may change the expression of autologous genes or induce the expression of introduced genes. By affecting the expression of similar autologous sequences in a plant that have the biological activity of the present sequences, or by introducing the present sequences into a plant, one may alter a plant's phenotype to one with improved traits. The sequences of the invention may also be used to transform a plant and introduce desirable traits not found in the wild-type cultivar or strain. Plants may then be selected for those that produce the most desirable degree of over- or under-expression of target genes of interest and coincident trait improvement.

The sequences of the present invention may be from any species, particularly plant species, in a naturally occurring form or from any source whether natural, synthetic, semi-synthetic or recombinant. The sequences of the invention may also include fragments of the present amino acid sequences. In this context, a “fragment” refers to a fragment of a polypeptide sequence which is at least 5 to about 15 amino acids in length, most preferably at least 14 amino acids, and which retain some biological activity of a transcription factor. Where “amino acid sequence” is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.

As one of ordinary skill in the art recognizes, transcription factors can be identified by the presence of a region or domain of structural similarity or identity to a specific consensus sequence or the presence of a specific consensus DNA-binding site or DNA-binding site motif (see, for example, Riechmann et al. (2000) Science 290: 2105-2110). The plant transcription factors may belong to one of the following transcription factor families: the AP2 (APETALA2) domain transcription factor family (Riechmann and Meyerowitz (1998) Biol. Chem. 379: 633-646); the MYB transcription factor family (ENBib; Martin and Paz-Ares (1997) Trends Genet. 13: 67-73); the MADS domain transcription factor family (Riechmann and Meyerowitz (1997) Biol. Chem. 378: 1079-1101); the WRKY protein family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244: 563-571); the ankyrin-repeat protein family (Zhang et al. (1992) Plant Cell 4: 1575-1588); the zinc finger protein (Z) family (Klug and Schwabe (1995) FASEB J. 9: 597-604); Takatsuji (1998) Cell. Mol. Life Sci. 54:582-596); the homeobox (HB) protein family (Buerglin (1994) in Guidebook to the Homeobox Genes, Duboule (ed.) Oxford University Press); the CAAT-element binding proteins (Forsburg and Guarente (1989) Genes Dev. 3: 1166-1178); the squamosa promoter binding proteins (SPB) (Klein et al. (1996) Mol. Gen. Genet. 1996 250: 7-16); the NAM protein family (Souer et al. (1996) Cell 85: 159-170); the IAA/AUX proteins (Abel et al. (1995) J Mol. Biol. 251: 533-549); the HLH/MYC protein family (Littlewood et al. (1994) Prot. Profile 1: 639-709); the DNA-binding protein (DBP) family (Tucker et al. (1994) EMBO J 13: 2994-3002); the bZIP family of transcription factors (Foster et al. (1994) FASEB J. 8: 192-200); the Box P-binding protein (the BPF-1) family (da Costa e Silva et al. (1993) Plant J. 4: 125-135); the high mobility group (HMG) family (Bustin and Reeves (1996) Prog. Nucl. Acids Res. Mol. Biol. 54: 35-100); the scarecrow (SCR) family (Di Laurenzio et al. (1996) Cell 86: 423-433); the GF14 family (Wu et al. (1997) Plant Physiol. 114: 1421-1431); the polycomb (PCOMB) family (Goodrich et al. (1997) Nature 386: 44-51); the teosinte branched (TEO) family (Luo et al. (1996) Nature 383: 794-799); the ABI3 family (Giraudat et al. (1992) Plant Cell 4: 1251-1261); the triple helix (TH) family (Dehesh et al. (1990) Science 250: 1397-1399); the EIL family (Chao et al. (1997) Cell 89: 1133-44); the AT-HOOK family (Reeves and Nissen (1990) J. Biol. Chem. 265: 8573-8582); the SIFA family (Zhou et al. (1995) Nucleic Acids Res. 23: 1165-1169); the bZIPT2 family (Lu and Ferl (1995) Plant Physiol. 109: 723); the YABBY family (Bowman et al. (1999) Development 126: 2387-96); the PAZ family (Bohmert et al. (1998) EMBO J 17: 170-80); a family of miscellaneous (MISC) transcription factors including the DPBF family (Kim et al. (1997) Plant J. 11: 1237-1251) and the SPF1 family (Ishiguro and Nakamura (1994) Mol. Gen. Genet. 244: 563-571); the GARP family (Hall et al. (1998) Plant Cell 10: 925-936), the TUBBY family (Boggin et al (1999) Science 286: 2119-2125), the heat shock family (Wu (1995) Annu. Rev. Cell Dev. Biol. 11: 441-469), the ENBP family (Christiansen et al. (1996) Plant Mol. Biol. 32: 809-821), the RING-zinc family (Jensen et al. (1998) FEBS Letters 436: 283-287), the PDBP family (Janik et al. (1989) Virology 168: 320-329), the PCF family (Cubas et al. Plant J. (1999) 18: 215-22), the SRS(SHI-related) family (Fridborg et al. (1999) Plant Cell 11: 1019-1032), the CPP (cysteine-rich polycomb-like) family (Cvitanich et al. (2000) Proc. Natl. Acad. Sci. 97: 8163-8168), the ARF (auxin response factor) family (Ulmasov et al. (1999) Proc. Natl. Acad. Sci. 96: 5844-5849), the SWI/SNF family (Collingwood et al. (1999) J. Mol. Endocrinol. 23: 255-275), the ACBF family (Seguin et al. (1997) Plant Mol. Biol. 35: 281-291), PCGL (CG-1 like) family (da Costa e Silva et al. (1994) Plant Mol. Biol. 25: 921-924) the ARID family (Vazquez et al. (1999) Development 126: 733-742), the Jumonji family (Balciunas et al. (2000), Trends Biochem. Sci. 25: 274-276), the bZIP-NIN family (Schauser et al. (1999) Nature 402: 191-195), the E2F family (Kaelin et al. (1992) Cell 70: 351-364) and the GRF-like family (Knaap et al. (2000) Plant Physiol. 122: 695-704). As indicated by any part of the list above and as known in the art, transcription factors have been sometimes categorized by class, family, and sub-family according to their structural content and consensus DNA-binding site motif, for example. Many of the classes and many of the families and sub-families are listed here. However, the inclusion of one sub-family and not another, or the inclusion of one family and not another, does not mean that the invention does not encompass polynucleotides or polypeptides of a certain family or sub-family. The list provided here is merely an example of the types of transcription factors and the knowledge available concerning the consensus sequences and consensus DNA-binding site motifs that help define them as known to those of skill in the art (each of the references noted above are specifically incorporated herein by reference). A transcription factor may include, but is not limited to, any polypeptide that can activate or repress transcription of a single gene or a number of genes. This polypeptide group includes, but is not limited to, DNA-binding proteins, DNA-binding protein binding proteins, protein kinases, protein phosphatases, protein methyltransferases, GTP-binding proteins, and receptors, and the like.

In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the invention described herein, the polynucleotides and polypeptides of the invention have a variety of additional uses. These uses include their use in the recombinant production (i.e., expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like; as substrates for cloning e.g., including digestion or ligation reactions; and for identifying exogenous or endogenous modulators of the transcription factors. A “polynucleotide” is a nucleic acid molecule comprising a plurality of polymerized nucleotides, e.g., at least about 15 consecutive polymerized nucleotides, optionally at least about 30 consecutive nucleotides, at least about 50 consecutive nucleotides. A polynucleotide may be a nucleic acid, oligonucleotide, nucleotide, or any fragment thereof. In many instances, a polynucleotide comprises a nucleotide sequence encoding a polypeptide (or protein) or a domain or fragment thereof. Additionally, the polynucleotide may comprise a promoter, an intron, an enhancer region, a polyadenylation site, a translation initiation site, 5′ or 3′ untranslated regions, a reporter gene, a selectable marker, or the like. The polynucleotide can be single stranded or double stranded DNA or RNA. The polynucleotide optionally comprises modified bases or a modified backbone. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can be combined with carbohydrate, lipids, protein, or other materials to perform a particular activity such as transformation or form a useful composition such as a peptide nucleic acid (PNA). The polynucleotide can comprise a sequence in either sense or antisense orientations. “Oligonucleotide” is substantially equivalent to the terms amplimer, primer, oligoiner, element, target, and probe and is preferably single stranded.

Definitions

A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid.

An “isolated polynucleotide” is a polynucleotide whether naturally occurring or recombinant, that is present outside the cell in which it is typically found in nature, whether purified or not. Optionally, an isolated polynucleotide is subject to one or more enrichment or purification procedures, e.g., cell lysis, extraction, centrifugation, precipitation, or the like.

A “polypeptide” is an amino acid sequence comprising a plurality of consecutive polymerized amino acid residues e.g., at least about 15 consecutive polymerized amino acid residues, optionally at least about 30 consecutive polymerized amino acid residues, at least about 50 consecutive polymerized amino acid residues. In many instances, a polypeptide comprises a polymerized amino acid residue sequence that is a transcription factor or a domain or portion or fragment thereof. A transcription factor can regulate gene expression and may increase or decrease gene expression in a plant. Additionally, the polypeptide may comprise 1) a localization domain, 2) an activation domain, 3) a repression domain, 4) an oligomerization domain, or 5) a DNA-binding domain, or the like. The polypeptide optionally comprises modified amino acid residues, naturally occurring amino acid residues not encoded by a codon, non-naturally occurring amino acid residues.

A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. A “synthetic polypeptide” is a polypeptide created by consecutive polymerization of isolated amino acid residues using methods well known in the art. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild-type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild-type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein.

“Identity” or “similarity” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases “percent identity” and “% identity” refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. “Sequence similarity” refers to the percent similarity in base pair sequence (as determined by any suitable method) between two or more polynucleotide sequences. Two or more sequences can be anywhere from 0-100% similar, or any integer value therebetween. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polynucleotide sequences is a function of the number of identical or matching nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at positions shared by the polypeptide sequences.

“Alignment” refers to a number of DNA or amino acid sequences aligned by lengthwise comparison so that components in common (i.e., nucleotide bases or amino acid residues) may be visually and readily identified. The fraction or percentage of components in common is related to the homology or identity between the sequences. Alignments such as those of FIG. 3, 4, or 5 may be used to identify conserved domains and relatedness within these domains. An alignment may suitably be determined by means of computer programs known in the art, such as MACVECTOR software (1999) (Accelrys, Inc., San Diego, Calif.).

The terms “highly stringent” or “highly stringent condition” refer to conditions that permit hybridization of DNA strands whose sequences are highly complementary, wherein these same conditions exclude hybridization of significantly mismatched DNAs. Polynucleotide sequences capable of hybridizing under stringent conditions with the polynucleotides of the present invention may be, for example, variants of the disclosed polynucleotide sequences, including allelic or splice variants, or sequences that encode orthologs or paralogs of presently disclosed polypeptides. Nucleic acid hybridization methods are disclosed in detail by Kashima et al. (1985) Nature 313:402-404, and Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y (“Sambrook”); and by Haymes et al., “Nucleic Acid Hybridization: A Practical Approach”, IRL Press, Washington, D.C. (1985), which references are incorporated herein by reference.

In general, stringency is determined by the temperature, ionic strength, and concentration of denaturing agents (e.g., formamide) used in a hybridization and washing procedure (for a more detailed description of establishing and determining stringency, see below). The degree to which two nucleic acids hybridize under various conditions of stringency is correlated with the extent of their similarity. Thus, similar nucleic acid sequences from a variety of sources, such as within a plant's genome (as in the case of paralogs) or from another plant (as in the case of orthologs) that may perform similar functions can be isolated on the basis of their ability to hybridize with known transcription factor sequences. Numerous variations are possible in the conditions and means by which nucleic acid hybridization can be performed to isolate transcription factor sequences having similarity to transcription factor sequences known in the art and are not limited to those explicitly disclosed herein. Such an approach may be used to isolate polynucleotide sequences having various degrees of similarity with disclosed transcription factor sequences, such as, for example, transcription factors having 60% identity, or more preferably greater than about 70% identity, most preferably 72% or greater identity with disclosed transcription factors.

The term “equivalog” describes members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families, and otherwise into protein families with other hierarchically defined homology types. This definition is provided at the Institute for Genomic Research (TIGR) website, www.tigr.org; “Terms associated with TIGRFAMs”.

The term “variant”, as used herein, may refer to polynucleotides or polypeptides that differ from the presently disclosed polynucleotides or polypeptides, respectively, in sequence from each other, and as set forth below.

With regard to polynucleotide variants, differences between presently disclosed polynucleotides and their variants are limited so that the nucleotide sequences of the former and the latter are closely similar overall and, in many regions, identical. The degeneracy of the genetic code dictates that many different variant polynucleotides can encode identical and/or substantially similar polypeptides in addition to those sequences illustrated in the Sequence Listing. Due to this degeneracy, differences between presently disclosed polynucleotides and variant nucleotide sequences may be silent in any given region or over the entire length of the polypeptide (i.e., the amino acids encoded by the polynucleotide are the same, and the variant polynucleotide sequence thus encodes the same amino acid sequence in that region or entire length of the presently disclosed polynucleotide. Variant nucleotide sequences may encode different amino acid sequences, in which case such nucleotide differences will result in amino acid substitutions, additions, deletions, insertions, truncations or fusions with respect to the similar disclosed polynucleotide sequences. These variations result in polynucleotide variants encoding polypeptides that share at least one functional characteristic (i.e., a presently disclosed transcription factor and a variant will confer at least one of the same functions to a plant).

Within the scope of the invention is a variant of a nucleic acid listed in the Sequence Listing (except CBF polynucleotide sequences SEQ ID NOs: 1955, 1957, 1959, or 2203), that is, one having a sequence that differs from the one of the polynucleotide sequences in the Sequence Listing, or a complementary sequence, that encodes a functionally equivalent polypeptide (i.e., a polypeptide having some degree of equivalent or similar biological activity) but differs in sequence from the sequence in the Sequence Listing, due to degeneracy in the genetic code.

“Allelic variant” or “polynucleotide allelic variant” refers to any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in phenotypic polymorphism within populations. Gene mutations may be “silent” or may encode polypeptides having altered amino acid sequences. “Allelic variant” and “polypeptide allelic variant” may also be used with respect to polypeptides, and in this case the terms refer to a polypeptide encoded by an allelic variant of a gene.

“Splice variant” or “polynucleotide splice variant” as used herein refers to alternative forms of RNA transcribed from a gene. Splice variation naturally occurs as a result of alternative sites being spliced within a single transcribed RNA molecule or between separately transcribed RNA molecules, and may result in several different forms of mRNA transcribed from the same gene. Thus, splice variants may encode polypeptides having different amino acid sequences, which, in the present context, will have at least one similar function in the organism (splice variation may also give rise to distinct polypeptides having different functions). “Splice variant” or “polypeptide splice variant” may also refer to a polypeptide encoded by a splice variant of a transcribed mRNA.

As used herein, “polynucleotide variants” may also refer to polynucleotide sequences that encode paralogs and orthologs of the presently disclosed polypeptide sequences. “Polypeptide variants” may refer to polypeptide sequences that are paralogs and orthologs of the presently disclosed polypeptide sequences.

Differences between presently disclosed polypeptides and polypeptide variants are limited so that the sequences of the former and the latter are closely similar overall and, in many regions, identical. Presently disclosed polypeptide sequences and similar polypeptide variants may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination. These differences may produce silent changes and result in a functionally equivalent transcription factor. Thus, it will be readily appreciated by those of skill in the art, that any of a variety of polynucleotide sequences is capable of encoding the transcription factors and transcription factor homolog polypeptides of the invention. A polypeptide sequence variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties. Deliberate amino acid substitutions may thus be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the functional or biological activity of the transcription factor is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine. For more detail on conservative substitutions, see Table 2. More rarely, a variant may have “non-conservative” changes, e.g., replacement of a glycine with a tryptophan. Similar minor variations may also include amino acid deletions or insertions, or both. Related polypeptides may comprise, for example, additions and/or deletions of one or more N-linked or O-linked glycosylation sites, or an addition and/or a deletion of one or more cysteine residues. Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted without abolishing functional or biological activity may be found using computer programs well known in the art, for example, DNASTAR software (see U.S. Pat. No. 5,840,544).

The term “plant” includes whole plants, shoot vegetative organs/structures (e.g., leaves, stems and tubers), roots, flowers and floral organs/stiuctures (e.g., bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g., vascular tissue, ground tissue, and the like) and cells (e.g., guard cells, egg cells, and the like), and progeny of same. The class of plants that can be used in the method of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, horsetails, psilophytes, lycophytes, bryophytes, and multicellular algae. (See for example, FIG. 1, adapted from Daly et al. (2001) Plant Physiol. 127: 1328-1333; FIG. 2, adapted from Ku et al. (2000) Proc. Natl. Acad. Sci. 97: 9121-9126; and see also Tudge, in The Variety of Life, Oxford University Press, New York, N.Y. (2000) pp. 547-606).

A “transgenic plant” refers to a plant that contains genetic material not found in a wild-type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes.

A transgenic plant may contain an expression vector or cassette. The expression cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible or constitutive regulatory sequences that allow for the expression of polypeptide. The expression cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant, including seedlings and mature plants, as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell.

“Fragment”, with respect to a polynucleotide, refers to a clone or any part of a polynucleotide molecule that retains a usable, functional characteristic. Useful fragments include oligonucleotides and polynucleotides that may be used in hybridization or amplification technologies or in the regulation of replication, transcription or translation. A polynucleotide fragment” refers to any subsequence of a polynucleotide, typically, of at least about 9 consecutive nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50 nucleotides, of any of the sequences provided herein. Exemplary polynucleotide fragments are the first sixty consecutive nucleotides of the transcription factor polynucleotides listed in the Sequence Listing. Exemplary fragments also include fragments that comprise a region that encodes a conserved domain of a transcription factor.

Fragments may also include subsequences of polypeptides and protein molecules, or a subsequence of the polypeptide. Fragments may have uses in that they may have antigenic potential. In some cases, the fragment or domain is a subsequence of the polypeptide that performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA-binding site or domain that binds to a DNA promoter region, an activation domain, or a domain for protein-protein interactions, and may initiate transcription. Fragments can vary in size from as few as 3 amino acids to the full length of the intact polypeptide, but are preferably at least about 30 amino acids in length and more preferably at least about 60 amino acids in length. Exemplary polypeptide fragments are the first twenty consecutive amino acids of a mammalian protein encoded by are the first twenty consecutive amino acids of the transcription factor polypeptides listed in the Sequence Listing.

Exemplary fragments also include fragments that comprise a conserved domain of a transcription factor. An example of such an exemplary fragment would include amino acid residues 59-124 of G867 (SEQ ID NO: 170), as noted in Table 5.

The invention also encompasses production of DNA sequences that encode transcription factors and transcription factor derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a sequence encoding transcription factors or any fragment thereof.

A “conserved domain” or “conserved region” as used herein refers to a region in heterologous polynucleotide or polypeptide sequences where there is a relatively high degree of sequence identity between the distinct sequences.

With respect to polynucleotides encoding presently disclosed transcription factors, a conserved region is preferably at least 10 base pairs (bp) in length.

A “conserved domain”, with respect to presently disclosed polypeptides refers to a domain within a transcription factor family that exhibits a higher degree of sequence homology, such as at least 26% sequence similarity, at least 16% sequence identity, preferably at least 40% sequence identity, preferably at least 65% sequence identity including conservative substitutions, and more preferably at least 80% sequence identity, and even more preferably at least 85%, or at least about 86%, or at least about 87%, or at least about 88%, or at least about 90%, or at least about 95%, or at least about 98% amino acid residue sequence identity of a polypeptide of consecutive amino acid residues. A fragment or domain can be referred to as outside a conserved domain, outside a consensus sequence, or outside a consensus DNA-binding site that is known to exist or that exists for a particular transcription factor class, family, or sub-family. In this case, the fragment or domain will not include the exact amino acids of a consensus sequence or consensus DNA-binding site of a transcription factor class, family or sub-family, or the exact amino acids of a particular transcription factor consensus sequence or consensus DNA-binding site. Furthermore, a particular fragment, region, or domain of a polypeptide, or a polynucleotide encoding a polypeptide, can be “outside a conserved domain” if all the amino acids of the fragment, region, or domain fall outside of a defined conserved domain(s) for a polypeptide or protein. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents.

As one of ordinary skill in the art recognizes, conserved domains of transcription factors may be identified as regions or domains of identity to a specific consensus sequence (see, for example, Riechmann et al. (2000) supra). Thus, by using alignment methods well known in the art, the conserved domains of the plant transcription factors for each of the following may be determined: the AP2 (APETALA2) domain transcription factor family (Riechmann and Meyerowitz (1998) supra; the MYB transcription factor family (ENBib; Martin and Paz-Ares (1997) supra); the MADS domain transcription factor family (Riechmann and Meyerowitz (1997) supra); the WRKY protein family (Ishiguro and Nakamura (1994) supra); the ankyrin-repeat protein family (Zhang et al. (1992) supra); the zinc finger protein (Z) family (Klug and Schwabe (1995) supra; Takatsuji (1998) supra); the homeobox (HB) protein family (Buerglin (1994) supra); the CAAT-element binding proteins (Forsburg and Guarente (1989) supra); the squamosa promoter binding proteins (SPB) (Klein et al. (1996) supra); the NAM protein family (Souer et al. (1996) supra); the IAA/AUX proteins (Abel et al. (1995) supra); the HLH/MYC protein family (Littlewood et al. (1994) supra); the DNA-binding protein (DBP) family (Tucker et al. (1994) supra); the bZIP family of transcription factors (Foster et al. (1994) supra); the Box P-binding protein (the BPF-1) family (da Costa e Silva et al. (1993) supra); the high mobility group (HMG) family (Bustin and Reeves (1996) supra); the scarecrow (SCR) family (Di Laurenzio et al. (1996) supra); the GF14 family (Wu et al. (1997) supra); the polycomb (PCOMB) family (Goodrich et al. (1997) supra); the teosinte branched (TEO) family (Luo et al. (1996) supra); the ABI3 family (Giraudat et al. (1992) supra); the triple helix (TH) family (Dehesh et al. (1990) supra); the EIL family (Chao et al. (1997) Cell supra); the AT-HOOK family (Reeves and Nissen (1990 supra); the SIFA family (Zhou et al. (1995) supra); the bZIPT2 family (Lu and Ferl (1995) supra); the YABBY family (Bowman et al. (1999) supra); the PAZ family (Bohmert et al. (1998) supra); a family of miscellaneous (MISC) transcription factors including the DPBF family (Kim et al. (1997) supra) and the SPF1 family (Ishiguro and Nakamura (1994) supra); the GARP family (Hall et al. (1998) supra), the TUBBY family (Boggin et al. (1999) supra), the heat shock family (Wu (1995 supra), the ENBP family (Christiansen et al. (1996) supra), the RING-zinc family (Jensen et al. (1998) supra), the PDBP family (Janik et al. (1989) supra), the PCF family (Cubas et al. (1999) supra), the SRS(SHI-related) family (Fridborg et al. (1999) supra), the CPP (cysteine-rich polycomb-like) family (Cvitanich et al. (2000) supra), the ARF (auxin response factor) family (Ulmasov et al. (1999) supra), the SWI/SNF family (Collingwood et al. (1999) supra), the ACBF family (Seguin et al. (1997) supra), PCGL (CG-1 like) family (da Costa e Silva et al. (1994) supra) the ARID family (Vazquez et al. (1999) supra), the Jumonji family, (Balciunas et al. (2000) supra), the bZIP-NIN family (Schauser et al. (1999) supra), the E2F family Kaelin et al. (1992) supra) and the GRF-like family (Knaap et al (2000) supra).

The conserved domains for each of polypeptides of SEQ ID NO: 2N, wherein N=1-229, are listed in Table 5 as described in Example VII. Also, many of the polypeptides of Table 5 have conserved domains specifically indicated by start and stop sites. A comparison of the regions of the polypeptides in SEQ ID NO: 2N, wherein N=1-229, or of those in Table 5, allows one of skill in the art to identify conserved domain(s) for any of the polypeptides listed or referred to in this disclosure, including those in Tables 4-8.

As used herein, a “gene” is a functional unit of inheritance, and in physical terms is a particular segment or sequence of nucleotides along a molecule of DNA (or RNA, in the case of RNA viruses) involved in producing a functional RNA molecule, such as one used for a structural or regulatory role, or a polypeptide chain, such as one used for a structural or regulatory role (an example of the latter would be transcription regulation, as by a transcription factor polypeptide). Polypeptides may then be subjected to subsequent processing such as splicing and/or folding to obtain a functional polypeptide. A gene may be isolated, partially isolated, or be found with an organism's genome. By way of example, a transcription factor gene encodes a transcription factor polypeptide, which may be functional withor without additional processing to function as an initiator of transcription.

Operationally, genes may be defined by the cis-trans test, a genetic test that determines whether two mutations occur in the same gene and which may be used to determine the limits of the genetically active unit (Rieger et al. (1976) Glossary of Genetics and Cytogenetics: Classical and Molecular, 4th ed., Springer Verlag. Berlin). A gene generally includes regions preceding (“leaders”; upstream) and following (“trailers”; downstream) of the coding region. A gene may also include intervening, non-coded sequences, referred to as “introns”, which are located between individual coding segments, referred to as “exons”. Most genes have an identifiable associated promoter region, a regulatory sequence 5′ or upstream of the transcription initiation codon. The function of a gene may also be regulated by enhancers, operators, and other regulatory elements.

A “trait” refers to a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by biochemical techniques, such as detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g. by measuring uptake of carbon dioxide, or by the observation of the expression level of a gene or genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays, or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield, or pathogen tolerance. Any technique can be used to measure the amount of, comparative level of, or difference in any selected chemical compound or macromolecule in the transgenic plants, however.

“Trait modification” refers to a detectable difference in a characteristic in a plant ectopically expressing a polynucleotide or polypeptide of the present invention relative to a plant not doing so, such as a wild-type plant. In some cases, the trait modification can be evaluated quantitatively. For example, the trait modification can entail at least about a 2% increase or decrease in an observed trait (difference), at least a 5% difference, at least about a 10% difference, at least about a 20% difference, at least about a 30%, at least about a 50%, at least about a 70%, or at least about a 100%, or an even greater difference compared with a wild-type plant. It is known that there can be a natural variation in the modified trait. Therefore, the trait modification observed entails a change of the normal distribution of the trait in the plants compared with the distribution observed in wild-type plant.

The term “transcript profile” refers to the expression levels of a set of genes in a cell in a particular state, particularly by comparison with the expression levels of that same set of genes in a cell of the same type in a reference state. For example, the transcript profile of a particular transcription factor in a suspension cell is the expression levels of a set of genes in a cell overexpressing that transcription factor compared with the expression levels of that same set of genes in a suspension cell that has normal levels of that transcription factor. The transcript profile can be presented as a list of those genes whose expression level is significantly different between the two treatments, and the difference ratios. Differences and similarities between expression levels may also be evaluated and calculated using statistical and clustering methods.

“Wild type”, as used herein, refers to a cell, tissue or plant that has not been genetically modified to knock out or overexpress one or more of the presently disclosed transcription factors. Wild-type cells, tissue or plants may be used as controls to compare levels of expression and the extent and nature of trait modification with modified (e.g., transgenic) cells, tissue or plants in which transcription factor expression is altered or ectopically expressed by, for example, knocking out or overexpressing a gene.

“Ectopic expression” or “altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild-type plant or a reference plant of the same species. The pattern of expression may also be compared with a reference expression pattern in a wild-type plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild-type plant, or by expression at a time other than at the time the sequence is expressed in the wild-type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild-type plant. Altered expression may be achieved by, for example, transformation of a plant with an expression cassette having a constitutive or inducible promoter element associated with a transcription factor gene. The resulting expression pattern can thus constitutive or inducible, and be stable or transient. Altered or ectopic expression may also refer to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression by, for example, knocking out a gene's expression by disrupting expression or regulation of the gene with an insertion element.

In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides.

The term “overexpression” as used herein refers to a greater expression level of a gene in a plant, plant cell or plant tissue, compared to expression in a wild-type plant, cell or tissue, at any developmental or temporal stage for the gene. Overexpression can occur when, for example, the genes encoding one or more transcription factors are under the control of a strong expression signal, such as one of the promoters described herein (e.g., the cauliflower mosaic virus 35S transcription initiation region). Overexpression may occur throughout a plant or in specific tissues of the plant, depending on the promoter used, as described below.

Overexpression may take place in plant cells normally lacking expression of polypeptides functionally equivalent or identical to the present transcription factors. Overexpression may also occur in plant cells where endogenous expression of the present transcription factors or functionally equivalent molecules normally occurs, but such normal expression is at a lower level than in the organism or tissues of the overexpressor. Overexpression thus results in a greater than normal production, or “overproduction” of the transcription factor in the plant, cell or tissue.

The term “phase change” refers to a plant's progression from embryo to adult, and, by some definitions, the transition wherein flowering plants gain reproductive competency. It is believed that phase change occurs either after a certain number of cell divisions in the shoot apex of a developing plant, or when the shoot apex achieves a particular distance from the roots. Thus, altering the timing of phase changes may affect a plant's size, which, in turn, may affect yield and biomass.

Traits That May Be Modified in Overexpressing or Knock-Out Plants

Trait modifications of particular interest include those to seed (such as embryo or endosperm), fruit, root, flower, leaf, stem, shoot, seedling or the like, including: enhanced tolerance to environmental conditions including freezing, chilling, heat, drought, water saturation, radiation and ozone; improved tolerance to microbial, fungal or viral diseases; improved tolerance to pest infestations, including insects, nematodes, mollicutes, parasitic higher plants or the like; decreased herbicide sensitivity; improved tolerance of heavy metals or enhanced ability to take up heavy metals; improved growth under poor photoconditions (e.g., low light and/or short day length), or changes in expression levels of genes of interest. Other phenotype that can be modified relate to the production of plant metabolites, such as variations in the production of taxol, tocopherol, tocotrienol, sterols, phytosterols, vitamins, wax monomers, anti-oxidants, amino acids, lignins, cellulose, tannins, prenyllipids (such as chlorophylls and carotenoids), glucosinolates, and terpenoids, enhanced or compositionally altered protein or oil production (especially in seeds), or modified sugar (insoluble or soluble) and/or starch composition. Physical plant characteristics that can be modified include cell development (such as the number of trichomes), fruit and seed size and number, yields of plant parts such as stems, leaves, inflorescences, and roots, the stability of the seeds during storage, characteristics of the seed pod (e.g., susceptibility to shattering), root hair length and quantity, internode distances, or the quality of seed coat. Plant growth characteristics that can be modified include growth rate, germination rate of seeds, vigor of plants and seedlings, leaf and flower senescence, male sterility, apomixis, flowering time, flower abscission, rate of nitrogen uptake, osmotic sensitivity to soluble sugar concentrations, biomass or transpiration characteristics, as well as plant architecture characteristics such as apical dominance, branching patterns, number of organs, organ identity, organ shape or size.

Transcription Factors Modify Expression of Endogenous Genes

Expression of genes that encode transcription factors that modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising isolated polynucleotides encoding transcription factors may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al. (1997) Genes and Development 11: 3194-3205, and Peng et al. (1999) Nature 400: 256-261. In addition, many others have demonstrated that an Arabidopsis transcription factor expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al. (2001) Plant Cell 13: 1791-1802; Nandi et al. (2000, Curr. Biol. 10: 215-218; Coupland (1995) Nature 377: 482-483; and Weigel and Nilsson (1995) Nature 377: 482-500.

In another example, Mandel et al. (1992) Cell 71-133-143 and Suzuki et al. (2001) Plant J. 28: 409-418, teach that a transcription factor expressed in another plant species elicits the same or very similar phenotypic response of the endogenous sequence, as often predicted in earlier studies of Arabidopsis transcription factors in Arabidopsis (see Mandel et al. (1992) supra; Suzuki et al. (2001) supra).

Other examples include Müller et al. (2001) Plant J. 28: 169-179; Kim et al. (2001) Plant J. 25: 247-259; Kyozuka and Shimamoto (2002) Plant Cell Physiol. 43: 130-135; Boss and Thomas (2002) Nature 416: 847-850; He et al. (2000) Transgenic Res. 9: 223-227; and Robson et al. (2001) Plant J. 28: 619-631.

In yet another example, Gilmour et al. (1998) Plant J. 16: 433-442, teach an Arabidopsis AP2 transcription factor, CBF1 (SEQ ID NO: 1956), which, when overexpressed in transgenic plants, increases plant freezing tolerance. Jaglo et al. (2001) Plant Physiol. 127: 910-917, further identified sequences in Brassica napus which encode CBF-like genes and that transcripts for these genes accumulated rapidly in response to low temperature. Transcripts encoding CBF-like proteins were also found to accumulate rapidly in response to low temperature in wheat, as well as in tomato. An alignment of the CBF proteins from Arabidopsis, B. napus, wheat, rye, and tomato revealed the presence of conserved consecutive amino acid residues, PKK/RPAGRxKFxETRHP and DSAWR, that bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family. (See Jaglo et al. supra).

Gao et al. (2002) Plant Molec. Biol. 49: 459-471) have recently described four CBF transcription factors from Brassica napus: BNCBFs 5, 7, 16 and 17. They note that the first three CBFs (GenBank Accession Numbers AAM18958, AAM18959, and AAM18960, respectively) are very similar to Arabidopsis CBF1, whereas BNCBF17 (GenBank Accession Number AAM 18961) is similar but contains two extra regions of 16 and 21 amino acids in its acidic activation domain. All four B. napus CBFs accumulate in leaves of the plants after cold-treatment, and BNCBFs 5, 7, 16 accumulated after salt stress treatment. The authors concluded that these BNCBFs likely function in low-temperature responses in B. napus.

In a functional study of CBF genes, Hsieh et al. ((2002) Plant Physiol. 129: 1086-1094) found that heterologous expression of Arabidopsis CBF1 in tomato plants confers increased tolerance to chilling and considerable tolerance to oxidative stress, which suggested to the authors that ectopic Arabidopsis CBF1 expression may induce several tomato stress responsive genes to protect the plants.

Polypeptides and Polynucleotides of the Invention

The present invention provides, among other things, transcription factors (TFs), and transcription factor homolog polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides, or novel sequence variant polypeptides or polynucleotides encoding novel variants of transcription factors derived from the specific sequences provided here. These polypeptides and polynucleotides may be employed to modify a plant's characteristics.

Exemplary polynucleotides encoding the polypeptides of the invention were identified in the Arabidopsis thaliana GenBank database using publicly available sequence analysis programs and parameters. Sequences initially identified were then further characterized to identify sequences comprising specified sequence strings corresponding to sequence motifs present in families of known transcription factors. In addition, further exemplary polynucleotides encoding the polypeptides of the invention were identified in the plant GenBank database using publicly available sequence analysis programs and parameters. Sequences initially identified were then further characterized to identify sequences comprising specified sequence strings corresponding to sequence motifs present in families of known transcription factors. Polynucleotide sequences meeting such criteria were confirmed as transcription factors.

Additional polynucleotides of the invention were identified by screening Arabidopsis thaliana and/or other plant cDNA libraries with probes corresponding to known transcription factors under low stringency hybridization conditions. Additional sequences, including full length coding sequences were subsequently recovered by the rapid amplification of cDNA ends (RACE) procedure, using a commercially available kit according to the manufacturer's instructions. Where necessary, multiple rounds of RACE are performed to isolate 5′ and 3′ ends. The full-length cDNA was then recovered by a routine end-to-end polymerase chain reaction (PCR) using primers specific to the isolated 5′ and 3′ ends. Exemplary sequences are provided in the Sequence Listing.

The polynucleotides of the invention can be or were ectopically expressed in overexpressor or knockout plants and the changes in the characteristic(s) or trait(s) of the plants observed. Therefore, the polynucleotides and polypeptides can be employed to improve the characteristics of plants.

The polynucleotides of the invention can be or were ectopically expressed in overexpressor plant cells and the changes in the expression levels of a number of genes, polynucleotides, and/or proteins of the plant cells observed. Therefore, the polynucleotides and polypeptides can be employed to change expression levels of a genes, polynucleotides, and/or proteins of plants.

Producing Polypeptides

The polynucleotides of the invention include sequences that encode transcription factors and transcription factor homolog polypeptides and sequences complementary thereto, as well as unique fragments of coding sequence, or sequence complementary thereto. Such polynucleotides can be, e.g., DNA or RNA, e.g., mRNA, cRNA, synthetic RNA, genomic DNA, cDNA synthetic DNA, oligonucleotides, etc. The polynucleotides are either double-stranded or single-stranded, and include either, or both sense (i.e., coding) sequences and antisense (i.e., non-coding, complementary) sequences. The polynucleotides include the coding sequence of a transcription factor, or transcription factor homolog polypeptide, in isolation, in combination with additional coding sequences (e.g., a purification tag, a localization signal, as a fusion-protein, as a pre-protein, or the like), in combination with non-coding sequences (e.g., introns or inteins, regulatory elements such as promoters, enhancers, terminators, and the like), and/or in a vector or host environment in which the polynucleotide encoding a transcription factor or transcription factor homolog polypeptide is an endogenous or exogenous gene.

A variety of methods exist for producing the polynucleotides of the invention. Procedures for identifying and isolating DNA clones are well known to those of skill in the art, and are described in, e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, vol. 152 Academic Press, Inc., San Diego, Calif. (“Berger”); Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., and Current Protocols in Molecular Biology, Ausubel et al. eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2000) (“Ausubel”).

Alternatively, polynucleotides of the invention, can be produced by a variety of in vitro amplification methods adapted to the present invention by appropriate selection of specific or degenerate primers. Examples of protocols sufficient to direct persons of skill through in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qbeta-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA), e.g., for the production of the homologous nucleic acids of the invention are found in Berger (supra), Sambrook (supra), and Ausubel (supra), as well as Mullis et al. (1987) PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Improved methods for cloning in vitro amplified nucleic acids are described in Wallace et al. U.S. Pat. No. 5,426,039. Improved methods for amplifying large nucleic acids by PCR are summarized in Cheng et al. (1994) Nature 369: 684-685 and the references cited therein, in which PCR amplicons of up to 40 kb are generated. One of skill will appreciate that essentially any RNA can be converted into a double stranded DNA suitable for restriction digestion, PCR expansion and sequencing using reverse transcriptase and a polymerase. See, e.g., Ausubel, Sambrook and Berger, all supra.

Alternatively, polynucleotides and oligonucleotides of the invention can be assembled from fragments produced by solid-phase synthesis methods. Typically, fragments of up to approximately 100 bases are individually synthesized and then enzymatically or chemically ligated to produce a desired sequence, e.g., a polynucleotide encoding all or part of a transcription factor. For example, chemical synthesis using the phosphoramidite method is described, e.g., by Beaucage et al. (1981) Tetrahedron Letters 22: 1859-1869; and Matthes et al. (1984) EMBO J. 3: 801-805. According to such methods, oligonucleotides are synthesized, purified, annealed to their complementary strand, ligated and then optionally cloned into suitable vectors. And if so desired, the polynucleotides and polypeptides of the invention can be custom ordered from any of a number of commercial suppliers.

Homologous Sequences

Sequences homologous, i.e., that share significant sequence identity or similarity, to those provided in the Sequence Listing (except CBF sequences SEQ ID NOs: 1955-1960), derived from Arabidopsis thaliana or from other plants of choice, are also an aspect of the invention. Homologous sequences can be derived from any plant including monocots and dicots and in particular agriculturally important plant species, including but not limited to, crops such as soybean, wheat, corn (maize), potato, cotton, rice, rape, oilseed rape (including canola), sunflower, alfalfa, clover, sugarcane, and turf; or fruits and vegetables, such as banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, tomatillo, watermelon, rosaceous fruits (such as apple, peach, pear, cherry and plum) and vegetable brassicas (such as broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi). Other crops, including fruits and vegetables, whose phenotype can be changed and which comprise homologous sequences include barley; rye; millet; sorghum; currant; avocado; citrus fruits such as oranges, lemons, grapefruit and tangerines, artichoke, cherries; nuts such as the walnut and peanut; endive; leek; roots such as arrowroot, beet, cassaya, turnip, radish, yam, and sweet potato; and beans. The homologous sequences may also be derived from woody species, such pine, poplar and eucalyptus, or mint or other labiates. In addition, homologous sequences may be derived from plants that are evolutionarily-related to crop plants, but which may not have yet been used as crop plants. Examples include deadly nightshade (Atropa belladona), related to tomato; jimson weed (Datura strommium), related to peyote; and teosinte (Zea species), related to corn (maize).

Orthologs and Paralogs

Homologous sequences as described above can comprise orthologous or paralogous sequences. Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. Three general methods for defining orthologs and paralogs are described; an ortholog or paralog, including equivalogs, may be identified by one or more of the methods described below.

Orthologs and paralogs are evolutionarily related genes that have similar sequence and similar functions. Orthologs are structurally related genes in different species that are derived by a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event.

Within a single plant species, gene duplication may cause two copies of a particular gene, giving rise to two or more genes with similar sequence and often similar function known as paralogs. A paralog is therefore a similar gene formed by duplication within the same species. Paralogs typically cluster together or in the same clade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLU.S.TAL (Thompson et al. (1994) Nucleic Acids Res. 22: 4673-4680; Higgins et al. (1996) Methods Enzymol. 266: 383-402). Groups of similar genes can also be identified with pair-wise BLAST analysis (Feng and Doolittle (1987) J. Mol. Evol. 25: 351-360). For example, a lade of very similar MADS domain transcription factors from Arabidopsis all share a common function in flowering time (Ratcliffe et al. (2001) Plant Physiol. 126: 122-132), and a group of very similar AP2 domain transcription factors from Arabidopsis are involved in tolerance of plants to freezing (Gilmour et al. (1998) Plant J. 16: 433-442). Analysis of groups of similar genes with similar function that fall within one lade can yield sub-sequences that are particular to the lade. These sub-sequences, known as consensus sequences, can not only be used to define the sequences within each lade, but define the functions of these genes; genes within a lade may contain paralogous sequences, or orthologous sequences that share the same function (see also, for example, Mount (2001), in Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., page 543.)

Speciation, the production of new species from a parental species, can also give rise to two or more genes with similar sequence and similar function. These genes, termed orthologs, often have an identical function within their host plants and are often interchangeable between species without losing function. Because plants have common ancestors, many genes in any plant species will have a corresponding orthologous gene in another plant species. Once a phylogenic tree for a gene family of one species has been constructed using a program such as CLU.S.TAL (Thompson et al. (1994) Nucleic Acids Res. 22: 4673-4680; Higgins et al. (1996) supra) potential orthologous sequences can be placed into the phylogenetic tree and their relationship to genes from the species of interest can be determined. Orthologous sequences can also be identified by a reciprocal BLAST strategy. Once an orthologous sequence has been identified, the function of the ortholog can be deduced from the identified function of the reference sequence.

Transcription factor gene sequences are conserved across diverse eukaryotic species lines (Goodrich et al. (1993) Cell 75: 519-530; Lin et al. (1991) Nature 353: 569-571; Sadowski et al. (1988) Nature 335: 563-564).et al. Plants are no exception to this observation; diverse plant species possess transcription factors that have similar sequences and functions.

Orthologous genes from different organisms have highly conserved functions, and very often essentially identical functions (Lee et al. (2002) Genome Res. 12: 493-502; Remm et al. (2001) J. Mol. Biol. 314: 1041-1052). Paralogous genes, which have diverged through gene duplication, may retain similar functions of the encoded proteins. In such cases, paralogs can be used interchangeably with respect to certain embodiments of the instant invention (for example, transgenic expression of a coding sequence). An example of such highly related paralogs is the CBF family, with three well-defined members in Arabidopsis and at least one ortholog in Brassica napus (SEQ ID NOs: 1956, 1958, 1960, or 2204, respectively), all of which control pathways involved in both freezing and drought stress (Gilmour et al. (1998) Plant J. 16: 433-442; Jaglo et al. (1998) Plant Physiol. 127: 910-917).

The following references represent a small sampling of the many studies that demonstrate that conserved transcription factor genes from diverse species are likely to function similarly (i.e., regulate similar target sequences and control the same traits), and that transcription factors may be transformed into diverse species to confer or improve traits.

(1) The Arabidopsis NPR1 gene regulates systemic acquired resistance (SAR); over-expression of NPR1 leads to enhanced resistance in Arabidopsis. When either Arabidopsis NPR1 or the rice NPR1 ortholog was overexpressed in rice (which, as a monocot, is diverse from Arabidopsis), challenge with the rice bacterial blight pathogen Xanthomonas oryzae pv. Oryzae, the transgenic plants displayed enhanced resistance (Chern et al. (2001) Plant J. 27: 101-113). NPR1 acts through activation of expression of transcription factor genes, such as TGA2 (Fan and Dong (2002) Plant Cell 14: 1377-1389).

(2) E2F genes are involved in transcription of plant genes for proliferating cell nuclear antigen (PCNA). Plant E2Fs share a high degree of similarity in amino acid sequence between monocots and dicots, and are even similar to the conserved domains of the animal E2Fs. Such conservation indicates a functional similarity between plant and animal E2Fs. E2F transcription factors that regulate meristem development act through common cis-elements, and regulate related (PCNA) genes (Kosugi and Ohashi, (2002) Plant J. 29: 45-59).

(3) The ABI5 gene (abscisic acid (ABA) insensitive 5) encodes a basic leucine zipper factor required for ABA response in the seed and vegetative tissues. Co-transformation experiments with ABI5 cDNA constructs in rice protoplasts resulted in specific transactivation of the ABA-inducible wheat, Arabidopsis, bean, and barley promoters. These results demonstrate that sequentially similar ABI5 transcription factors are key targets of a conserved ABA signaling pathway in diverse plants. (Gampala et al. (2001) J. Biol. Chem. 277: 1689-1694).

(4) Sequences of three Arabidopsis GAMYB-like genes were obtained on the basis of sequence similarity to GAMYB genes from barley, rice, and L. temulentum. These three Arabadopsis genes were determined to encode transcription factors (AtMYB33, AtMYB65, and AtMYB 101) and could substitute for a barley GAMYB and control alpha-amylase expression (Gocal et al. (2001) Plant Physiol. 127: 1682-1693).

(5) The floral control gene LEAFY from Arabidopsis can dramatically accelerate flowering in numerous dictoyledonous plants. Constitutive expression of Arabidopsis LEAFY also caused early flowering in transgenic rice (a monocot), with a heading date that was 26-34 days earlier than that of wild-type plants. These observations indicate that floral regulatory genes from Arabidopsis are useful tools for heading date improvement in cereal crops (He et al. (2000) Transgenic Res. 9: 223-227).

(6) Bioactive gibberellins (GAs) are essential endogenous regulators of plant growth. GA signaling tends to be conserved across the plant kingdom. GA signaling is mediated via GAI, a nuclear member of the GRAS family of plant transcription factors. Arabidopsis GAI has been shown to function in rice to inhibit gibberellin response pathways (Fu et al. (2001) Plant Cell 13: 1791-1802).

(7) The Arabidopsis gene SUPERMAN (SUP), encodes a putative transcription factor that maintains the boundary between stamens and carpels. By over-expressing Arabidopsis SUP in rice, the effect of the gene's presence on whorl boundaries was shown to be conserved. This demonstrated that SUP is a conserved regulator of floral whorl boundaries and affects cell proliferation (Nandi et al. (2000) Curr. Biol. 10: 215-218).

(8) Maize, petunia and Arabidopsis myb transcription factors that regulate flavonoid biosynthesis are very genetically similar and affect the same trait in their native species, therefore sequence and function of these myb transcription factors correlate with each other in these diverse species (Borevitz et al. (2000) Plant Cell 12: 2383-2394).

(9) Wheat reduced height-1 (Rht-B1/Rht-D1) and maize dwarf-8 (d8) genes are orthologs of the Arabidopsis gibberellin insensitive (GAI) gene. Both of these genes have been used to produce dwarf grain varieties that have improved grain yield. These genes encode proteins that resemble nuclear transcription factors and contain an SH2-like domain, indicating that phosphotyrosine may participate in gibberellin signaling. Transgenic rice plants containing a mutant GAI allele from Arabidopsis have been shown to produce reduced responses to gibberellin and are dwarfed, indicating that mutant GAI orthologs could be used to increase yield in a wide range of crop species (Peng et al. (1999) Nature 400: 256-261).

Transcription factors that are homologous to the listed sequences will typically share, in at least one conserved domain, at least about 70% amino acid sequence identity, and with regard to zinc finger transcription factors, at least about 50% amino acid sequence identity. More closely related transcription factors can share at least about 70%, or about 75% or about 80% or about 90% or about 95% or about 98% or more sequence identity with the listed sequences, or with the listed sequences but excluding or outside a known consensus sequence or consensus DNA-binding site, or with the listed sequences excluding one or all conserved domain. Factors that are most closely related to the listed sequences share, e.g., at least about 85%, about 90% or about 95% or more % sequence identity to the listed sequences, or to the listed sequences but excluding or outside a known consensus sequence or consensus DNA-binding site or outside one or all conserved domain. At the nucleotide level, the sequences will typically share at least about 40% nucleotide sequence identity, preferably at least about 50%, about 60%, about 70% or about 80% sequence identity, and more preferably about 85%, about 90%, about 95% or about 97% or more sequence identity to one or more of the listed sequences, or to a listed sequence but excluding or outside a known consensus sequence or consensus DNA-binding site, or outside one or all conserved domain. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein. Conserved domains within a transcription factor family may exhibit a higher degree of sequence homology, such as at least 65% amino acid sequence identity including conservative substitutions, and preferably at least 80% sequence identity, and more preferably at least 85%, or at least about 86%, or at least about 87%, or at least about 88%, or at least about 90%, or at least about 95%, or at least about 98% sequence identity. Transcription factors that are homologous to the listed sequences should share at least 30%, or at least about 60%, or at least about 75%, or at least about 80%, or at least about 90%, or at least about 95% amino acid sequence identity over the entire length of the polypeptide or the homolog.

Percent identity can be determined electronically, e.g., by using the MEGALIGN program (DNASTAR, Inc. Madison, Wis.). The MEGALIGN program can create alignments between two or more sequences according to different methods, for example, the clustal method. (See, for example, Higgins and Sharp (1988) Gene 73: 237-244.) The clustal algorithm groups sequences into clusters by examining the distances between all pairs. The clusters are aligned pairwise and then in groups. Other alignment algorithms or programs may be used, including FASTA, BLAST, or ENTREZ, FASTA and BLAST, and which may be used to calculate percent similarity. These are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with or without default settings. ENTREZ is available through the National Center for Biotechnology Information. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences (see U.S. Pat. No. 6,262,333).

Other techniques for alignment are described in Doolittle, R. F. (1996) Methods in Enzymology: Computer Methods for Macromolecular Sequence Analysis, vol. 266, Academic Press, Orlando, Fla., U.S.A. Preferably, an alignment program that permits gaps in the sequence is utilized to align the sequences. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments (see Shpaer (1997) Methods Mol. Biol. 70: 173-187). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. An alternative search strategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves ability to pick up distantly related matches, and is especially tolerant of small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases.

The percentage similarity between two polypeptide sequences, e.g., sequence A and sequence B, is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the two amino acid sequences are not included in determining percentage similarity. Percent identity between polynucleotide sequences can also be counted or calculated by other methods known in the art, e.g., the Jotun Hein method. (See, e.g., Hein (1990) Methods Enzymol. 183: 626-645.) Identity between sequences can also be determined by other methods known in the art, e.g., by varying hybridization conditions (see U.S. patent application Ser. No. 20010010913).

The percent identity between two conserved domains of a transcription factor DNA-binding domain consensus polypeptide sequence can be as low as 16%, as exemplified in the case of GATA1 family of eukaryotic Cys2/Cys2-type zinc finger transcription factors. The DNA-binding domain consensus polypeptide sequence of the GATA1 family is CX2CX17CX2C, where X is any amino acid residue. (See, for example, Takatsuji, supra.) Other examples of such conserved consensus polypeptide sequences with low overall percent sequence identity are well known to those of skill in the art.

Thus, the invention provides methods for identifying a sequence similar or paralogous or orthologous or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an internet or intranet) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions.

In addition, one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to search against a BLOCKS (Bairoch et al. (1997) Nucleic Acids Res. 25: 217-221), PFAM, and other databases which contain previously identified and annotated motifs, sequences and gene functions. Methods that search for primary sequence patterns with secondary structure gap penalties (Smith et al. (1992) Protein Engineering 5: 35-51) as well as algorithms such as Basic Local Alignment Search Tool (BLAST; Altschul (1993) J. Mol. Evol. 36: 290-300; Altschul et al. (1990) supra), BLOCKS (Henikoff and Henikoff (1991) Nucleic Acids Res. 19: 6565-6572), Hidden Markov Models (HMM; Eddy (1996) Curr. Opin. Str. Biol. 6: 361-365; Sonnhammer et al. (1997) Proteins 28: 405-420), and the like, can be used to manipulate and analyze polynucleotide and polypeptide sequences encoded by polynucleotides. These databases, algorithms and other methods are well known in the art and are described in Ausubel et al. (1997; Short Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., unit 7.7) and in Meyers (1995; Molecular Biology and Biotechnology, Wiley VCH, New York, N.Y., p 856-853).

Furthermore, methods using manual alignment of sequences similar or homologous to one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to identify regions of similarity and conserved domains. Such manual methods are well-known of those of skill in the art and can include, for example, comparisons of tertiary structure between a polypeptide sequence encoded by a polynucleotide which comprises a known function with a polypeptide sequence encoded by a polynucleotide sequence which has a function not yet determined. Such examples of tertiary structure may comprise predicted alpha helices, beta-sheets, amphipathic helices, leucine zipper motifs, zinc finger motifs, proline-rich regions, cysteine repeat motifs, and the like.

Orthologs and paralogs of presently disclosed transcription factors may be cloned using compositions provided by the present invention according to methods well known in the art. cDNAs can be cloned using mRNA from a plant cell or tissue that expresses one of the present transcription factors. Appropriate mRNA sources may be identified by interrogating Northern blots with probes designed from the present transcription factor sequences, after which a library is prepared from the mRNA obtained from a positive cell or tissue. Transcription factor-encoding cDNA is then isolated using, for example, PCR, using primers designed from a presently disclosed transcription factor gene sequence, or by probing with a partial or complete cDNA or with one or more sets of degenerate probes based on the disclosed sequences. The cDNA library may be used to transform plant cells. Expression of the cDNAs of interest is detected using, for example, methods disclosed herein such as microarrays, Northern blots, quantitative PCR, or any other technique for monitoring changes in expression. Genomic clones may be isolated using similar techniques to those.

Identifying Polynucleotides or Nucleic Acids by Hybridization

Polynucleotides homologous to the sequences illustrated in the Sequence Listing and tables can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Single stranded polynucleotides hybridize when they associate based on a variety of well characterized physical-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. The stringency of a hybridization reflects the degree of sequence identity of the nucleic acids involved, such that the higher the stringency, the more similar are the two polynucleotide strands. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations (and number thereof, as described in more detail in the references cited above.

Encompassed by the invention are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the transcription factor polynucleotides within the Sequence Listing (excluding CBF sequences SEQ ID NOs: 1955, 1957, 1959, or 2203), and fragments thereof under various conditions of stringency (See, for example, Wahl and Berger (1987) Methods Enzymol. 152: 399-407; and Kimmel (1987) Methods Enzymol. 152: 507-511). In addition to the nucleotide sequences listed in Tables 4 and 5, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.

With regard to hybridization, conditions that are highly stringent, and means for achieving them, are well known in the art. See, for example, Sambrook et al. (1989) “Molecular Cloning: A Laboratory Manual” (2nd ed., Cold Spring Harbor Laboratory); Berger and Kimmel, eds., (1987) “Guide to Molecular Cloning Techniques”, In Methods in Enzymology:152: 467-469; and Anderson and Young (1985) “Quantitative Filter Hybridisation.” In: Hames and Higgins, ed., Nucleic Acid Hybridisation, A Practical Approach. Oxford, IRL Press, 73-111.

Stability of DNA duplexes is affected by such factors as base composition, length, and degree of base pair mismatch. Hybridization conditions may be adjusted to allow DNAs of different sequence relatedness to hybridize. The melting temperature (Tm) is defined as the temperature when 50% of the duplex molecules have dissociated into their constituent single strands. The melting temperature of a perfectly matched duplex, where the hybridization buffer contains formamide as a denaturing agent, may be estimated by the following equation:
DNA-DNA: TmC.)=81.5+16.6(log [Na+])+0.41(% G+C)−0.62(% formamide)−500/L  (1)
DNA-RNA: TmC.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C)2−0.5(% formamide)−820/L  (2)
RNA-RNA: TmC.)=79.8+18.5(log [Na+])+0.58(%G+C)+0.12(%G+C)2−0.35(% formamide)−820/L  (3)

    • where L is the length of the duplex formed, [Na+] is the molar concentration of the sodium ion in the hybridization or washing solution, and % G+C is the percentage of (guanine+cytosine) bases in the hybrid. For imperfectly matched hybrids, approximately 1° C. is required to reduce the melting temperature for each 1-% mismatch.

Hybridization experiments are generally conducted in a buffer of pH between 6.8 to 7.4, although the rate of hybridization is nearly independent of pH at ionic strengths likely to be used in the hybridization buffer (Anderson et al. (1985) supra). In addition, one or more of the following may be used to reduce non-specific hybridization: sonicated salmon sperm DNA or another non-complementary DNA, bovine serum albumin, sodium pyrophosphate, sodium dodecylsulfate (SDS), polyvinyl-pyrrolidone, ficoll and Denhardt's solution. Dextran sulfate and polyethylene glycol 6000 act to exclude DNA from solution, thus raising the effective probe DNA concentration and the hybridization signal within a given unit of time. In some instances, conditions of even greater stringency may be desirable or required to reduce non-specific and/or background hybridization. These conditions may be created with the use of higher temperature, lower ionic strength and higher concentration of a denaturing agent such as formamide.

Stringency conditions can be adjusted to screen for moderately similar fragments such as homologous sequences from distantly related organisms, or to highly similar fragments such as genes that duplicate functional enzymes from closely related organisms. The stringency can be adjusted either during the hybridization step or in the post-hybridization washes. Salt concentration, formamide concentration, hybridization temperature and probe lengths are variables that can be used to alter stringency (as described by the formula above). As a general guidelines high stringency is typically performed at Tm−5oC to Tm−20oC, moderate stringency at Tm−20oC to Tm−35oC and low stringency at Tm−35oC to Tm−50oC for duplex>150 base pairs. Hybridization may be performed at low to moderate stringency (25-50oC below Tm), followed by post-hybridization washes at increasing stringencies. Maximum rates of hybridization in solution are determined empirically to occur at Tm−25oC for DNA-DNA duplex and Tm−15oC for RNA-DNA duplex. Optionally, the degree of dissociation may be assessed after each wash step to determine the need for subsequent, higher stringency wash steps.

High stringency conditions may be used to select for nucleic acid sequences with high degrees of identity to the disclosed sequences. An example of stringent hybridization conditions obtained in a filter-based method such as a Southern or northern blot for hybridization of complementary nucleic acids that have more than 100 complementary residues is about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Conditions used for hybridization may include about 0.02 M to about 0.15 M sodium chloride, about 0.5% to about 5% casein, about 0.02% SDS or about 0.1% N-laurylsarcosine, about 0.001 M to about 0.03 M sodium citrate, at hybridization temperatures between about 50° C. and about 70° C. More preferably, high stringency conditions are about 0.02 M sodium chloride, about 0.5% casein, about 0.02% SDS, about 0.001 M sodium citrate, at a temperature of about 50° C. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire DNA molecule or selected portions, e.g., to a unique subsequence, of the DNA.

Stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate. Increasingly stringent conditions may be obtained with less than about 500 mM NaCl and 50 mM trisodium citrate, to even greater stringency with less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, whereas high stringency hybridization may be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., more preferably of at least about 37° C., and most preferably of at least about 42° C. with formamide present. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS) and ionic strength, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In a preferred embodiment, hybridization will occur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In a more preferred embodiment, hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide. In a most preferred embodiment, hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide. Useful variations on these conditions will be readily apparent to those skilled in the art.

The washing steps that follow hybridization may also vary in stringency; the post-hybridization wash steps primarily determine hybridization specificity, with the most critical factors being temperature and the ionic strength of the final wash solution. Wash stringency can be increased by decreasing salt concentration or by increasing temperature. Stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate. For example, the wash conditions may be under conditions of 0.1×SSC to 2.0×SSC and 0.1% SDS at 50-65° C., with, for example, two steps of 10-30 min. One example of stringent wash conditions includes about 2.0×SSC, 0.1% SDS at 65° C. and washing twice, each wash step being about 30 min. A higher stringency wash is about 0.2×SSC, 0.1% SDS at 65° C. and washing twice for 30 min. A still higher stringency wash is about 0.1×SSC, 0.1% SDS at 65° C. and washing twice for 30 min. The temperature for the wash solutions will ordinarily be at least about 25° C., and for greater stringency at least about 42° C. Hybridization stringency may be increased further by using the same conditions as in the hybridization steps, with the wash temperature raised about 3° C. to about 5° C., and stringency may be increased even further by using the same conditions except the wash temperature is raised about 6° C. to about 9° C. For identification of less closely related homolog, wash steps may be performed at a lower temperature, e.g., 50° C.

An example of a low stringency wash step employs a solution and conditions of at least 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS over 30 min. Greater stringency may be obtained at 42° C. in 15 mM NaCl, with 1.5 mM trisodium citrate, and 0.1% SDS over 30 min. Even higher stringency wash conditions are obtained at 65° C.-68° C. in a solution of 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Wash procedures will generally employ at least two final wash steps. Additional variations on these conditions will be readily apparent to those skilled in the art (see, for example, U.S. patent application Ser. No. 20010010913).

Stringency conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-10× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a transcription factor known as of the filing date of the application. It may be desirable to select conditions for a particular assay such that a higher signal to noise ratio, that is, about 15× or more, is obtained. Accordingly, a subject nucleic acid will hybridize to a unique coding oligonucleotide with at least a 2× or greater signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a calorimetric label, a radioactive label, or the like. Labeled hybridization or PCR probes for detecting related polynucleotide sequences may be produced by oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.

Identifying Polynucleotides or Nucleic Acids with Expression Libraries

In addition to hybridization methods, transcription factor homolog polypeptides can be obtained by screening an expression library using antibodies specific for one or more transcription factors. With the provision herein of the disclosed transcription factor, and transcription factor homolog nucleic acid sequences, the encoded polypeptide(s) can be expressed and purified in a heterologous expression system (e.g., E. coli) and used to raise antibodies (monoclonal or polyclonal) specific for the polypeptide(s) in question. Antibodies can also be raised against synthetic peptides derived from transcription factor, or transcription factor homolog, amino acid sequences. Methods of raising antibodies are well known in the art and are described in Harlow and Lane (1988), Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. Such antibodies can then be used to screen an expression library produced from the plant from which it is desired to clone additional transcription factor homologs, using the methods described above. The selected cDNAs can be confirmed by sequencing and enzymatic activity.

Sequence Variations

It will readily be appreciated by those of skill in the art, that any of a variety of polynucleotide sequences are capable of encoding the transcription factors and transcription factor homolog polypeptides of the invention. Due to the degeneracy of the genetic code, many different polynucleotides can encode identical and/or substantially similar polypeptides in addition to those sequences illustrated in the Sequence Listing (except CBF polypeptide sequences SEQ ID NOs: 1956, 1958, 1960, or 2204). Nucleic acids having a sequence that differs from the sequences shown in the Sequence Listing, or complementary sequences, that encode functionally equivalent peptides (i.e., peptides having some degree of equivalent or similar biological activity) but differ in sequence from the sequence shown in the Sequence Listing due to degeneracy in the genetic code, are also within the scope of the invention.

Altered polynucleotide sequences encoding polypeptides include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polynucleotide encoding a polypeptide with at least one functional characteristic of the instant polypeptides. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding the instant polypeptides, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding the instant polypeptides.

Allelic variant refers to any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in phenotypic polymorphism within populations. Gene mutations can be silent (i.e., no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequence. The term allelic variant is also used herein to denote a protein encoded by an allelic variant of a gene. Splice variant refers to alternative forms of RNA transcribed from a gene. Splice variation arises naturally through use of alternative splicing sites within a transcribed RNA molecule, or less commonly between separately transcribed RNA molecules, and may result in several mRNAs transcribed from the same gene. Splice variants may encode polypeptides having altered amino acid sequence. The term splice variant is also used herein to denote a protein encoded by a splice variant of an mRNA transcribed from a gene.

Those skilled in the art would recognize that, for example, G28, SEQ ID NO: 10, represents a single transcription factor; allelic variation and alternative splicing may be expected to occur. Allelic variants of SEQ ID NO: 9 can be cloned by probing cDNA or genomic libraries from different individual organisms according to standard procedures. Allelic variants of the DNA sequence shown in SEQ ID NO: 9, including those containing silent mutations and those in which mutations result in amino acid sequence changes, are within the scope of the present invention, as are proteins which are allelic variants of SEQ ID NO: 10. cDNAs generated from alternatively spliced mRNAs, which retain the properties of the transcription factor are included within the scope of the present invention, as are polypeptides encoded by such cDNAs and mRNAs. Allelic variants and splice variants of these sequences can be cloned by probing cDNA or genomic libraries from different individual organisms or tissues according to standard procedures known in the art (see U.S. Pat. No. 6,388,064).

Thus, in addition to the sequences set forth in the Sequence Listing (except CBF sequences), the invention also encompasses related nucleic acid molecules that include allelic or splice variants of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO: 459-466; 468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538-539; 541-557; 560-568; 570-586; 595-596; 598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834; 838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965; 968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 1134-1138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 1271-1287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 1393-1394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 1523-1527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 1647-1654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 1738-1742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 1806-1812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 1921-1928; 1931-1936; 1940-1941; 1944-1946, or SEQ ID NO: 2N-1, wherein N=974-1101, and include sequences which are complementary to any of the above nucleotide sequences. Related nucleic acid molecules also include nucleotide sequences encoding a polypeptide comprising or consisting essentially of a substitution, modification, addition and/or deletion of one or more amino acid residues compared to the polypeptide as set forth in any of SEQ ID NO: 2N, wherein N=1-229, SEQ ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537; 540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720-721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910-913; 922-923; 926; 933-934; 943; 953-960; 966-967; 987-988; 994; 1011; 1035-1042; 1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 1176-1186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 1310-1314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 1399-1418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504; 1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 1621-1624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727; 1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813; 1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920; 1929-1930; 1937-1939; 1942-1943; or SEQ ID NO: 2N, wherein N=974-1101. Such related polypeptides may comprise, for example, additions and/or deletions of one or more N-linked or O-linked glycosylation sites, or an addition and/or a deletion of one or more cysteine residues.

For example, Table 1 illustrates, e.g., that the codons AGC, AGT, TCA, TCC, TCG, and TCT all encode the same amino acid: serine. Accordingly, at each position in the sequence where there is a codon encoding serine, any of the above trinucleotide sequences can be used without altering the encoded polypeptide.

TABLE 1 Amino acid Possible Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys C TGC TGT Aspartic acid Asp D GAC GAT Glutamic acid Glu B GAA GAG Phenylalanine Phe F TTC TTT Glycine Gly C GGA GGC GGG GGT Histidine His H CAC CAT Isoleucine Ile I ATA ATC ATT Lysine Lys K AAA AAG Leucine Leu L TTA TTG CTA CTC CTG CTT Methionine Met M ATG Asparagine Asn N AAC AAT Proline Pro P CCA CCC CCG CCT Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGT Serine Ser S AGC AGT TCA TCC TCG TCT Threonine Thr T ACA ACC ACG ACT Valine Val V GTA GTC GTG GTT Tryptophan Trp W TGG Tyrosine Tyr Y TAC TAT

Sequence alterations that do not change the amino acid sequence encoded by the polynucleotide are termed “silent” variations. With the exception of the codons ATG and TGG, encoding methionine and tryptophan, respectively, any of the possible codons for the same amino acid can be substituted by a variety of techniques, e.g., site-directed mutagenesis, available in the art. Accordingly, any and all such variations of a sequence selected from the above table are a feature of the invention.

In addition to silent variations, other conservative variations that alter one, or a few amino acids in the encoded polypeptide, can be made without altering the function of the polypeptide, these conservative variants are, likewise, a feature of the invention.

For example, substitutions, deletions and insertions introduced into the sequences provided in the Sequence Listing (except CBF polypeptide sequences SEQ ID NOs: 1956, 1958, 1960, or 2204, listed therein), are also envisioned by the invention. Such sequence modifications can be engineered into a sequence by site-directed mutagenesis (Wu (ed.) Methods Enzymol. (1993) vol. 217, Academic Press) or the other methods noted below. Amino acid substitutions are typically of single residues; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. In preferred embodiments, deletions or insertions are made in adjacent pairs, e.g., a deletion of two residues or insertion of two residues. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a sequence. The mutations that are made in the polynucleotide encoding the transcription factor should not place the sequence out of reading frame and should not create complementary regions that could produce secondary mRNA structure. Preferably, the polypeptide encoded by the DNA performs the desired function.

Conservative substitutions are those in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 2 when it is desired to maintain the activity of the protein. Table 2 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions.

TABLE 2 Conservative Residue Substitutions Ala Ser Arg Lys Asn Gln; His Asp Glu Gln Asn Cys Ser Glu Asp Gly Pro His Asn; Gln Ile Leu, Val Leu Ile; Val Lys Arg; Gln Met Leu; Ile Phe Met; Leu; Tyr Ser Thr; Gly Thr Ser; Val Trp Tyr Tyr Trp; Phe Val Ile; Leu

Similar substitutions are those in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 3 when it is desired to maintain the activity of the protein. Table 3 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as structural and functional substitutions. For example, a residue in column 1 of Table 3 may be substituted with a residue in column 2; in addition, a residue in column 2 of Table 3 may be substituted with the residue of column 1.

TABLE 3 Residue Similar Substitutions Ala Ser; Thr; Gly; Val; Leu; Ile Arg Lys; His; Gly Asn Gln; His; Gly; Ser; Thr Asp Glu, Ser; Thr Gln Asn; Ala Cys Ser; Gly Glu Asp Gly Pro; Arg His Asn; Gln; Tyr; Phe; Lys; Arg Ile Ala; Leu; Val; Gly; Met Leu Ala; Ile; Val; Gly; Met Lys Arg; His; Gln; Gly; Pro Met Leu; Ile; Phe Phe Met; Leu; Tyr; Trp; His; Val; Ala Ser Thr; Gly; Asp; Ala; Val; Ile; His Thr Ser; Val; Ala; Gly Trp Tyr; Phe; His Tyr Trp; Phe; His Val Ala; Ile; Leu; Gly; Thr; Ser; Glu

Substitutions that are less conservative than those in Table 2 can be selected by picking residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in protein properties will be those in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

Further Modifying Sequences of the Invention—Mutation/Forced Evolution

In addition to generating silent or conservative substitutions as noted, above, the present invention optionally includes methods of modifying the sequences of the Sequence Listing. In the methods, nucleic acid or protein modification methods are used to alter the given sequences to produce new sequences and/or to chemically or enzymatically modify given sequences to change the properties of the nucleic acids or proteins.

Thus, in one embodiment, given nucleic acid sequences are modified, e.g., according to standard mutagenesis or artificial evolution methods to produce modified sequences. The modified sequences may be created using purified natural polynucleotides isolated from any organism or may be synthesized from purified compositions and chemicals using chemical means well know to those of skill in the art. For example, Ausubel, supra, provides additional details on mutagenesis methods. Artificial forced evolution methods are described, for example, by Stemmer (1994) Nature 370: 389-391, Stemmer (1994) Proc. Natl. Acad. Sci. 91: 10747-10751, and U.S. Pat. Nos. 5,811,238, 5,837,500, and 6,242,568. Methods for engineering synthetic transcription factors and other polypeptides are described, for example, by Zhang et al. (2000) J. Biol. Chem. 275: 33850-33860, Liu et al. (2001) J. Biol. Chem. 276: 11323-11334, and Isalan et al. (2001) Nature Biotechnol. 19: 656-660. Many other mutation and evolution methods are also available and expected to be within the skill of the practitioner.

Similarly, chemical or enzymatic alteration of expressed nucleic acids and polypeptides can be performed by standard methods. For example, sequence can be modified by addition of lipids, sugars, peptides, organic or inorganic compounds, by the inclusion of modified nucleotides or amino acids, or the like. For example, protein modification techniques are illustrated in Ausubel, supra. Further details on chemical and enzymatic modifications can be found herein. These modification methods can be used to modify any given sequence, or to modify any sequence produced by the various mutation and artificial evolution modification methods noted herein.

Accordingly, the invention provides for modification of any given nucleic acid by mutation, evolution, chemical or enzymatic modification, or other available methods, as well as for the products produced by practicing such methods, e.g., using the sequences herein as a starting substrate for the various modification approaches.

For example, optimized coding sequence containing codons preferred by a particular prokaryotic or eukaryotic host can be used e.g., to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced using a non-optimized sequence. Translation stop codons can also be modified to reflect host preference. For example, preferred stop codons for Saccharomyces cerevisiae and mammals are TAA and TGA, respectively. The preferred stop codon for monocotyledonous plants is TGA, whereas insects and E. coli prefer to use TAA as the stop codon.

The polynucleotide sequences of the present invention can also be engineered in order to alter a coding sequence for a variety of reasons, including but not limited to, alterations which modify the sequence to facilitate cloning, processing and/or expression of the gene product. For example, alterations are optionally introduced using techniques which are well known in the art, e.g., site-directed mutagenesis, to insert new restriction sites, to alter glycosylation patterns, to change codon preference, to introduce splice sites, etc.

Furthermore, a fragment or domain derived from any of the polypeptides of the invention can be combined with domains derived from other transcription factors or synthetic domains to modify the biological activity of a transcription factor. For instance, a DNA-binding domain derived from a transcription factor of the invention can be combined with the activation domain of another transcription factor or with a synthetic activation domain. A transcription activation domain assists in initiating transcription from a DNA-binding site. Examples include the transcription activation region of VP16 or GAL4 (Moore et al. (1998) Proc. Natl. Acad. Sci. 95: 376-381; Aoyama et al. (1995) Plant Cell 7: 1773-1785), peptides derived from bacterial sequences (Ma and Ptashne (1987) Cell 51: 113-119) and synthetic peptides (Giniger and Ptashne (1987) Nature 330: 670-672).

Expression and Modification of Polypeptides

Typically, polynucleotide sequences of the invention are incorporated into recombinant DNA (or RNA) molecules that direct expression of polypeptides of the invention in appropriate host cells, transgenic plants, in vitro translation systems, or the like. Due to the inherent degeneracy of the genetic code, nucleic acid sequences which encode substantially the same or a functionally equivalent amino acid sequence can be substituted for any listed sequence to provide for cloning and expressing the relevant homolog.

The transgenic plants of the present invention comprising recombinant polynucleotide sequences are generally derived from parental plants, which may themselves be non-transformed (or non-transgenic) plants. These transgenic plants may either have a transcription factor gene “knocked out” (for example, with a genomic insertion by homologous recombination, an antisense or ribozyme construct) or expressed to a normal or wild-type extent. However, overexpressing transgenic “progeny” plants will exhibit greater mRNA levels, wherein the mRNA encodes a transcription factor, that is, a DNA-binding protein that is capable of binding to a DNA regulatory sequence and inducing transcription, and preferably, expression of a plant trait gene. Preferably, the mRNA expression level will be at least three-fold greater than that of the parental plant, or more preferably at least ten-fold greater mRNA levels compared to said parental plant, and most preferably at least fifty-fold greater compared to said parental plant.

Vectors, Promoters, and Expression Systems

The present invention includes recombinant constructs comprising one or more of the nucleic acid sequences herein. The constructs typically comprise a vector, such as a plasmid, a cosmid, a phage, a virus (e.g., a plant virus), a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), or the like, into which a nucleic acid sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available.

General texts that describe molecular biological techniques useful herein, including the use and production of vectors, promoters and many other relevant topics, include Berger, Sambrook, supra and Ausubel, supra. Any of the identified sequences can be incorporated into a cassette or vector, e.g., for expression in plants. A number of expression vectors suitable for stable transformation of plant cells or for the establishment of transgenic plants have been described including those described in Weissbach and Weissbach (1989) Methods for Plant Molecular Biology, Academic Press, and Gelvin et al. (1990) Plant Molecular Biology Manual, Kluwer Academic Publishers. Specific examples include those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed by Herrera-Estrella et al. (1983) Nature 303: 209, Bevan (1984) Nucleic Acids Res. 12: 8711-8721, Klee (1985) Bio/Technology 3: 637-642, for dicotyledonous plants.

Alternatively, non-Ti vectors can be used to transfer the DNA into monocotyledonous plants and cells by using free DNA delivery techniques. Such methods can involve, for example, the use of liposomes, electroporation, microprojectile bombardment, silicon carbide whiskers, and viruses. By using these methods transgenic plants such as wheat, rice (Christou (1991) Bio/Technology 9: 957-962) and corn (Gordon-Kamm (1990) Plant Cell 2: 603-618) can be produced. An immature embryo can also be a good target tissue for monocots for direct DNA delivery techniques by using the particle gun (Weeks et al. (1993) Plant Physiol. 102: 1077-1084; Vasil (1993) Bio/Technology 10: 667-674; Wan and Lemeaux (1994) Plant Physiol. 104: 37-48, and for Agrobacterium-mediated DNA transfer (Ishida et al. (1996) Nature Biotechnol. 14: 745-750).

Typically, plant transformation vectors include one or more cloned plant coding sequence (genomic or cDNA) under the transcriptional control of 5′ and 3′ regulatory sequences and a dominant selectable marker. Such plant transformation vectors typically also contain a promoter (e.g., a regulatory region controlling inducible or constitutive, environmentally-or developmentally-regulated, or cell- or tissue-specific expression), a transcription initiation start site, an RNA processing signal (such as intron splice sites), a transcription termination site, and/or a polyadenylation signal.

A potential utility for the transcription factor polynucleotides disclosed herein is the isolation of promoter elements from these genes that can be used to program expression in plants of any genes. Each transcription factor gene disclosed herein is expressed in a unique fashion, as determined by promoter elements located upstream of the start of translation, and additionally within an intron of the transcription factor gene or downstream of the termination codon of the gene. As is well known in the art, for a significant portion of genes, the promoter sequences are located entirely in the region directly upstream of the start of translation. In such cases, typically the promoter sequences are located within 2.0 kb of the start of translation, or within 1.5 kb of the start of translation, frequently within 1.0 kb of the start of translation, and sometimes within 0.5 kb of the start of translation.

The promoter sequences can be isolated according to methods known to one skilled in the art.

Examples of constitutive plant promoters which can be useful for expressing the TF sequence include: the cauliflower mosaic virus (CaMV) 35S promoter, which confers constitutive, high-level expression in most plant tissues (see, e.g., Odell et al. (1985) Nature 313: 810-812); the nopaline synthase promoter (An et al. (1988) Plant Physiol. 88: 547-552); and the octopine synthase promoter (Fromm et al. (1989) Plant Cell 1: 977-984).

A variety of plant gene promoters that regulate gene expression in response to environmental, hormonal, chemical, developmental signals, and in a tissue-active manner can be used for expression of a TF sequence in plants. Choice of a promoter is based largely on the phenotype of interest and is determined by such factors as tissue (e.g., seed, fruit, root, pollen, vascular tissue, flower, carpel, etc.), inducibility (e.g., in response to wounding, heat, cold, drought, light, pathogens, etc.), timing, developmental stage, and the like. Numerous known promoters have been characterized and can favorably be employed to promote expression of a polynucleotide of the invention in a transgenic plant or cell of interest. For example, tissue specific promoters include: seed-specific promoters (such as the napin, phaseolin or DC3 promoter described in U.S. Pat. No. 5,773,697), fruit-specific promoters that are active during fruit ripening (such as the dru 1 promoter (U.S. Pat. No. 5,783,393), or the 2A11 promoter (U.S. Pat. No. 4,943,674) and the tomato polygalacturonase promoter (Bird et al. (1988) Plant Mol. Biol. 11: 651-662), root-specific promoters, such as those disclosed in U.S. Pat. Nos. 5,618,988, 5,837,848 and 5,905,186, pollen-active promoters such as PTA29, PTA26 and PTA 13 (U.S. Pat. No. 5,792,929), promoters active in vascular tissue (Ringli and Keller (1998) Plant Mol. Biol. 37: 977-988), flower-specific (Kaiser et al. (1995) Plant Mol. Biol. 28: 231-243), pollen (Baerson et al. (1994) Plant Mol. Biol. 26: 1947-1959), carpels (Ohl et al. (1990) Plant Cell 2: 837-848), pollen and ovules (Baerson et al. (1993) Plant Mol. Biol. 22: 255-267), auxin-inducible promoters (such as that described in van der Kop et al. (1999) Plant Mol Biol. 39: 979-990 or Baumann et al. (1999) Plant Cell 11: 323-334), cytokinin-inducible promoter (Guevara-Garcia (1998) Plant Mol. Biol. 38: 743-753), promoters responsive to gibberellin (Shi et al. (1998) Plant Mol. Biol. 38: 1053-1060, Willmott et al. (1998) 38: 817-825) and the like. Additional promoters are those that elicit expression in response to heat (Ainley et al. (1993) Plant Mol. Biol. 22: 13-23), light (e.g., the pea rbcS-3A promoter, Kuhlemeier et al. (1989) Plant Cell 1: 471-478, and the maize rbcS promoter, Schaffner and Sheen (1991) Plant Cell 3: 997-1012); wounding (e.g., wunI, Siebertz et al. (1989) Plant Cell 1: 961-968); pathogens (such as the PR-1 promoter described in Buchel et al. (1999) Plant Mol. Biol. 40: 387-396, and the PDF1.2 promoter described in Manners et al. (1998) Plant Mol. Biol. 38: 1071-1080), and chemicals such as methyl jasmonate or salicylic acid (Gatz (1997) Annu. Rev. Plant Physiol. Plant Mol. Biol. 48: 89-108). In addition, the timing of the expression can be controlled by using promoters such as those acting at senescence (Gan and Amasino (1995) Science 270: 1986-1988); or late seed development (Odell et al. (1994) Plant Physiol. 106: 447-458).

Plant expression vectors can also include RNA processing signals that can be positioned within, upstream or downstream of the coding sequence. In addition, the expression vectors can include additional regulatory sequences from the 3′-untranslated region of plant genes, e.g., a 3′ terminator region to increase mRNA stability of the mRNA, such as the PI-II terminator region of potato or the octopine or nopaline synthase 3′ terminator regions.

Additional Expression Elements

Specific initiation signals can aid in efficient translation of coding sequences. These signals can include, e.g., the ATG initiation codon and adjacent sequences. In cases where a coding sequence, its initiation codon and upstream sequences are inserted into the appropriate expression vector, no additional translational control signals may be needed. However, in cases where only coding sequence (e.g., a mature protein coding sequence), or a portion thereof, is inserted, exogenous transcriptional control signals including the ATG initiation codon can be separately provided. The initiation codon is provided in the correct reading frame to facilitate transcription. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers appropriate to the cell system in use.

Expression Hosts

The present invention also relates to host cells which are transduced with vectors of the invention, and the production of polypeptides of the invention (including fragments thereof) by recombinant techniques. Host cells are genetically engineered (i.e., nucleic acids are introduced, e.g., transduced, transformed or transfected) with the vectors of this invention, which may be, for example, a cloning vector or an expression vector comprising the relevant nucleic acids herein. The vector is optionally a plasmid, a viral particle, a phage, a naked nucleic acid, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the relevant gene. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art and in the references cited herein, including, Sambrook, supra and Ausubel, supra.

The host cell can be a eukaryotic cell, such as a yeast cell, or a plant cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Plant protoplasts are also suitable for some applications. For example, the DNA fragments are introduced into plant tissues, cultured plant cells or plant protoplasts by standard methods including electroporation (Fromm et al. (1985) Proc. Natl. Acad. Sci. 82: 5824-5828, infection by viral vectors such as cauliflower mosaic virus (CaMV) (Hohn et al. (1982) Molecular Biology of Plant Tumors Academic Press, New York, N.Y., pp. 549-560; U.S. Pat. No. 4,407,956), high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (Klein et al. (1987) Nature 327: 70-73), use of pollen as vector (WO 85/01856), or use of Agrobacterium tumefaciens or A. rhizogenes carrying a T-DNA plasmid in which DNA fragments are cloned. The T-DNA plasmid is transmitted to plant cells upon infection by Agrobacterium tumefaciens, and a portion is stably integrated into the plant genome (Horsch et al. (1984) Science 233: 496-498; Fraley et al. (1983) Proc. Natl. Acad. Sci. 80: 4803-4807).

The cell can include a nucleic acid of the invention that encodes a polypeptide, wherein the cell expresses a polypeptide of the invention. The cell can also include vector sequences, or the like. Furthermore, cells and transgenic plants that include any polypeptide or nucleic acid above or throughout this specification, e.g., produced by transduction of a vector of the invention, are an additional feature of the invention.

For long-term, high-yield production of recombinant proteins, stable expression can be used. Host cells transformed with a nucleotide sequence encoding a polypeptide of the invention are optionally cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein or fragment thereof produced by a recombinant cell may be secreted, membrane-bound, or contained intracellularly, depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides encoding mature proteins of the invention can be designed with signal sequences which direct secretion of the mature polypeptides through a prokaryotic or eukaryotic cell membrane.

Modified Amino Acid Residues

Polypeptides of the invention may contain one or more modified amino acid residues. The presence of modified amino acids may be advantageous in, for example, increasing polypeptide half-life, reducing polypeptide antigenicity or toxicity, increasing polypeptide storage stability, or the like. Amino acid residue(s) are modified, for example, co-translationally or post-translationally during recombinant production or modified by synthetic or chemical means.

Non-limiting examples of a modified amino acid residue include incorporation or other use of acetylated amino acids, glycosylated amino acids, sulfated amino acids, prenylated (e.g., farnesylated, geranylgeranylated) amino acids, PEG modified (e.g., “PEGylated”) amino acids, biotinylated amino acids, carboxylated amino acids, phosphorylated amino acids, etc. References adequate to guide one of skill in the modification of amino acid residues are replete throughout the literature.

The modified amino acid residues may prevent or increase affinity of the polypeptide for another molecule, including, but not limited to, polynucleotide, proteins, carbohydrates, lipids and lipid derivatives, and other organic or synthetic compounds.

Identification of Additional Factors

A transcription factor provided by the present invention can also be used to identify additional endogenous or exogenous molecules that can affect a phentoype or trait of interest. On the one hand, such molecules include organic (small or large molecules) and/or inorganic compounds that affect expression of (i.e., regulate) a particular transcription factor. Alternatively, such molecules include endogenous molecules that are acted upon either at a transcriptional level by a transcription factor of the invention to modify a phenotype as desired. For example, the transcription factors can be employed to identify one or more downstream genes that are subject to a regulatory effect of the transcription factor. In one approach, a transcription factor or transcription factor homolog of the invention is expressed in a host cell, e.g., a transgenic plant cell, tissue or explant, and expression products, either RNA or protein, of likely or random targets are monitored, e.g., by hybridization to a microarray of nucleic acid probes corresponding to genes expressed in a tissue or cell type of interest, by two-dimensional gel electrophoresis of protein products, or by any other method known in the art for assessing expression of gene products at the level of RNA or protein. Alternatively, a transcription factor of the invention can be used to identify promoter sequences (such as binding sites on DNA sequences) involved in the regulation of a downstream target. After identifying a promoter sequence, interactions between the transcription factor and the promoter sequence can be modified by changing specific nucleotides in the promoter sequence or specific amino acids in the transcription factor that interact with the promoter sequence to alter a plant trait. Typically, transcription factor DNA-binding sites are identified by gel shift assays. After identifying the promoter regions, the promoter region sequences can be employed in double-stranded DNA arrays to identify molecules that affect the interactions of the transcription factors with their promoters (Bulyk et al. (1999) Nature Biotechnol. 17: 573-577).

The identified transcription factors are also useful to identify proteins that modify the activity of the transcription factor. Such modification can occur by covalent modification, such as by phosphorylation, or by protein-protein (homo or -heteropolymer) interactions. Any method suitable for detecting protein-protein interactions can be employed. Among the methods that can be employed are co-immunoprecipitation, cross-linking and co-purification through gradients or chromatographic columns, and the two-hybrid yeast system.

The two-hybrid system detects protein interactions in vivo and is described in Chien et al. (1991) Proc. Natl. Acad. Sci. 88: 9578-9582, and is commercially available from Clontech (Palo Alto, Calif.). In such a system, plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to the TF polypeptide and the other consists of the transcription activator protein's activation domain fused to an unknown protein that is encoded by a cDNA that has been recombined into the plasmid as part of a cDNA library. The DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., lacZ) whose regulatory region contains the transcription activator's binding site. Either hybrid protein alone cannot activate transcription of the reporter gene. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product. Then, the library plasmids responsible for reporter gene expression are isolated and sequenced to identify the proteins encoded by the library plasmids. After identifying proteins that interact with the transcription factors, assays for compounds that interfere with the TF protein-protein interactions can be preformed.

Identification of Modulators

In addition to the intracellular molecules described above, extracellular molecules that alter activity or expression of a transcription factor, either directly or indirectly, can be identified. For example, the methods can entail first placing a candidate molecule in contact with a plant or plant cell. The molecule can be introduced by topical administration, such as spraying or soaking of a plant, or incubating a plant in a solution containing the molecule, and then the molecule's effect on the expression or activity of the TF polypeptide or the expression of the polynucleotide monitored. Changes in the expression of the TF polypeptide can be monitored by use of polyclonal or monoclonal antibodies, gel electrophoresis or the like. Changes in the expression of the corresponding polynucleotide sequence can be detected by use of microarrays, Northerns, quantitative PCR, or any other technique for monitoring changes in mRNA expression. These techniques are exemplified in Ausubel et al. (eds.) Current Protocols in Molecular Biology, John Wiley & Sons (1998, and supplements through 2001).Changes in the activity of the transcription factor can be monitored, directly or indirectly, by assaying the function of the transcription factor, for example, by measuring the expression of promoters known to be controlled by the transcription factor (using promoter-reporter constructs), measuring the levels of transcripts using microarrays, Northern blots, quantitative PCR, etc. Such changes in the expression levels can be correlated with modified plant traits and thus identified molecules can be useful for soaking or spraying on fruit, vegetable and grain crops to modify traits in plants.

Essentially any available composition can be tested for modulatory activity of expression or activity of any nucleic acid or polypeptide herein. Thus, available libraries of compounds such as chemicals, polypeptides, nucleic acids and the like can be tested for modulatory activity. Often, potential modulator compounds can be dissolved in aqueous or organic (e.g., DMSO-based) solutions for easy delivery to the cell or plant of interest in which the activity of the modulator is to be tested. Optionally, the assays are designed to screen large modulator composition libraries by automating the assay steps and providing compounds from any convenient source to assays, which are typically run in parallel (e.g., in microtiter formats on microplates in robotic assays).

In one embodiment, high throughput screening methods involve providing a combinatorial library containing a large number of potential compounds (potential modulator compounds). Such “combinatorial chemical libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as target compounds.

A combinatorial chemical library can be, e.g., a collection of diverse chemical compounds generated by chemical synthesis or biological synthesis. For example, a combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks (e.g., in one example, amino acids) in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound of a set length). Exemplary libraries include peptide libraries, nucleic acid libraries, antibody libraries (see, e.g., Vaughn et al. (1996) Nature Biotechnol. 14: 309-314 and PCT/U.S.96/10287), carbohydrate libraries (see, e.g., Liang et al. Science (1996) 274: 1520-1522 and U.S. Pat. No. 5,593,853), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), and small organic molecule libraries (see, e.g., benzodiazepines, in Baum Chem. & Engineering News Jan. 18, 1993, page 33; isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506,337) and the like.

Preparation and screening of combinatorial or other libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175; Furka, (1991) Int. J. Pept. Prot. Res. 37: 487-493; and Houghton et al. (1991) Nature 354: 84-88). Other chemistries for generating chemical diversity libraries can also be used.

In addition, as noted, compound screening equipment for high-throughput screening is generally available, e.g., using any of a number of well known robotic systems that have also been developed for solution phase chemistries useful in assay systems. These systems include automated workstations including an automated synthesis apparatus and robotic systems utilizing robotic arms. Any of the above devices are suitable for use with the present invention, e.g., for high-throughput screening of potential modulators. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art.

Indeed, entire high-throughput screening systems are commercially available. These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. Similarly, microfluidic implementations of screening are also commercially available.

The manufacturers of such systems provide detailed protocols the various high throughput. Thus, for example, Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like. The integrated systems herein, in addition to providing for sequence alignment and, optionally, synthesis of relevant nucleic acids, can include such screening apparatus to identify modulators that have an effect on one or more polynucleotides or polypeptides according to the present invention.

In some assays it is desirable to have positive controls to ensure that the components of the assays are working properly. At least two types of positive controls are appropriate. That is, known transcriptional activators or inhibitors can be incubated with cells or plants, for example, in one sample of the assay, and the resulting increase/decrease in transcription can be detected by measuring the resulting increase in RNA levels and/or protein expression, for example, according to the methods herein. It will be appreciated that modulators can also be combined with transcriptional activators or inhibitors to find modulators that inhibit transcriptional activation or transcriptional repression. Either expression of the nucleic acids and proteins herein or any additional nucleic acids or proteins activated by the nucleic acids or proteins herein, or both, can be monitored.

In an embodiment, the invention provides a method for identifying compositions that modulate the activity or expression of a polynucleotide or polypeptide of the invention. For example, a test compound, whether a small or large molecule, is placed in contact with a cell, plant (or plant tissue or explant), or composition comprising the polynucleotide or polypeptide of interest and a resulting effect on the cell, plant, (or tissue or explant) or composition is evaluated by monitoring, either directly or indirectly, one or more of: expression level of the polynucleotide or polypeptide, activity (or modulation of the activity) of the polynucleotide or polypeptide. In some cases, an alteration in a plant phenotype can be detected following contact of a plant (or plant cell, or tissue or explant) with the putative modulator, e.g., by modulation of expression or activity of a polynucleotide or polypeptide of the invention. Modulation of expression or activity of a polynucleotide or polypeptide of the invention may also be caused by molecular elements in a signal transduction second messenger pathway and such modulation can affect similar elements in the same or another signal transduction second messenger pathway.

Subsequences

Also contemplated are uses of polynucleotides, also referred to herein as oligonucleotides, typically having at least 12 bases, preferably at least 15, more preferably at least 20, 30, or 50 bases, which hybridize under at least highly stringent (or ultra-high stringent or ultra-ultra-high stringent conditions) conditions to a polynucleotide sequence described above. The polynucleotides may be used as probes, primers, sense and antisense agents, and the like, according to methods as noted supra.

Subsequences of the polynucleotides of the invention, including polynucleotide fragments and oligonucleotides are useful as nucleic acid probes and primers. An oligonucleotide suitable for use as a probe or primer is at least about 15 nucleotides in length, more often at least about 18 nucleotides, often at least about 21 nucleotides, frequently at least about 30 nucleotides, or about 40 nucleotides, or more in length. A nucleic acid probe is useful in hybridization protocols, e.g., to identify additional polypeptide homologs of the invention, including protocols for microarray experiments. Primers can be annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, and then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods. See Sambrook, supra, and Ausubel, supra.

In addition, the invention includes an isolated or recombinant polypeptide including a subsequence of at least about 15 contiguous amino acids encoded by the recombinant or isolated polynucleotides of the invention. For example, such polypeptides, or domains or fragments thereof, can be used as immunogens, e.g., to produce antibodies specific for the polypeptide sequence, or as probes for detecting a sequence of interest. A subsequence can range in size from about 15 amino acids in length up to and including the full length of the polypeptide.

To be encompassed by the present invention, an expressed polypeptide which comprises such a polypeptide subsequence performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA binding domain that activates transcription, e.g., by binding to a specific DNA promoter region an activation domain, or a domain for protein-protein interactions.

Production of Transgenic Plants

Modification of Traits

The polynucleotides of the invention are favorably employed to produce transgenic plants with various traits, or characteristics, that have been modified in a desirable manner, e.g., to improve the seed characteristics of a plant. For example, alteration of expression levels or patterns (e.g., spatial or temporal expression patterns) of one or more of the transcription factors (or transcription factor homologs) of the invention, as compared with the levels of the same protein found in a wild-type plant, can be used to modify a plant's traits. An illustrative example of trait modification, improved characteristics, by altering expression levels of a particular transcription factor is described further in the Examples and the Sequence Listing.

Arabidopsis as a Model System

Arabidopsis thaliana is the object of rapidly growing attention as a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz et al. eds., et al. Methods in Arabidopsis Research (1992) et al. World Scientific, New Jersey, N.J., in “Preface”). Because of its small size, short life cycle, obligate autogamy and high fertility, Arabidopsis is also a choice organism for the isolation of mutants and studies in morphogenetic and development pathways, and control of these pathways by transcription factors (Koncz supra, p. 72). A number of studies introducing transcription factors into A. thaliana have demonstrated the utility of this plant for understanding the mechanisms of gene regulation and trait alteration in plants. (See, for example, Koncz supra, and U.S. Pat. No. 6,417,428).

Arabidopsis Genes in Transgenic Plants.

Expression of genes which encode transcription factors modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising isolated polynucleotides encoding transcription factors may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al. (1997) et al. Genes and Development 11: 3194-3205, and Peng et al. (1999) Nature 400: 256-261. In addition, many others have demonstrated that an Arabidopsis transcription factor expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al. (2001) Plant Cell 13: 1791-1802; Nandi et al. (2000) Curr. Biol. 10: 215-218; Coupland (1995) Nature 377: 482-483; and Weigel and Nilsson (1995) Nature 377: 482-500.

Homologous Genes Introduced into Transgenic Plants.

Homologous genes that may be derived from any plant, or from any source whether natural, synthetic, semi-synthetic or recombinant, and that share significant sequence identity or similarity to those provided by the present invention, may be introduced into plants, for example, crop plants, to confer desirable or improved traits. Consequently, transgenic plants may be produced that comprise a recombinant expression vector or cassette with a promoter operably linked to one or more sequences homologous to presently disclosed sequences. The promoter may be, for example, a plant or viral promoter.

The invention thus provides for methods for preparing transgenic plants, and for modifying plant traits. These methods include introducing into a plant a recombinant expression vector or cassette comprising a functional promoter operably linked to one or more sequences homologous to presently disclosed sequences. Plants and kits for producing these plants that result from the application of these methods are also encompassed by the present invention.

Transcription Factors of Interest for the Modification of Plant Traits

Currently, the existence of a series of maturity groups for different latitudes represents a major barrier to the introduction of new valuable traits. Any trait (e.g. disease resistance) has to be bred into each of the different maturity groups separately, a laborious and costly exercise. The availability of single strain, which could be grown at any latitude, would therefore greatly increase the potential for introducing new traits to crop species such as soybean and cotton.

For many of the specific effects, traits and utilities listed in Table 4 and Table 6 that may be conferred to plants, one or more transcription factor genes may be used to increase or decrease, advance or delay, or improve or prove deleterious to a given trait. Overexpressing or suppressing one or more genes can impart significant differences in production of plant products, such as different fatty acid ratios. For example, overexpression of G720 caused a plant to become more freezing tolerant, but knocking out the same transcription factor imparted greater susceptibility to freezing. Thus, suppressing a gene that causes a plant to be more sensitive to cold may improve a plant's tolerance of cold. More than one transcription factor gene may be introduced into a plant, either by transforming the plant with one or more vectors comprising two or more transcription factors, or by selective breeding of plants to yield hybrid crosses that comprise more than one introduced transcription factor.

A listing of specific effects and utilities that the presently disclosed transcription factor genes have on plants, as determined by direct observation and assay analysis, is provided in Table 4. Table 4 shows the polynucleotides identified by SEQ ID NO; Mendel Gene ID No. (GID); and if the polynucleotide was tested in a transgenic assay. The first column shows the polynucleotide SEQ ID NO; the second column shows the GID; the third column shows whether the gene was overexpressed (OF) or knocked out (KO) in plant studies; the fourth column shows the trait(s) resulting from the knock out or overexpression of the polynucleotide in the transgenic plant; the fifth column shows the category of the trait; and the sixth column (“Comment”), includes specific observations made with respect to the polynucleotide of the first column.

TABLE 4 Traits, trait categories, and effects and utilities that transcription factor genes have on plants. Polynucleotide GID OE/ SEQ ID NO: No. KO Trait(s) Category Observations 1 G8 OE Flowering time Flowering time Late flowering 3 G19 OE Erysiphe Disease Increased tolerance to Erysiphe; repressed by methyl jasmonate and induced by 1-aminocyclopropane 1- carboxylic acid (ACC) 5 G22 OE Sodium chloride Abiotic stress Increased tolerance to high salt 7 G24 OE Morphology: other Dev and morph Reduced size and necrotic patches 9 G28 OE Botrytis Disease Increased tolerance to Botrytis Sclerotinia Disease Increased tolerance to Sclerotinia Erysiphe Disease Increased resistance to Erysiphe 11 G47 OE Stem Dev and morph Altered structure of vascular tissues Osmotic Abiotic stress Better root growth under osmotic Flowering time Flowering time stress Architecture Dev and morph Late flowering Architecture Dev and morph Altered architecture and inflorescence development Reduced apical dominance 13 G156 KO Seed Dev and morph Seed color alteration 15 G157 OE Flowering time Flowering time Altered flowering time (modest level of overexpression triggers early flowering, whereas a larger increase delays flowering) 17 G162 OE Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Increased seed protein content 19 G175 OE Osmotic Abiotic stress Increased tolerance to osmotic stress 21 G180 OE Seed oil content Seed biochemistry Decreased seed oil Flowering time Flowering time Early flowering 23 G183 OE Flowering time Flowering time Early flowering Light response Dev and morph Constitutive photomorphogenesis 25 G188 KO Fusarium Disease Increased susceptibility to Fusarium Osmotic Abiotic stress Better germination under osmotic stress 27 G189 OE Size Dev and morph Increased leaf size 29 G192 OE Flowering time Flowering time Late flowering Seed oil content Seed biochemistry Decreased seed oil content 31 G196 OE Sodium chloride Abiotic stress Increased tolerance to high salt 33 G211 OE Leaf insoluble sugars Leaf biochemistry Increase in leaf xylose Architecture Dev and morph Reduced apical dominance Leaf Dev and morph Altered leaf shape 35 G214 OE Flowering time Flowering time Late flowering Leaf fatty acids Leaf biochemistry Increased leaf fatty acids Seed prenyl lipids Seed biochemistry Increased seed lutein Leaf prenyl lipids Leaf biochemistry Increased leaf chlorophyll and carotenoids 37 G226 OE Seed protein content Seed biochemistry Increased seed protein Trichome Dev and morph Glabrous, lack of trichomes Root Dev and morph Increased root hairs Sodium chloride Abiotic stress Increased tolerance to high salt Nutrient uptake Abiotic stress Increased tolerance to nitrogen- limited medium 39 G241 KO Seed protein content Seed biochemistry Increased seed protein content Seed oil content Seed biochemistry Decreased seed oil Sugar sensing Sugar sensing Decreased germination and growth on glucose medium 41 G248 OE Botrytis Disease Increased susceptibility to Botrytis 43 G254 OE Sugar sensing Sugar sensing Decreased germination and growth on glucose medium 45 G256 OE Cold, chilling Abiotic stress Better germination and growth in cold 47 G278 OE Sclerotinia Disease Increased susceptibility to Sclerotinia 49 G291 OE Seed oil content Seed biochemistry Increased seed oil content 51 G303 OE Osmotic Abiotic stress Better germination on high sucrose and high NaCl 53 G312 OE Sodium chloride Abiotic stress Better germination on high NaCl 55 G325 OE Osmotic Abiotic stress Better germination on high sucrose and NaCl 57 G343 OE Glyphosate Herbicide sensitivity Increased resistance to glyphosate Size Dev and morph Small plant 59 G353 OE Osmotic Abiotic stress Increased seedling vigor on polyethylene glycol (PEG) Size Dev and morph Reduced size Leaf Dev and morph Altered leaf development Flower Dev and morph Short pedicels, downward pointing siliques 61 G354 OE Size Dev and morph Reduced size Light response Dev and morph Constitutive photomorphogenesis Flower Dev and morph Short pedicels, downward pointing siliques 63 G361 OE Flowering time Flowering time Late flowering 65 G362 OE Flowering time Flowering time Late flowering Size Dev and morph Reduced size Trichome Dev and morph Ectopic trichome formation, increased trichome number Morphology: other Dev and morph Increased pigmentation in seed and embryos, and in other organs 67 G371 OE Botrytis Disease Increased susceptibility to Botrytis 69 G390 OE Architecture Dev and morph Altered shoot development 71 G391 OE Architecture Dev and morph Altered shoot development 73 G409 OE Erysiphe Disease Increased tolerance to Erysiphe 75 G427 OE Seed oil content Seed biochemistry Increased oil content Seed protein content Seed biochemistry Decreased protein content 77 G438 KO Stem Dev and morph Reduced lignin Architecture Dev and morph Reduced branching 79 G450 OE Seed Dev and morph Increased seed size 81 G464 OE Heat Abiotic stress Better germination and growth in heat 83 G470 OE Fertility Dev and morph Short stamen filaments 85 G477 OE Sclerotinia Disease Increased susceptibility to Oxidative Abiotic stress Sclerotinia Increased sensitivity to oxidative stress 87 G481 OE Sugar sensing Sugar sensing Better germination on sucrose media Drought Abiotic stress Increased tolerance to drought 89 G482 OE Sodium chloride Abiotic stress Increased tolerance to high salt 91 G484 KO Seed glucosinolates Seed biochemistry Altered glucosinolate profile 93 G489 OE Osmotic Abiotic stress Increased tolerance to osmotic stress 95 G490 OE Flowering time Flowering time Early flowering 97 G504 OE Seed oil composition Seed biochemistry Decreased seed oil composition and content; increase in 18:2 fatty acid and decrease in 20:1 fatty acid 99 G509 KO Seed oil content Seed biochemistry Increased total seed oil and protein Seed protein content Seed biochemistry content 101 G519 OE Seed oil content Seed biochemistry Increased seed oil content 103 G545 OE Sodium chloride Abiotic stress Susceptible to high salt Erysiphe Disease Increased susceptibility to Erysiphe Pseudomonas Disease Increased susceptibility to Fusarium Disease Pseudomonas Nutrient uptake Abiotic stress Increased susceptibility to Fusarium Increased tolerance to phosphate-free medium 105 G546 OE Hormone sensitivity Hormone sensitivity Decreased sensitivity to abscisic acid (ABA) 107 G561 OE Seed oil content Seed biochemistry Increased seed oil content Nutrient uptake Abiotic stress Increased tolerance to potassium-free medium 109 G562 OE Flowering time Flowering time Late flowering 111 G567 OE Seed oil content Seed biochemistry Increased total seed oil/protein Seed protein content Seed biochemistry content Sugar sensing Sugar sensing Increased total seed oil/protein content Decreased seedling vigor on high glucose 113 G568 OE Architecture Dev and morph Altered branching 115 G584 OE Seed Dev and morph Large seeds 117 G585 OE Trichome Dev and morph Reduced trichome density 119 G590 KO Seed oil content Seed biochemistry Increased seed oil content OE Flowering time Flowering time Early flowering 121 G594 OE Sclerotinia Disease Increased susceptibility to Sclerotinia 123 G597 OE Seed protein content Seed biochemistry Altered seed protein content 125 G598 OE Seed oil content Seed biochemistry Increased seed oil 127 G634 OE Trichome Dev and morph Increased trichome density and size 129 G635 OE Variegation Dev and morph Altered coloration 131 G636 OE Senescence Dev and morph Premature senescence 133 G638 OE Flower Dev and morph Altered flower development 135 G652 KO Seed prenyl lipids Seed biochemistry Increase in alpha-tocopherol 137 G663 OE Biochemistry: other Biochem: misc Increased anthocyanins in leaf, root, seed 139 G664 OE Cold, chilling Abiotic stress Better germination and growth in cold 141 G674 OE Leaf Dev and morph Dark green, upwardly oriented leaves 143 G676 OE Trichome Dev and morph Reduced trichome number, ectopic trichome formation 145 G680 OE Sugar sensing Sugar sensing Reduced germination on glucose medium 147 G682 OE Trichome Dev and morph Glabrous, lack of trichomes Heat Abiotic stress Better germination and growth in Root Dev and morph heat Increased root hairs 149 G715 OE Seed oil content Seed biochemistry Increased seed oil content 151 G720 OE Freezing Abiotic stress More freezing tolerant KO Freezing Abiotic stress Increased susceptibility to freezing 153 G736 OE Flowering time Flowering time Late flowering Leaf Dev and morph Altered leaf shape 155 G748 OE Seed prenyl lipids Seed biochemistry Increased lutein content Stem Dev and morph More vascular bundles in stem Flowering time Flowering time Late flowering 157 G779 OE Fertility Dev and morph Reduced fertility Flower Dev and morph Homeotic transformations 159 G789 OE Flowering time Flowering time Early flowering 161 G801 OE Sodium chloride Abiotic stress Better germination on high NaCl 163 G849 KO Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Altered seed protein content 165 G859 OE Flowering time Flowering time Late flowering 167 G864 OE Heat Abiotic stress Better germination in heat 169 G867 OE Sodium chloride Abiotic stress Better seedling vigor on high salt Sugar sensing Sugar sensing Better seedling vigor on high sucrose 171 G869 OE Seed oil composition Seed biochemistry Altered seed fatty acids 173 G877 KO Embryo lethal Dev and morph Embryo lethal phenotype: potential herbicide target 175 G881 OE Erysiphe Disease Increased susceptibility to Erysiphe 177 G892 KO Seed protein content Seed biochemistry Altered seed protein content Seed oil content Seed biochemistry Altered seed oil content 179 G896 KO Fusarium Disease Increased susceptibility to Fusarium 181 G910 OE Flowering time Flowering time Late flowering 183 G911 OE Nutrient uptake Abiotic stress Increased growth on potassium-free medium 185 G912 OE Freezing Abiotic stress Freezing tolerant Drought Abiotic stress Increased survival in drought Morphology: other Dev and morph conditions Sugar sensing Sugar sensing Dark green color Reduced cotyledon expansion in glucose 187 G913 OE Freezing Abiotic stress Increased tolerance to freezing Flowering time Flowering time Late flowering Drought Abiotic stress Increased tolerance to drought 189 G922 OE Osmotic Abiotic stress Better germination on high sucrose Sodium chloride Abiotic stress Better germination, increased root growth on high salt 191 G926 KO Hormone sensitivity Hormone sensitivity Reduced sensitivity to ABA Osmotic Abiotic stress Increased tolerance to osmotic stress (salt and sucrose) 193 G961 KO Seed oil content Seed biochemistry Increased seed oil content 195 G971 OE Flowering time Flowering time Late flowering 197 G974 OE Seed oil content Seed biochemistry Altered seed oil content 199 G975 OE Leaf fatty acids Leaf biochemistry Increased wax in leaves 201 G979 KO Seed Dev and morph Altered seed development, ripening, and germination 203 G987 KO Leaf fatty acids Leaf biochemistry Reduction in 16:3 fatty acids Leaf prenyl lipids Leaf biochemistry Altered chlorophyll, tocopherol, carotenoid 205 G988 OE Seed protein content Seed biochemistry Increased seed protein content Flower Dev and morph Enlarged floral organs, short pedicels Architecture Dev and morph Reduced lateral branching Stem Dev and morph Thicker stem, altered distribution of vascular bundles 207 G1040 OE Seed Dev and morph Smaller and more rounded seeds 209 G1047 OE Fusarium Disease Increased tolerance to Fusarium 211 G1051 OE Flowering time Flowering time Late flowering 213 G1052 OE Flowering time Flowering time Late flowering 215 G1062 KO Seed Dev and morph Altered seed shape 217 G1063 OE Leaf Dev and morph Altered leaf shape, dark green color Inflorescence Dev and morph Altered inflorescence development Flower Dev and morph Altered flower development, ectopic carpel tissue 219 G1064 OE Botrytis Disease Increased sensitivity to Botrytis 221 G1069 OE Hormone sensitivity Hormone sensitivity Reduced ABA sensitivity Osmotic Abiotic stress Better germination under osmotic stress 223 G1073 OE Size Dev and morph Substantially increased plant size Seed Dev and morph Increased seed yield Drought Abiotic stress Increased tolerance to drought 225 G1075 OE Flower Dev and morph Reduced or absent petals, sepals and stamens 227 G1084 OE Botrytis Disease Increased susceptibility to Botrytis 229 G1089 KO Osmotic Abiotic stress Better germination under osmotic stress 231 G1134 OE Hormone sensitivity Hormone sensitivity Altered response to ethylene: longer hypocotyls and lack of apical hook 233 G1140 OE Flower Dev and morph Altered flower development 235 G1143 OE Seed oil content Seed biochemistry Altered seed oil content 237 G1146 OE Leaf Dev and morph Altered leaf development 239 G1196 KO Botrytis Disease Increased susceptibility to Botrytis 241 G1198 OE Seed oil content Seed biochemistry Increased seed oil content 243 G1225 OE Flowering time Flowering time Early flowering Sugar sensing Sugar sensing Better germination on sucrose and glucose media 245 G1226 OE Seed oil content Seed biochemistry Increased seed oil content 247 G1229 OE Seed oil content Seed biochemistry Decreased seed oil content 249 G1255 OE Botrytis Disease Increased susceptibility to Botrytis Seed Dev and morph Increased seed size Morphology: other Dev and morph Reduced apical dominance 251 G1266 OE Erysiphe Disease Increased tolerance to Erysiphe 253 G1275 OE Architecture Dev and morph Reduced apical dominance 255 G1305 OE Heat Abiotic stress Reduced chlorosis in heat 257 G1322 OE Chilling Abiotic stress Increased seedling vigor in cold Size Dev and morph Reduced size Leaf glucosinolates Leaf biochemistry Increase in M39480 Light response Dev and morph Photomorphogenesis in the dark 259 G1323 OE Seed oil content Seed biochemistry Decreased seed oil Seed protein content Seed biochemistry Increased seed protein 261 G1330 OE Hormone sensitivity Hormone sensitivity Ethylene insensitive when germinated in the dark on ACC 263 G1331 OE Light response Dev and morph Constitutive photomorphogenesis 265 G1332 OE Trichome Dev and morph Reduced trichome density 267 G1363 OE Fusarium Disease Increased tolerance to Fusarium 269 G1411 OE Architecture Dev and morph Loss of apical dominance 271 G1417 KO Seed oil composition Seed biochemistry Increase in 18:2, decrease in 18:3 fatty acids 273 G1419 OE Seed protein content Seed biochemistry Increased seed protein 275 G1449 OE Flower Dev and morph Altered flower structure 277 G1451 OE Morphology: other Dev and morph Increased plant size OE Leaf Dev and morph Large leaf size KO Seed oil content Seed biochemistry Altered seed oil content 279 G1452 OE Trichome Dev and morph Reduced trichome density Leaf Dev and morph Altered leaf shape, dark green color Hormone sensitivity Hormone sensitivity Reduced sensitivity to ABA Osmotic Abiotic stress Better germination on sucrose and Flowering time Flowering time salt Late flowering 281 G1463 OE Senescence Dev and morph Premature senescence 283 G1471 OE Seed oil content Seed biochemistry Increased seed oil content 285 G1478 OE Seed protein content Seed biochemistry Decreased seed protein content Flowering time Flowering time Late flowering Seed oil content Seed biochemistry Increased seed oil content 287 G1482 KO Biochemistry: other Biochem: misc Increased anthocyanins OE Root Dev and morph Increased root growth 289 G1488 OE Seed protein content Seed biochemistry Altered seed protein content Light response Dev and morph Constitutive photomorphogenesis Architecture Dev and morph Reduced apical dominance, shorter stems 291 G1494 OE Flowering time Flowering time Early flowering Light response Dev and morph Long hypocotyls, altered leaf shape Leaf Dev and morph Pale green leaves, altered leaf shape 293 G1496 OE Seed oil content Seed biochemistry Altered seed oil content 295 G1499 OE Morphology: other Dev and morph Dark green color Architecture Dev and morph Altered plant architecture Flower Dev and morph Altered floral organ identity and development 297 G1519 KO Embryo lethal Dev and morph Embryo lethal phenotype: potential herbicide target 299 G1526 KO Seed oil content Seed biochemistry Increased seed oil content 301 G1540 OE Morphology: other Dev and morph Reduced cell differentiation in meristem 303 G1543 OE Architecture Dev and morph Altered architecture, compact plant Morphology: other Dev and morph Dark green color Seed oil content Seed biochemistry Decreased seed oil Leaf prenyl lipids Leaf biochemistry Increase in chlorophyll a and b 305 G1634 OE Seed oil content Seed biochemistry Increased seed oil content Seed protein content Decreased seed protein content 307 G1637 OE Seed protein content Seed biochemistry Altered seed protein content 309 G1640 OE Seed oil content Seed biochemistry Increased seed oil 311 G1645 OE Inflorescence Dev and morph Altered inflorescence structure 313 G1646 OE Seed oil content Seed biochemistry Increased seed oil content 315 G1652 OE Seed protein content Seed biochemistry Increased seed protein content 317 G1672 OE Seed oil content Seed biochemistry Altered seed oil content 319 G1677 OE Seed protein content Seed biochemistry Altered seed protein content Seed oil content Seed biochemistry Altered seed oil content 321 G1749 OE Morphology: other Dev and morph Formation of necrotic lesions 323 G1750 OE Seed oil content Seed biochemistry Increased seed oil content 325 G1756 OE Botrytis Disease Increased susceptibility to Botrytis 327 G1765 OE Seed oil content Seed biochemistry Increased seed oil content 329 G1777 OE Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Decreased seed protein content 331 G1792 OE Leaf Dev and morph Dark green, shiny leaves Erysiphe Disease Increased resistance to Erysiphe Botrytis Disease Increased resistance to Botrytis Fusarium Disease Increased resistance to Fusarium Nutrient uptake Abiotic stress Increased tolerance to nitrogen- limited medium 333 G1793 OE Seed oil content Seed biochemistry Increased seed oil content 335 G1794 OE Architecture Dev and morph Altered architecture, bushier plant Architecture Dev and morph Reduced apical dominance Light response Dev and morph Constitutive photomorphogenesis Osmotic Abiotic stress Increased sensitivity to high PEG Nutrient uptake Abiotic stress Reduced root growth 337 G1804 OE Flowering time Flowering time Late flowering Sugar sensing Sugar sensing Altered sugar sensing: more sensitive to glucose in germination assays 339 G1818 OE Seed protein content Seed biochemistry Increased protein content 341 G1820 OE Flowering time Flowering time Early flowering Hormone sensitivity Hormone sensitivity Reduced ABA sensitivity Seed protein content Seed biochemistry Increased seed protein content Osmotic Abiotic stress Better germination in high NaCl Drought Abiotic stress Increased tolerance to drought 343 G1836 OE Sodium chloride Abiotic stress Better germination in high salt Drought Abiotic stress Increased tolerance to drought 345 G1838 OE Seed oil content Seed biochemistry Increased seed oil content 347 G1841 OE Heat Abiotic stress Better germination under heat stress Flowering time Flowering time Early flowering 349 G1842 OE Flowering time Flowering time Early flowering 351 G1843 OE Flowering time Flowering time Early flowering 353 G1852 OE Osmotic Abiotic stress Better root growth under osmotic stress 355 G1863 OE Leaf Dev and morph Altered leaf shape and coloration 357 G1880 KO Botrytis Disease Increased resistance to Botrytis 359 G1895 OE Flowering time Flowering time Late flowering 361 G1902 OE Seed oil content Seed biochemistry Increased seed oil content 363 G1903 OE Seed protein content Seed biochemistry Decreased seed protein content 365 G1919 OE Botrytis Disease Increased tolerance to Botrytis 367 G1927 OE Sclerotinia Disease Increased tolerance to Sclerotinia 369 G1930 OE Osmotic Abiotic stress Better germination under osmotic stress 371 G1936 KO Sclerotinia Disease Increased susceptibility to Botrytis Disease Sclerotinia Increased susceptibility to Botrytis 373 G1944 OE Senescence Dev and morph Early senescence 375 G1946 OE Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Decreased seed protein content Flowering time Flowering time Early flowering Nutrient uptake Abiotic stress Increased root growth on phosphate- free media 377 G1947 KO Fertility Dev and morph Reduced fertility 379 G1948 OE Seed oil content Seed biochemistry Increased seed oil content 381 G1950 OE Botrytis Disease Increased tolerance to Botrytis 383 G1958 KO Morphology: other Dev and morph Reduced size and root mass Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Increased seed protein content. 385 G2007 OE Flowering time Flowering time Late flowering 387 G2010 OE Flowering time Flowering time Early flowering 389 G2053 OE Osmotic Abiotic stress Increased root growth under osmotic stress 391 G2059 OE Seed oil content Seed biochemistry Altered seed oil content Seed protein content Seed biochemistry Altered seed protein content 393 G2085 OE Seed Dev and morph Increased seed size and altered seed color 395 G2105 OE Seed Dev and morph Large, pale seeds 397 G2110 OE Sodium chloride Abiotic stress Increased tolerance to high salt 399 G2114 OE Seed Dev and morph Increased seed size 401 G2117 OE Seed protein content Seed biochemistry Increased seed protein content 403 G2123 OE Seed oil content Seed biochemistry Increased seed oil content 405 G2130 OE Heat Abiotic stress Better germination in heat 407 G2133 OE Glyphosate Herbicide sensitivity Increased tolerance to glyphosate Flowering time Flowering time Late flowering 409 G2138 OE Seed oil content Seed biochemistry Increased seed oil content 411 G2140 OE Hormone sensitivity Hormone sensitivity Decreased sensitivity to ABA Osmotic Abiotic stress Better germination on high NaCl and sucrose 413 G2143 OE Inflorescence Dev and morph Altered inflorescence development Leaf Dev and morph Altered leaf shape, dark green color Flower Dev and morph Altered flower development, ectopic carpel tissue 415 G2144 OE Flowering time Flowering time Early flowering Leaf Dev and morph Pale green leaves, altered leaf shape Light response Dev and morph Long hypocotyls, altered leaf shape 417 G2153 OE Osmotic Abiotic stress Better germination under osmotic stress 419 G2155 OE Flowering time Flowering time Late flowering 421 G2192 OE Seed oil composition Seed biochemistry Altered seed fatty acid composition 423 G2295 OE Flowering time Flowering time Early flowering 425 G2340 OE Seed glucosinolates Seed biochemistry Altered glucosinolate profile 427 G2343 OE Seed oil content Seed biochemistry Increased seed oil content 429 G2346 OE Morphology: other Dev and morph Enlarged seedlings 431 G2347 OE Flowering time Flowering time Early flowering 433 G2379 OE Osmotic Abiotic stress Increased seedling vigor on high sucrose media 435 G2430 OE Heat Abiotic stress Increased tolerance to heat Size Dev and morph Increased leaf size, faster development 437 G2505 OE Drought Abiotic stress Increased tolerance to drought 439 G2509 OE Seed oil content Seed biochemistry Decreased seed oil content Seed protein content Seed biochemistry Increased seed protein content Seed prenyl lipids Seed biochemistry Increase in alpha-tocopherol Architecture Dev and morph Reduced apical dominance Flowering time Flowering time Early flowering 441 G2517 OE Glyphosate Herbicide sensitivity Increased tolerance to glyphosate 443 G2520 OE Seed prenyl lipids Seed biochemistry Altered tocopherol composition 445 G2555 OE Light response Dev and morph Constitutive photomorphogenesis Botrytis Disease Increased susceptibility to Botrytis 447 G2557 OE Leaf Dev and morph Altered leaf shape, dark green color Flower Dev and morph Altered flower development, ectopic carpel tissue 449 G2583 OE Leaf Dev and morph Glossy, shiny leaves 451 G2701 OE Osmotic Abiotic stress Better germination on high NaCl and sucrose 453 G2719 OE Osmotic Abiotic stress Increased seedling vigor on high sucrose 455 G2789 OE Osmotic Abiotic stress Better germination on high sucrose Hormone sensitivity Hormone sensitivity Reduced ABA sensitivity 457 G2830 KO Seed oil content Seed biochemistry Increased seed oil content 1951 G12 KO Hormone sensitivity Hormone sensitivity Increased sensitivity to ACC OE Morphology: other Dev and morph Leaf and hypocotyl necrosis 1953 G30 OE Leaf Dev and morph Glossy green leaves Light response Dev and morph Shade avoidance 1975 G231 OE Leaf fatty acids Leaf biochemistry Increased leaf unsaturated fatty acids Seed oil content Seed biochemistry Increased seed oil content Seed protein content Seed biochemistry Decreased seed protein content 1979 G247 OE Trichome Dev and morph Altered trichome distribution, reduced trichome density 1991 G370 KO Size Dev and morph Reduced size, shiny leaves OE Trichome Dev and morph Ectropic trichome formation 2009 G485 OE Flowering time Flowering time Early flowering KO Flowering time Flowering time Late flowering 2061 G839 OE Nutrient uptake Abiotic stress Increased tolerance to nitrogen- limited medium 2099 G1357 OE Leaf Dev and morph Altered leaf shape, dark green leaves Chilling Abiotic stress Increased tolerance to cold Hormone sensitivity Hormone sensitivity Insensitive to ABA Flowering time Flowering time Late flowering 2126 G1646 OE Seed oil content Seed oil content Increased seed oil content 2142 G1816 OE Sugar sensing Sugar sensing Increased tolerance to glucose Nutrient uptake Abiotic stress Altered C/N sensing; less Osmotic Abiotic stress anthocyanin Root Dev and morph on nitrogen-limited medium Trichome Dev and morph Increased tolerance to osmotic stress Nutrient uptake Abiotic stress Increased root hairs Glabrous leaves Increased tolerance to nitrogen- limited medium 2147 G1888 OE Size Dev and morph Reduced size, dark green leaves 2153 G1945 OE Flowering time Flowering time Late flowering Leaf Dev and morph Altered leaf shape 2195 G2826 OE Flower Dev and morph Aerial rosettes Trichome Dev and morph Ectropic trichome formation 2197 G2838 OE Trichome Dev and morph Increased trichome density Flowering time Flowering time Late flowering Flower Dev and morph Flower: multiple alterations Flower Dev and morph Aerial rosettes Leaves Dev and morph Dark green leaves Size Dev and morph Increased seedling size 2199 G2839 OE Osmotic stress Dev and morph Better germination on high sucrose Inflorescence Dev and morph Downward pedicels Size Abiotic stress Reduced size

Table 5 shows the polypeptides identified by SEQ ID NO; Mendel Gene ID (GID) No.; the transcription factor family to which the polypeptide belongs, and conserved domains of the polypeptide. The first column shows the polypeptide SEQ ID NO; the third column shows the transcription factor family to which the polynucleotide belongs; and the fourth column shows the amino acid residue positions of the conserved domain in amino acid (AA) co-ordinates.

TABLE 5 Gene families and conserved domains Polypeptide GID Conserved Domains in SEQ ID NO: No. Family Amino Acid Coordinates 2 G8 AP2 151-217, 243-296 4 G19 AP2  76-145 6 G22 AP2  89-157 8 G24 AP2  25-93 10 G28 AP2 145-213 12 G47 AP2  11-80 14 G156 MADS  2-57 16 G157 MADS  2-57 18 G162 MADS  2-57 20 G175 WRKY 178-234, 372-428 22 G180 WRKY 118-174 24 G183 WRKY 307-363 26 G188 WRKY 175-222 28 G189 WRKY 240-297 30 G192 WRKY 128-185 32 G196 WRKY 223-283 34 G211 MYB-R1 R2R3  24-137 36 G214 MYB-related  22-71 38 G226 MYB-related  28-78 40 G241 MYB-R1 R2R3  14-114 42 G248 MYB-R1 R2R3 264-332 44 G254 MYB-related  62-106 46 G256 MYB-R1 R2R3  13-115 48 G278 AKR  2-593 50 G291 MISC 132-160 52 G303 HLH/MYC  92-161 54 G312 SCR 320-336 56 G325 Z-CO-like  5-28, 48-71 58 G343 GATA/Zn 178-214 60 G353 Z-C2H2  41-61, 84-104 62 G354 Z-C2H2  42-62, 88-109 64 G361 Z-C2H2  43-63 66 G362 Z-C2H2  62-82 68 G371 RING/C3HC4  21-74 70 G390 HB  18-81 72 G391 HB  25-85 74 G409 HB  64-124 76 G427 HB 307-370 78 G438 HB  22-85 80 G450 IAA  6-14, 78-89, 112-128, 180-213 82 G464 IAA  20-28, 71-82, 126-142, 187-224 84 G470 ARF  61-393 86 G477 SBP 108-233 88 G481 CAAT  20-109 90 G482 CAAT  25-116 92 G484 CAAT  11-104 94 G489 CAAT  57-156 96 G490 CAAT  48-143 98 G504 NAC  19-174 100 G509 NAC  13-169 102 G519 NAC  11-104 104 G545 Z-C2H2  82-102, 136-154 106 G546 RING/C3H2C3 114-155 108 G561 bZIP 248-308 110 G562 bZIP 253-315 112 G567 bZIP 210-270 114 G568 bZIP 215-265 116 G584 HLH/MYC 401-494 118 G585 HLH/MYC 436-501 120 G590 HLH/MYC 202-254 122 G594 HLH/MYC 140-204 124 G597 AT-hook  97-104, 137-144 126 G598 DBP 205-263 128 G634 TH  62-147, 189-245 130 G635 TH 239-323 132 G636 TH  55-145, 405-498 134 G638 TH 119-206 136 G652 Z-CLDSH  28-49, 137-151, 182-196 138 G663 MYB-R1 R2R3  9-111 140 G664 MYB-R1 R2R3  13-116 142 G674 MYB-R1 R2R3  20-120 144 G676 MYB-R1 R2R3  17-119 146 G680 MYB-related  24-70 148 G682 MYB-related  27-63 150 G715 CAAT  60-132 152 G720 GARP 301-349 154 G736 Z-Dof  54-111 156 G748 Z-Dof 112-140 158 G779 HLH/MYC 126-182 160 G789 HLH/MYC 253-313 162 G801 PCF  32-93 164 G849 BPF-1 324-413, 504-583 166 G859 MADS  3-56 168 G864 AP2 119-186 170 G867 AP2  59-124 172 G869 AP2 109-177 174 G877 WRKY 272-328, 487-603 176 G881 WRKY 176-233 178 G892 RING/C3H2C3 177-270 180 G896 Z-LSDlike  18-39 182 G910 Z-CO-like  14-37, 77-103 184 G911 RING/C3H2C3  86-129 186 G912 AP2  51-118 188 G913 AP2  62-128 190 G922 SCR 225-242 192 G926 CAAT 131-225 194 G961 NAC  15-140 196 G971 AP2 120-186 198 G974 AP2  81-140 200 G975 AP2  4-71 202 G979 AP2  63-139, 165-233 204 G987 SCR 428-432, 704-708 206 G988 SCR 178-195 208 G1040 GARP 109-158 210 G1047 bZIP 129-180 212 G1051 bZIP 189-250 214 G1052 bZIP 201-261 216 G1062 HLH/MYC 308-359 218 G1063 HLH/MYC 131-182 220 G1064 PCF 116-179 222 G1069 AT-hook  67-74 224 G1073 AT-hook  33-42, 78-175 226 G1075 AT-hook  78-85 228 G1084 BZIPT2  1-53, 490-619 230 G1089 BZIPT2 425-500 232 G1134 HLH/MYC 198-247 234 G1140 MADS  2-57 236 G1143 HLH/MYC  33-82 238 G1146 PAZ 886-896 240 G1196 AKR 179-254 242 G1198 bZIP 173-223 244 G1225 HLH/MYC  78-147 246 G1226 HLH/MYC 115-174 248 G1229 HLH/MYC 102-160 250 G1255 Z-CO-like  18-56 252 G1266 AP2  79-147 254 G1275 WRKY 113-169 256 G1305 MYB-R1 R2R3  15-118 258 G1322 MYB-R1 R2R3  26-130 260 G1323 MYB-R1 R2R3  15-116 262 G1330 MYB-R1 R2R3  28-134 264 G1331 MYB-R1 R2R3  8-109 266 G1332 MYB-R1 R2R3  13-116 268 G1363 CAAT 174-226 270 G1411 AP2  87-154 272 G1417 WRKY 239-296 274 G1419 AP2  69-137 276 G1449 IAA  48-53, 74-107, 122-152 278 G1451 ARF  22-357 280 G1452 NAC  30-177 282 G1463 NAC  9-156 284 G1471 Z-C2H2  49-70 286 G1478 Z-CO-like  32-76 288 G1482 Z-CO-like  5-63 290 G1488 GATA/Zn 221-246 292 G1494 HLH/MYC 261-311 294 G1496 HLH/MYC 184-248 296 G1499 HLH/MYC 118-181 298 G1519 RING/C3HC4 327-364 300 G1526 SWI/SNF 493-620, 864-1006 302 G1540 HB  35-98 304 G1543 HB 135-195 306 G1634 MYB-related 129-180 308 G1637 MYB-related 109-173 310 G1640 MYB-R1 R2R3  14-115 312 G1645 MYB-R1 R2R3  90-210 314 G1646 CAAT  72-162 316 G1652 HLH/MYC 143-215 318 G1672 NAC  41-194 320 G1677 NAC  17-181 322 G1749 AP2  84-155 324 G1750 AP2 107-173 326 G1756 WRKY 141-197 328 G1765 NAC  20-140 330 G1777 RING/C3HC4 124-247 332 G1792 AP2  17-85 334 G1793 AP2 179-255, 281-349 336 G1794 AP2 182-249 338 G1804 bZIP 357-407 340 G1818 CAAT  36-113 342 G1820 CAAT  70-133 344 G1836 CAAT  30-164 346 G1838 AP2 229-305, 330-400 348 G1841 AP2  83-150 350 G1842 MADS  2-57 352 G1843 MADS  2-57 354 G1852 AKR  1-600 356 G1863 GRF-like  77-186 358 G1880 Z-C2H2  69-89, 111-139 360 G1895 Z-Dof  55-110 362 G1902 Z-Dof  31-59 364 G1903 Z-Dof 134-180 366 G1919 RING/C3HC4 214-287 368 G1927 NAC  17-188 370 G1930 AP2  59-124 372 G1936 PCF  64-129 374 G1944 AT-hook  87-100 376 G1946 HS  32-130 378 G1947 HS  37-120 380 G1948 AKR  75-126, 120-148, 152-181, 186-215, 261-311, 312-363 382 G1950 AKR  65-228 384 G1958 GARP 230-278 386 G2007 MYB-R1 R2R3  14-116 388 G2010 SBP  53-127 390 G2053 NAC  10-149 392 G2059 AP2 184-254 394 G2085 RING/C3HC4 214-241 396 G2105 TH 100-153 398 G2110 WRKY 239-298 400 G2114 AP2 221-297, 323-393 402 G2117 bZIP  46-106 404 G2123 GF14  99-109 406 G2130 AP2  93-160 408 G2133 AP2  11-83 410 G2138 AP2  76-148 412 G2140 HLH/MYC 167-242 414 G2143 HLH/MYC 128-179 416 G2144 HLH/MYC 203-283 418 G2153 AT-hook  75-94, 162-206 420 G2155 AT-hook  18-38 422 G2192 bZIP-NIN 600-700 424 G2295 MADS  2-57 426 G2340 MYB-R1 R2R3  14-120 428 G2343 MYB-R1 R2R3  14-116 430 G2346 SBP  59-135 432 G2347 SBP  60-136 434 G2379 TH  19-110, 173-232 436 G2430 GARP 425-478 438 G2505 NAC  10-159 440 G2509 AP2  89-156 442 G2517 WRKY 118-174 444 G2520 HLH/MYC 135-206 446 G2555 HLH/MYC 175-245 448 G2557 HLH/MYC 278-328 450 G2583 AP2  4-71 452 G2701 MYB-related  33-81, 129-183 454 G2719 MYB-R1 R2R3  56-154 456 G2789 AT-hook  53-73, 121-165 458 G2830 Z-C2H2 245-266

Examples of some of the utilities that may be desirable in plants, and that may be provided by transforming the plants with the presently disclosed sequences, are listed in Table 6. Many of the transcription factors listed in Table 6 may be operably linked with a specific promoter that causes the transcription factor to be expressed in response to environmental, tissue-specific or temporal signals. For example, G362 induces ectopic trichomes on flowers but also produces small plants. The former may be desirable to produce insect or herbivore resistance, or increased cotton yield, but the latter may be undesirable in that it may reduce biomass. However, by operably linking G362 with a flower-specific promoter, one may achieve the desirable benefits of the genes without affecting overall biomass to a significant degree. For examples of flower specific promoters, see Kaiser et al. (supra). For examples of other tissue-specific, temporal-specific or inducible promoters, see the above discussion under the heading “Vectors, Promoters, and Expression Systems”.

TABLE 6 Genes, traits and utilities that affect plant characteristics Transcription factor genes Trait Category Phenotype(s) that impact traits Utility Abiotic stress Effect of chilling on plants Increased tolerance: G256; G664; G1322 Improved germination, growth rate, earlier planting, yield Germination in cold Increased tolerance: G256; G664 Earlier planting; improved survival, yield Freezing tolerance G720 (G720 KO is more Earlier planting; susceptible); G912; G913 improved quality, survival, yield Drought Increased tolerance: G912; G913; G1820; G1836; Improved survival, G2505 vigor, appearance, yield Heat Increased tolerance: G464; G682; G864; G1305; Improved germination, G1841; G2130; G2430 growth rate, later planting, yield Osmotic stress Increased sensitivity: G1794 Abiotic stress response manipulation Increased tolerance: G47; G175; G188; G303; G325; Improved germination G353; G489; G922; G926; rate, seedling vigor, G1069; G1089; G1452; G1816; survival, yield G1820; G1852; G1930; G2053; G2140; G2153; G2379; G2701; G2719; G2789; G2839 Salt tolerance More susceptible: G545 Manipulation of response to high salt conditions Increased tolerance: G22; G196; G226; G312; G482; Improved germination G801; G867; G922; G1836; rate, survival, yield; G2110 extended growth range Nitrogen stress Sensitivity to N limitation: G1794 Manipulation of response to low nutrient conditions Tolerance to N limitation: G225; G226; G839; G1792; Improved yield and G1816 nutrient stress tolerance, decreased fertilizer usage Phosphate stress Tolerance to P limitation: G545; G561; G911; G1946 Improved yield and nutrient stress tolerance, decreased fertilizer usage Oxidative stress G477 Improved yield, quality, ultraviolet and chemical stress tolerance Herbicide Glyphosate G343; G2133; G2517 Generation of glyphosate-resistant plants to improve weed control Hormone Abscisic acid (ABA) sensitivity sensitivity Reduced sensitivity to ABA: G546; G926; G1069; G1357; Modification of seed G1452; G1820; G2140; G2789 development, improved seed dormancy, cold and dehydration tolerance Sensitivity to ethylene Altered response: G1134 Manipulation of fruit ripening Insensitive to ethylene: G1330 Disease Botrytis Increased susceptibility: G248; G371; G1064; G1084; Manipulation of G1196; G1255; G1756; G1936; response to disease G2555 organism Increased resistance or G28; G1792; G1880; G1919; Improved yield, tolerance: G1950 appearance, survival, extended range Fusarium Increased susceptibility: G188; G545; G896 Manipulation of response to disease organism Increased resistance or G1047; G1792 Improved yield, tolerance: appearance, survival, extended range Erysiphe Increased susceptibility: G545; G881 Manipulation of response to disease organism Increased resistance or G19; G28; G409; G1266; Improved yield, tolerance: G1363; G1792 appearance, survival, extended range Pseudomonas Increased susceptibility: G545 Manipulation of response to disease organism Sclerotinia Increased susceptibility: G278; G477; G594; G1936 Manipulation of response to disease organism Increased resistance or G28; G1927 Improved yield, tolerance: appearance, survival, extended range Growth regulator Altered sugar sensing Alteration of energy Decreased tolerance to sugars: G241; G254; G567; G680; balance, photosynthetic G912; G1804 rate, carbohydrate accumulation, biomass Increased tolerance to sugars: G481; G867; G1225; G1816 production, source-sink relationships, senescence; alteration of storage compound accumulation in seeds Altered C/N sensing G1816 Flowering time Early flowering G157; G180; G183; G485 (OE); Faster generation time; G490; G590; G789; G1225; synchrony of flowering; G1494; G1820; G1841; G1842; additional harvests G1843; G1946; G2010; G2144; within a growing season, G2295; G2347; G2509 shortening of breeding programs Late flowering G8; G47; G157; G192; G214; Increased yield or G231; G361; G362; G485 (KO); biomass, alleviate risk of G562; G736; G748; G859; transgenic pollen escape, G910; G913; G971; G1051; synchrony of flowering G1052; G1357; G1452; G1478; G1804; G1895; G1945; G2007; G2133; G2155; G2838 General Altered flower structure Ornamental development and Stamen: G988; G1075; G1140; G1499; modification of plant morphology G2557 architecture, improved Sepal: G1075; G1140; G2557 or reduced fertility to Petal: G638; G1075; G1140; G1449; mitigate escape of G1499; G2557 transgenic pollen, Pedicel: G353; G354; G988 improved fruit size, Carpel: G1063; G1140; G2143; G2143; shape, number or yield G2557 Multiple alterations: G638; G988; G1063; G1140; G1449; G1499; G2143; G2557 G988; G1449; G2838 Enlarged floral organs: G353; G354 Siliques: G470; G779; G988; G1075; G1140; G1499; G1947; G2143; G2557 Reduced fertility: G638; G779; G1140; G1499 Aerial rosettes G1995; G2826; G2838 Inflorescence architectural Ornamental change modification of flower Altered branching pattern: G47; G1063; G1645; G2143 architecture; timing of Short internodes/bushy G47 flowering; altered plant inflorescences: habit for yield or Internode elongation: G1063 harvestability benefit; Lack of inflorescence: G1499; G2143 reduction in pollen production of genetically modified plants; manipulation of seasonality and annual or perennial habit; manipulation of determinate vs. indeterminate growth Altered shoot meristem Ornamental development modification of plant Stem bifurcations: G390; G391 architecture, manipulation of growth and development, increase in leaf numbers, modulation of branching patterns to provide improved yield or biomass Altered branching pattern G427; G568; G988; G1543; Ornamental G1794 modification of plant architecture, improved lodging resistance Apical dominance Ornamental Reduced apical dominance: G47; G211; G1255; G1275; modification of plant G1411; G1488; G1794; G2509 architecture Altered trichome density; Ornamental development, or structure modification of plant architecture, increased Reduced or no trichomes: G225; G226; G247; G585; plant product (e.g., G676; G682; G1332; G1452; diterpenes, cotton) G1816 productivity, insect and herbivore resistance Ectopic trichomes/altered G247; G362; G370; G676; trichome development/cell G2826 fate: Increase in trichome number, G362; G634; G838; G2838 size or density: Stem morphology and altered G47; G438; G748; G988; Modulation of lignin vascular tissue structure G1488 content; improvement of wood, palatability of fruits and vegetables Root development Improved yield, stress Increased root growth and G1482 tolerance; anchorage proliferation: Increased root hairs: G225; G226; G1816 Altered seed development, G979 ripening and germination Cell differentiation and cell G1540 Increase in carpel or proliferation fruit development; improve regeneration of shoots from callus in transformation or micro- propagation systems Rapid development G2430 Promote faster development and reproduction in plants Senescence Improvement in Premature senescence: G636; G1463; G1944 response to disease, fruit ripening Lethality when overexpressed G877; G1519 Herbicide target; ablation of specific tissues or organs such as stamen to prevent pollen escape Necrosis G12, G24 Disease resistance Plant size Increased plant size G1073; G1451 Improved yield, biomass, appearance Larger seedlings G2346; G2838 Increased survival and vigor of seedlings, yield Dwarfed or more compact G24; G343; G353; G354; G362; Dwarfism, lodging plants G370; G1008; G1277; G1543; resistance, manipulation G1794; G1958 of gibberellin responses Leaf morphology Dark green leaves G674; G912; G1063; G1357; Increased G1452; G1482; G1499; G1792; photosynthesis, biomass, G1863; G1888; G2143; G2557; appearance, yield G2838 Change in leaf shape G211; G353; G674; G736; Ornamental applications G1063; G1146; G1357; G1452; G1494; G1543; G1863; G2143; G2144 Altered leaf size: Increased yield, Increased leaf size, number or G189; G214; G1451; G2430 ornamental applications mass: Light green leaves G1494; G2144 Ornamental applications Variegation G635 Ornamental applications Glossy leaves G30; G1792; G2583 Ornamental applications, manipulation of wax composition, amount, or distribution Seed morphology Altered seed coloration G156; G2105; G2085 Appearance Seed size and shape Increased seed size: G450; G584; G1255; G2085; Yield, appearance G2105; G2114 Decreased seed size: G1040 Appearance Altered seed shape: G1040; G1062 Appearance Leaf biochemistry Increased leaf wax G975; G1792; G2583 Insect, pathogen resistance Leaf prenyl lipids Reduced chlorophyll: G987 Increase in tocopherols G652; G987; G2509 Increased lutein content G748 Increase in chlorophyll or G214; G1543 carotenoids: Leaf insoluble sugars Increase in leaf xylose G211 Increased leaf anthocyanins G663; G1482; G1888 Leaf fatty acids Reduction in leaf fatty acids: G987 Increase in leaf fatty acids: G214 Seed Seed oil content Improved oil yield biochemistry Increased oil content: G162; G291; G427; G509; Reduced caloric content G519; G561; G590; G598; G629; G715; G849; G961; G1198; G1226; G1471; G1478; G1526; G1640; G1646; G1750; G1765; G1777; G1793; G1838; G1902; G1946; G1948; G1958, G2123; G2138; G2343; G2830 Decreased oil content: G180; G192; G241; G504; G1143; G1229; G1323; G1543; G2509 Altered oil content: G567; G892; G974; G1451; G1496; G1646; G1672; G1677 Altered fatty acid content: G869; G1417; G2192 Seed protein content Improved protein yield, Increased protein content: G162; G226; G241; G509; nutritional value G988; G1323; G1419; G1652; Reduced caloric content G1818; G1820; G1958; G2117; G2509 Decreased protein content: G427; G1478; G1777; G1903; G1946 Altered protein content: G162; G567; G597; G849; G892; G1634; G1637; G1677 Altered seed prenyl lipid G652; G2509; G2520 Improved antioxidant content or composition and vitamin E content Seed glucosinolate Altered profile: G484; G2340 Increased seed anthocyanins G362; G663 Root Increased root anthocyanins G663 Biochemistry Light Altered cotyledon, hypocotyl, G183; G354; G1322; G1331; Potential for increased response/shade petiole development; altered G1488; G1494; G1794; G2144; planting densities and avoidance leaf orientation; constitutive G2555 yield enhancement photomorphogenesis; photomorphogenesis in low light Pigment Increased anthocyanin level G362; G663; G1482 Enhanced health benefits, improved ornamental appearance, increased stress resistance, attraction of pollinating and seed- dispersing animals
Abbreviations:

N = nitrogen

P = phosphate

ABA = abscisic acid

C/N = carbon/nitrogen balance

Detailed Description of Genes, Traits and Utilities that Affect Plant Characteristics

The following descriptions of traits and utilities associated with the present transcription factors offer a more comprehensive description than that provided in Table 6.

Abiotic Stress, General Considerations

Plant transcription factors can modulate gene expression, and, in turn, be modulated by the environmental experience of a plant. Significant alterations in a plant's environment invariably result in a change in the plant's transcription factor gene expression pattern. Altered transcription factor expression patterns generally result in phenotypic changes in the plant. Transcription factor gene product(s) in transgenic plants then differ(s) in amounts or proportions from that found in wild-type or non-transformed plants, and those transcription factors likely represent polypeptides that are used to alter the response to the environmental change. By way of example, it is well accepted in the art that analytical methods based on altered expression patterns may be used to screen for phenotypic changes in a plant far more effectively than can be achieved using traditional methods.

Abiotic stress: adult stage chilling. Enhanced chilling tolerance may extend the effective growth range of chilling sensitive crop species by allowing earlier planting or later harvest. Improved chilling tolerance may be conferred by increased expression of glycerol-3-phosphate acetyltransferase in chloroplasts (see, for example, Wolter et al. (1992) et al. EMBO J. 4685-4692, and Murata et al. (1992) Nature 356: 710-713).

Chilling tolerance could also serve as a model for understanding how plants adapt to water deficit. Both chilling and water stress share similar signal transduction pathways and tolerance/adaptation mechanisms. For example, acclimation to chilling temperatures can be induced by water stress or treatment with abscisic acid. Genes induced by low temperature include dehydrins (or LEA proteins). Dehydrins are also induced by salinity, abscisic acid, water stress, and during the late stages of embryogenesis.

Another large impact of chilling occurs during post-harvest storage. For example, some fruits and vegetables do not store well at low temperatures (for example, bananas, avocados, melons, and tomatoes). The normal ripening process of the tomato is impaired if it is exposed to cool temperatures. Transcription factor genes conferring resistance to chilling temperatures, including G256, G664, and G1322 may thus enhance tolerance during post-harvest storage.

Abiotic stress: cold germination. Several of the presently disclosed transcription factor genes confer better germination and growth in cold conditions. For example, the improved germination in cold conditions seen with G256 and G664 indicates a role in regulation of cold responses by these genes and their equivalogs. These genes might be engineered to manipulate the response to low temperature stress. Genes that would allow germination and seedling vigor in the cold would have highly significant utility in allowing seeds to be planted earlier in the season with a high rate of survival. Transcription factor genes that confer better survival in cooler climates allow a grower to move up planting time in the spring and extend the growing season further into autumn for higher crop yields. Germination of seeds and survival at temperatures significantly below that of the mean temperature required for germination of seeds and survival of non-transformed plants would increase the potential range of a crop plant into regions in which it would otherwise fail to thrive.

Abiotic stress: freezing tolerance and osmotic stress. Presently disclosed transcription factor genes, including G47, G175, G188, G303, G325, G353, G489, G922, G926, G1069, G1089, G1452, G1820, G1852, G1930, G2053, G2140, G2153, G2379, G2701, G2719, G2789, G2839 and their equivalogs, that increase germination rate and/or growth under adverse osmotic conditions, could impact survival and yield of seeds and plants. Osmotic stresses may be regulated by specific molecular control mechanisms that include genes controlling water and ion movements, functional and structural stress-induced proteins, signal perception and transduction, and free radical scavenging, and many others (Wang et al. (2001) Acta Hort. (ISHS) 560: 285-292). Instigators of osmotic stress include freezing, drought and high salinity, each of which are discussed in more detail below.

In many ways, freezing, high salt and drought have similar effects on plants, not the least of which is the induction of common polypeptides that respond to these different stresses. For example, freezing is similar to water deficit in that freezing reduces the amount of water available to a plant. Exposure to freezing temperatures may lead to cellular dehydration as water leaves cells and forms ice crystals in intercellular spaces (Buchanan, supra). As with high salt concentration and freezing, the problems for plants caused by low water availability include mechanical stresses caused by the withdrawal of cellular water. Thus, the incorporation of transcription factors that modify a plant's response to osmotic stress or improve tolerance to (e.g., by G720, G912, G913 or their equivalogs) into, for example, a crop or ornamental plant, may be useful in reducing damage or loss. Specific effects caused by freezing, high salt and drought are addressed below.

Abiotic stress: drought and low humidity tolerance. Exposure to dehydration invokes similar survival strategies in plants as does freezing stress (see, for example, Yelenosky (1989) Plant Physiol 89: 444-451) and drought stress induces freezing tolerance (see, for example, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy et al. (1992) Planta 188:265-270). In addition to the induction of cold-acclimation proteins, strategies that allow plants to survive in low water conditions may include, for example, reduced surface area, or surface oil or wax production. A number of presently disclosed transcription factor genes, e.g., G912, G913, G1820, G1836 and G2505 increase a plant's tolerance to low water conditions and, along with their functional equivalogs, would provide the benefits of improved survival, increased yield and an extended geographic and temporal planting range.

Abiotic stress: heat stress tolerance. The germination of many crops is also sensitive to high temperatures. Presently disclosed transcription factor genes that provide increased heat tolerance, including G464, G682, G864, G1305, G1841, G2130, G2430 and their equivalogs, would be generally useful in producing plants that germinate and grow in hot conditions, may find particular use for crops that are planted late in the season, or extend the range of a plant by allowing growth in relatively hot climates.

Abiotic stress: salt. The genes in Table 6 that provide tolerance to salt may be used to engineer salt tolerant crops and trees that can flourish in soils with high saline content or under drought conditions. In particular, increased salt tolerance during the germination stage of a plant enhances survival and yield. Presently disclosed transcription factor genes, including G22, G1196, G226, G312, G482, G801, G867, G922, G1836, G2110, and their equivalogs that provide increased salt tolerance during germination, the seedling stage, and throughout a plant's life cycle, would find particular value for imparting survival and yield in areas where a particular crop would not normally prosper.

Nutrient uptake and utilization: nitrogen and phosphorus. Presently disclosed transcription factor genes introduced into plants provide a means to improve uptake of essential nutrients, including nitrogenous compounds, phosphates, potassium, and trace minerals. The enhanced performance of, for example, G225, G226, G839, G1792, and other overexpressing lines under low nitrogen, and G545, G561, G911, G1946 under low phosphorous conditions indicate that these genes and their equivalogs can be used to engineer crops that could thrive under conditions of reduced nutrient availability. Phosphorus, in particular, tends to be a limiting nutrient in soils and is generally added as a component in fertilizers. Young plants have a rapid intake of phosphate and sufficient phosphate is important for yield of root crops such as carrot, potato and parsnip.

The effect of these modifications is to increase the seedling germination and range of ornamental and crop plants. The utilities of presently disclosed transcription factor genes conferring tolerance to conditions of low nutrients also include cost savings to the grower by reducing the amounts of fertilizer needed, environmental benefits of reduced fertilizer runoff into watersheds; and improved yield and stress tolerance. In addition, by providing improved nitrogen uptake capability, these genes can be used to alter seed protein amounts and/or composition in such a way that could impact yield as well as the nutritional value and production of various food products.

A number of the transcription factor-overexpressing lines make less anthocyanin on high sucrose plus glutamine indicates that these genes can be used to modify carbon and nitrogen status, and hence assimilate partitioning (assimilate partitioning refers to the manner in which an essential element, such as nitrogen, is distributed among different pools inside a plant, generally in a reduced form, for the purpose of transport to various tissues).

Increased tolerance of plants to oxidative stress. In plants, as in all living things, abiotic and biotic stresses induce the formation of oxygen radicals, including superoxide and peroxide radicals. This has the effect of accelerating senescence, particularly in leaves, with the resulting loss of yield and adverse effect on appearance. Generally, plants that have the highest level of defense mechanisms, such as, for example, polyunsaturated moieties of membrane lipids, are most likely to thrive under conditions that introduce oxidative stress (e.g., high light, ozone, water deficit, particularly in combination). Introduction of the presently disclosed transcription factor genes, including G477 and its equivalogs, that increase the level of oxidative stress defense mechanisms would provide beneficial effects on the yield and appearance of plants. One specific oxidizing agent, ozone, has been shown to cause significant foliar injury, which impacts yield and appearance of crop and ornamental plants. In addition to reduced foliar injury that would be found in ozone resistant plant created by transforming plants with some of the presently disclosed transcription factor genes, the latter have also been shown to have increased chlorophyll fluorescence (Yu-Sen Changet al. (2001) Bot. Bull. Acad. Sin. 42: 265-272).

Decreased herbicide sensitivity. Presently disclosed transcription factor genes, including G343, G2133, G2517 and their equivalogs, that confer resistance or tolerance to herbicides (e.g., glyphosate) will find use in providing means to increase herbicide applications without detriment to desirable plants. This would allow for the increased use of a particular herbicide in a local environment, with the effect of increased detriment to undesirable species and less harm to transgenic, desirable cultivars.

Knockouts of a number of the presently disclosed transcription factor genes have been shown to be lethal to developing embryos. Thus, these genes are potentially useful as herbicide targets.

Hormone sensitivity. ABA plays regulatory roles in a host of physiological processes in all higher as well as in lower plants (Davies et al. (1991) Abscisic Acid: Physiology and Biochemistry. Bios Scientific Publishers, Oxford, UK; Zeevaart et al. (1988) Ann Rev Plant Physiol. Plant Mol. Biol. 49: 439-473; Shimizu-Sato et al. (2001) Plant Physiol 127: 1405-1413). ABA mediates stress tolerance responses in higher plants, is a key signal compound that regulates stomatal aperture and, in concert with other plant signaling compounds, is implicated in mediating responses to pathogens and wounding or oxidative damage (for example, see Larkindale et al. (2002) Plant Physiol. 128: 682-695). In seeds, ABA promotes seed development, embryo maturation, synthesis of storage products (proteins and lipids), desiccation tolerance, and is involved in maintenance of dormancy (inhibition of germination), and apoptosis (Zeevaart et al. (1988) Ann Rev Plant Physiol. Plant Mol. Biol. 49: 439-473; Davies (1991), supra; Thomas (1993) Plant Cell 5: 1401-1410; and Bethke et al. (1999) Plant Cell 11: 1033-1046). ABA also affects plant architecture, including root growth and morphology and root-to-shoot ratios. ABA action and metabolism is modulated not only by environmental signals but also by endogenous signals generated by metabolic feedback, transport, hormonal cross-talk and developmental stage. Manipulation of ABA levels, and hence by extension the sensitivity to ABA, has been described as a very promising means to improve productivity, performance and architecture in plants Zeevaart (1999) in: Biochemistry and Molecular Biology of Plant Hormones, Hooykaas et al. eds, Elsevier Science pp 189-207; and Cutler et al. (1999) Trends Plant Sci. 4: 472-478).

A number of the presently disclosed transcription factor genes affect plant abscisic acid (ABA) sensitivity, including G546, G926, 1069, G1357, G1452, G1820, G2140, G2789. Thus, by affecting ABA sensitivity, these introduced transcription factor genes and their equivalogs would affect cold, drought, oxidative and other stress sensitivities, plant architecture, and yield.

Several other of the present transcription factor genes have been used to manipulate ethylene signal transduction and response pathways. These genes can thus be used to manipulate the processes influenced by ethylene, such as seed germination or fruit ripening, and to improve seed or fruit quality.

Diseases, pathogens and pests. A number of the presently disclosed transcription factor genes have been shown to or are likely to affect a plants response to various plant diseases, pathogens and pests. The offending organisms include fungal pathogens Fusarium oxysporum, Botrytis cinerea, Sclerotinia sclerotiorum, and Erysiphe orontii. Bacterial pathogens to which resistance may be conferred include Pseudomonas syringae. Other problem organisms may potentially include nematodes, mollicutes, parasites, or herbivorous arthropods. In each case, one or more transformed transcription factor genes may provide some benefit to the plant to help prevent or overcome infestation, or be used to manipulate any of the various plant responses to disease. These mechanisms by which the transcription factors work could include increasing surface waxes or oils, surface thickness, or the activation of signal transduction pathways that regulate plant defense in response to attacks by herbivorous pests (including, for example, protease inhibitors). Another means to combat fungal and other pathogens is by accelerating local cell death or senescence, mechanisms used to impair the spread of pathogenic microorganisms throughout a plant. For instance, the best known example of accelerated cell death is the resistance gene-mediated hypersensitive response, which causes localized cell death at an infection site and initiates a systemic defense response. Because many defenses, signaling molecules, and signal transduction pathways are common to defense against different pathogens and pests, such as fungal, bacterial, oomycete, nematode, and insect, transcription factors that are implicated in defense responses against the fungal pathogens tested may also function in defense against other pathogens and pests. These transcription factors include, for example, G28, G1792, G1880, G1919, G1950 (improved resistance or tolerance to Botrytis), G1047, G1792 (improved resistance or tolerance to Fusarium), G19, G28, G409, G1266, G1363, G1792 (improved resistance or tolerance to Erysiphe), G545 (improved resistance or tolerance to Pseudomonas), G28, G1927 (improved resistance or tolerance to Sclerotinia), and their equivalogs.

Growth regulator: sugar sensing. In addition to their important role as an energy source and structural component of the plant cell, sugars are central regulatory molecules that control several aspects of plant physiology, metabolism and development (Hsieh et al. (1998) Proc. Natl. Acad. Sci. 95: 13965-13970). It is thought that this control is achieved by regulating gene expression and, in higher plants, sugars have been shown to repress or activate plant genes involved in many essential processes such as photosynthesis, glyoxylate metabolism, respiration, starch and sucrose synthesis and degradation, pathogen response, wounding response, cell cycle regulation, pigmentation, flowering and senescence. The mechanisms by which sugars control gene expression are not understood.

Because sugars are important signaling molecules, the ability to control either the concentration of a signaling sugar or how the plant perceives or responds to a signaling sugar could be used to control plant development, physiology or metabolism. For example, the flux of sucrose (a disaccharide sugar used for systemically transporting carbon and energy in most plants) has been shown to affect gene expression and alter storage compound accumulation in seeds. Manipulation of the sucrose signaling pathway in seeds may therefore cause seeds to have more protein, oil or carbohydrate, depending on the type of manipulation. Similarly, in tubers, sucrose is converted to starch which is used as an energy store. It is thought that sugar signaling pathways may partially determine the levels of starch synthesized in the tubers. The manipulation of sugar signaling in tubers could lead to tubers with a higher starch content.

Thus, the presently disclosed transcription factor genes that manipulate the sugar signal transduction pathway, including G241, G254, G567, G680, G912, G1804, G481, G867, G1225, along with their equivalogs, may lead to altered gene expression to produce plants with desirable traits. In particular, manipulation of sugar signal transduction pathways could be used to alter source-sink relationships in seeds, tubers, roots and other storage organs leading to increase in yield.

Growth regulator: C/N sensing. Nitrogen and carbon metabolism are tightly linked in almost every biochemical pathway in the plant. Carbon metabolites regulate genes involved in N acquisition and metabolism, and are known to affect germination and the expression of photosynthetic genes (Coruzzi et al. (2001) Plant Physiol. 125: 61-64) and hence growth. Early studies on nitrate reductase (NR) in 1976 showed that NR activity could be affected by Glc/Suc (Crawford (1995) Plant Cell 7: 859-886; Daniel-Vedele et al. (1996) CR Acad Sci Paris 319: 961-968). Those observations were supported by later experiments that showed sugars induce NR mRNA in dark-adapted, green seedlings (Cheng CL, et al. (1992) Proc Natl Acad Sci U.S.A 89: 1861-1864). C and N may have antagonistic relationships as signaling molecules; light induction of NR activity and mRNA levels can be mimicked by C metabolites and N-metabolites cause repression of NR induction in tobacco (Vincentz et al. (1992) Plant J 3: 315-324). Gene regulation by C/N status has been demonstrated for a number of N-metabolic genes (Stitt (1999) Curr. Opin. Plant. Biol. 2: 178-186); Coruzzi et al. (2001) supra). Thus, transcription factor genes that affect C/N sensing, such as G1816, can be used to alter or improve germination and growth under nitrogen-limiting conditions.

Flowering time: early and late flowering. Presently disclosed transcription factor genes that accelerate flowering, which include G157, G180, G183, G485, G490, G590, G789, G1225, G1494, G1820, G1841, G1842, G1843, G1946, G2010, G2144, G2295, G2347, G2509, and their functional equivalogs, could have valuable applications in such programs, since they allow much faster generation times. In a number of species, for example, broccoli, cauliflower, where the reproductive parts of the plants constitute the crop and the vegetative tissues are discarded, it would be advantageous to accelerate time to flowering. Accelerating flowering could shorten crop and tree breeding programs. Additionally, in some instances, a faster generation time would allow additional harvests of a crop to be made within a given growing season. A number of Arabidopsis genes have already been shown to accelerate flowering when constitutively expressed. These include LEAFY, APETALA1 and CONSTANS (Mandel et al. (1995) Nature 377: 522-524; Weigel and Nilsson (1995) Nature 377:et al. 495-500; Simon et al. (1996) Nature 384: 59-62).

By regulating the expression of potential flowering using inducible promoters, flowering could be triggered by application of an inducer chemical. This would allow flowering to be synchronized across a crop and facilitate more efficient harvesting. Such inducible systems could also be used to tune the flowering of crop varieties to different latitudes. At present, species such as soybean and cotton are available as a series of maturity groups that are suitable for different latitudes on the basis of their flowering time (which is governed by day-length). A system in which flowering could be chemically controlled would allow a single high-yielding northern maturity group to be grown at any latitude. In southern regions such plants could be grown for longer periods before flowering was induced, thereby increasing yields. In more northern areas, the induction would be used to ensure that the crop flowers prior to the first winter frosts.

In a sizeable number of species, for example, root crops, where the vegetative parts of the plants constitute the crop and the reproductive tissues are discarded, it is advantageous to identify and incorporate transcription factor genes that delay or prevent flowering in order to prevent resources being diverted into reproductive development. For example, G8, G47, G157, G192, G214, G231; G361, G362, G562, G736, G748, G859, G910, G913, G971, G1051, G1052, G1357, G1452, G1478, G1804, G1895, G1945, G2007, G2133, G2155, G2838 and equivalogs, delay flowering time in transgenic plants. Extending vegetative development with presently disclosed transcription factor genes could thus bring about large increases in yields. Prevention of flowering can help maximize vegetative yields and prevent escape of genetically modified organism (GMO) pollen.

Presently disclosed transcription factors that extend flowering time have utility in engineering plants with longer-lasting flowers for the horticulture industry, and for extending the time in which the plant is fertile.

A number of the presently disclosed transcription factors may extend flowering time, and delay flower abscission, which would have utility in engineering plants with longer-lasting flowers for the horticulture industry. This would provide a significant benefit to the ornamental industry, for both cut flowers and woody plant varieties (of, for example, maize), as well as have the potential to lengthen the fertile period of a plant, which could positively impact yield and breeding programs.

General development and morphology: flower structure and inflorescence: architecture, altered flower organs, reduced fertilitv, multiple alterations, aerial rosettes, branching, internode distance, terminal flowers and phase change. Presently disclosed transgenic transcription factors such as G353; G354, G638; G779; G988; G1063; G1075; G1140; G1449; G1499; G2143; 62557, G2838, G2839 and their equivalogs, may be used to create plants with larger flowers or arrangements of flowers that are distinct from wild-type or non-transformed cultivars. This would likely have the most value for the ornamental horticulture industry, where larger flowers or interesting floral configurations are generally preferred and command the highest prices.

Flower structure may have advantageous or deleterious effects on fertility, and could be used, for example, to decrease fertility by the absence, reduction or screening of reproductive components. In fact, plants that overexpress a sizable number of the presently disclosed transcription factor genes e.g., G470, G779, G988, G1075, G1140, G1499, G1947, G2143, G2557 and their functional equivalogs, possess reduced fertility; flowers are infertile and fail to yield seed. These could be desirable traits, as low fertility could be exploited to prevent or minimize the escape of the pollen of genetically modified organisms (GMOs) into the environment.

The alterations in shoot architecture seen in the lines transformed with G47, G1063, G1645, G2143, and their functional equivalogs indicates that these genes and their equivalogs can be used to manipulate inflorescence branching patterns. This could influence yield and offer the potential for more effective harvesting techniques. For example, a “self pruning” mutation of tomato results in a determinate growth pattern and facilitates mechanical harvesting (Pnueli et al. (2001) Plant Cell 13(12): 2687-702).

One interesting application for manipulation of flower structure, for example, by introduced transcription factors could be in the increased production of edible flowers or flower parts, including saffron, which is derived from the stigmas of Crocus sativus.

Genes that later silique conformation in brassicates may be used to modify fruit ripening processes in brassicates and other plants, which may positively affect seed or fruit quality.

A number of the presently disclosed transcription factors may affect the timing of phase changes in plants. Since the timing or phase changes generally affects a plant's eventual size, these genes may prove beneficial by providing means for improving yield and biomass.

General development and morphology: shoot meristem and branching patterns. Several of the presently disclosed transcription factor genes, including G390 and G391, and G1794, when introduced into plants, have been shown to cause stem bifurcations in developing shoots in which the shoot meristems split to form two or three separate shoots. These transcription factors and their functional equivalogs may thus be used to manipulate branching. This would provide a unique appearance, which may be desirable in ornamental applications, and may be used to modify lateral branching for use in the forestry industry. A reduction in the formation of lateral branches could reduce knot formation. Conversely, increasing the number of lateral branches could provide utility when a plant is used as a view- or windscreen.

General development and morphology: apical dominance: The modified expression of presently disclosed transcription factors (e.g., G47, G211, G1255, G1275, G1411, G1488, G1794, G2509 and their equivalogs) that reduce apical dominance could be used in ornamental horticulture, for example, to modify plant architecture, for example, to produce a shorter, more bushy stature than wild type. The latter form would have ornamental utility as well as provide increased resistance to lodging.

General development and morphology: trichome density, development or structure. Several of the presently disclosed transcription factor genes have been used to modify trichome number, density, trichome cell fate, amount of trichome products produced by plants, or produce ectopic trichome formation. These include G225; G226, G247; G362, G370; G585, G634, G676, G682, G1332, G1452, G1995, G2826, and G2838. In most cases where the metabolic pathways are impossible to engineer, increasing trichome density or size on leaves may be the only way to increase plant productivity. Thus, by increasing trichome density, size or type, these trichome-affecting genes and their functional equivalogs would have profound utilities in molecular farming practices by making use of trichomes as a manufacturing system for complex secondary metabolites.

Trichome glands on the surface of many higher plants produce and secrete exudates that give protection from the elements and pests such as insects, microbes and herbivores. These exudates may physically immobilize insects and spores, may be insecticidal or ant-microbial or they may act as allergens or irritants to protect against herbivores. By modifying trichome location, density or activity with presently disclosed transcription factors that modify these plant characteristics, plants that are better protected and higher yielding may be the result.

A potential application for these trichome-affecting genes and their equivalogs also exists in cotton: cotton fibers are modified unicellular trichomes that develop from the outer ovule epidermis. In fact, only about 30% of these epidermal cells develop into trichomes, but all have the potential to develop a trichome fate. Trichome-affecting genes can trigger an increased number of these cells to develop as trichomes and thereby increase the yield of cotton fibers. Since the mallow family is closely related to the Brassica family, genes involved in trichome formation will likely have homologs in cotton or function in cotton.

If the effects on trichome patterning reflect a general change in heterochronic processes, trichome-affecting transcription factors or their equivalogs can be used to modify the way meristems and/or cells develop during different phases of the plant life cycle. In particular, altering the timing of phase changes could afford positive effects on yield and biomass production.

General development and morphology: stem morphologv and altered vascular tissue structure. Plants transformed with transcription factor genes that modify stem morphology or lignin content may be used to affect overall plant architecture and the distribution of lignified fiber cells within the stem.

Modulating lignin content might allow the quality of wood used for furniture or construction to be improved. Lignin is energy rich; increasing lignin composition could therefore be valuable in raising the energy content of wood used for fuel. Conversely, the pulp and paper industries seek wood with a reduced lignin content. Currently, lignin must be removed in a costly process that involves the use of many polluting chemicals. Consequently, lignin is a serious barrier to efficient pulp and paper production (Tzfira et al. (1998) TIBTECH 16: 439-446; Robinson (1999) Nature Biotechnology 17: 27-30). In addition to forest biotechnology applications, changing lignin content by selectively expressing or repressing transcription factors in fruits and vegetables might increase their palatability.

Transcription factors that modify stem structure, including G47, G438, G748, G988, G1488 and their equivalogs, may also be used to achieve reduction of higher-order shoot development, resulting in significant plant architecture modification. Overexpression of the genes that encode these transcription factors in woody plants might result in trees that lack side branches, and have fewer knots in the wood. Altering branching patterns could also have applications amongst ornamental and agricultural crops. For example, applications might exist in any species where secondary shoots currently have to be removed manually, or where changes in branching pattern could increase yield or facilitate more efficient harvesting.

General development and morphology: altered root development. By modifying the structure or development of roots by transforming into a plant one or more of the presently disclosed transcription factor genes, including G225, G226, G1482, and their equivalogs, plants may be produced that have the capacity to thrive in otherwise unproductive soils. For example, grape roots extending further into rocky soils would provide greater anchorage, greater coverage with increased branching, or would remain viable in waterlogged soils, thus increasing the effective planting range of the crop and/or increasing yield and survival. It may be advantageous to manipulate a plant to produce short roots, as when a soil in which the plant will be growing is occasionally flooded, or when pathogenic fungi or disease-causing nematodes are prevalent.

General development and morphology: seed development, ripening and germination rate. A number of the presently disclosed transcription factor genes (e.g., G979) have been shown to modify seed development and germination rate, including when the seeds are in conditions normally unfavorable for germination (e.g., cold, heat or salt stress, or in the presence of ABA), and may, along with functional equivalogs, thus be used to modify and improve germination rates under adverse conditions.

General development and morphology: cell differentiation and cell proliferation. Several of the disclosed transcription factors regulate cell proliferation and/or differentiation, including G1540 and its functional equivalogs. Control of these processes could have valuable applications in plant transformation, cell culture or micro-propagation systems, as well as in control of the proliferation of particular useful tissues or cell types. Transcription factors that induce the proliferation of undifferentiated cells can be operably linked with an inducible promoter to promote the formation of callus that can be used for transformation or production of cell suspension cultures. Transcription factors that prevent cells from differentiating, such as G1540 or its equivalogs, could be used to confer stem cell identity to cultured cells. Transcription factors that promote differentiation of shoots could be used in transformation or micro-propagation systems, where regeneration of shoots from callus is currently problematic. In addition, transcription factors that regulate the differentiation of specific tissues could be used to increase the proportion of these tissues in a plant. Genes that promote the differentiation of carpet tissue could be introduced into commercial species to induce formation of increased numbers of carpets or fruits. A particular application might exist in saffron, one of the world's most expensive spices. Saffron filaments, or threads, are actually the dried stigmas of the saffron flower, Crocus sativus Linneaus. Each flower contains only three stigmas, and more than 75,000 of these flowers are needed to produce just one pound of saffron filaments. An increase in carpel number would increase the quantity of stigmatic tissue and improve yield.

General development and morphology: cell expansion. Plant growth results from a combination of cell division and cell expansion. Transcription factors may be useful in regulation of cell expansion. Altered regulation of cell expansion could affect stem length, an important agronomic characteristic. For instance, short cultivars of wheat contributed to the Green Revolution, because plants that put fewer resources into stem elongation allocate more resources into developing seed and produce higher yield. These plants are also less vulnerable to wind and rain damage. These cultivars were found to be altered in their sensitivity to gibberellins, hormones that regulate stem elongation through control of both cell expansion and cell division. Altered cell expansion in leaves could also produce novel and ornamental plant forms.

General development and morphology: phase change and floral reversion. Transcription factors that regulate phase change can modulate the developmental programs of plants and regulate developmental plasticity of the shoot meristem. In particular, these genes might be used to manipulate seasonality and influence whether plants display an annual or perennial habit.

General development and morphology: rapid development. A number of the presently disclosed transcription factor genes, including G2430, have been shown to have significant effects on plant growth rate and development. These observations have included, for example, more rapid or delayed growth and development of reproductive organs. Thus, by causing more rapid development, G2430 and its functional equivalogs would prove useful for regions with short growing seasons; other transcription factors that delay development may be useful for regions with longer growing seasons. Accelerating plant growth would also improve early yield or increase biomass at an earlier stage, when such is desirable (for example, in producing forestry products or vegetable sprouts for consumption). Transcription factors that promote faster development such as G2430 and its functional equivalogs may also be used to modify the reproductive cycle of plants.

General development and morphology: slow growth rate. A number of the presently disclosed transcription factor genes, including G652 and G1335, have been shown to have significant effects on retarding plant growth rate and development. These observations have included, for example, delayed growth and development of reproductive organs. Slow growing plants may be highly desirable to ornamental horticulturists, both for providing house plants that display little change in their appearance over time, or outdoor plants for which wild-type or rapid growth is undesirable (e.g., ornamental palm trees). Slow growth may also provide for a prolonged fruiting period, thus extending the harvesting season, particularly in regions with long growing seasons. Slow growth could also provide a prolonged period in which pollen is available for improved self- or cross-fertilization, or cross-fertilization of cultivars that normally flower over non-overlapping time periods. The latter aspect may be particularly useful to plants comprising two or more distinct grafted cultivars (e.g., fruit trees) with normally non-overlapping flowering periods.

General development and morphology: senescence. Presently disclosed transcription factor genes may be used to alter senescence responses in plants. Although leaf senescence is thought to be an evolutionary adaptation to recycle nutrients, the ability to control senescence in an agricultural setting has significant value. For example, a delay in leaf senescence in some maize hybrids is associated with a significant increase in yields and a delay of a few days in the senescence of soybean plants can have a large impact on yield. In an experimental setting, tobacco plants engineered to inhibit leaf senescence had a longer photosynthetic lifespan, and produced a 50% increase in dry weight and seed yield (Gan and Amasino (1995) Science 270: 1986-1988). Delayed flower senescence caused by overexpression of transcription factors may generate plants that retain their blossoms longer and this may be of potential interest to the ornamental horticulture industry, and delayed foliar and fruit senescence could improve post-harvest shelf-life of produce.

Premature senescence caused by, for example, G636, G1463, G1944 and their equivalogs may be used to improve a plant's response to disease and hasten fruit ripening.

Growth rate and development: lethality and necrosis. Overexpression of transcription factors, for example, G12, G24, G877, G1519 and their equivalogs that have a role in regulating cell death may be used to induce lethality in specific tissues or necrosis in response to pathogen attack. For example, if a transcription factor gene inducing lethality or necrosis was specifically active in gametes or reproductive organs, its expression in these tissues would lead to ablation and subsequent male or female sterility. Alternatively, under pathogen-regulated expression, a necrosis-inducing transcription factor can restrict the spread of a pathogen infection through a plant.

Plant size: large plants. Plants overexpressing G1073 and G1451, for example, have been shown to be larger than controls. For some ornamental plants, the ability to provide larger varieties with these genes or their equivalogs may be highly desirable. For many plants, including fruit-bearing trees, trees that are used for lumber production, or trees and shrubs that serve as view or wind screens, increased stature provides improved benefits in the forms of greater yield or improved screening. Crop species may also produce higher yields on larger cultivars, particularly those in which the vegetative portion of the plant is edible.

Plant size: large seedlings. Presently disclosed transcription factor genes, that produce large seedlings can be used to produce crops that become established faster. Large seedlings are generally hardier, less vulnerable to stress, and better able to out-compete weed species. Seedlings transformed with presently disclosed transcription factors, including G2346 and G2838, for example, have been shown to possess larger cotyledons and were more developmentally advanced than control plants. Rapid seedling development made possible by manipulating expression of these genes or their equivalogs is likely to reduce loss due to diseases particularly prevalent at the seedling stage (e.g., damping off) and is thus important for survivability of plants germinating in the field or in controlled environments.

Plant size: dwarfed plants. Presently disclosed transcription factor genes, including G24; G343, G353, G354, G362, G370; G1008, G1277, G1543, G1794, G1958 and their equivalogs, for example, that can be used to decrease plant stature are likely to produce plants that are more resistant to damage by wind and rain, have improved lodging resistance, or more resistant to heat or low humidity or water deficit. Dwarf plants are also of significant interest to the ornamental horticulture industry, and particularly for home garden applications for which space availability may be limited.

Plant size: fruit size and number. Introduction of presently disclosed transcription factor genes that affect fruit size will have desirable impacts on fruit size and number, which may comprise increases in yield for fruit crops, or reduced fruit yield, such as when vegetative growth is preferred (e.g., with bushy ornamentals, or where fruit is undesirable, as with ornamental olive trees).

Leaf morphology: dark leaves. Color-affecting components in leaves include chlorophylls (generally green), anthocyanins (generally red to blue) and carotenoids (generally yellow to red). Transcription factor genes that increase these pigments in leaves, including G674, G912, G1063, G1357, G1452, G1482, G1499, G1792, G1863, G1888, G2143, G2557, G2838 and their equivalogs, may positively affect a plant's value to the ornamental horticulture industry. Variegated varieties, in particular, would show improved contrast. Other uses that result from overexpression of transcription factor genes include improvements in the nutritional value of foodstuffs. For example, lutein is an important nutraccutical; lutein-rich diets have been shown to help prevent age-related macular degeneration (ARMD), the leading cause of blindness in elderly people. Consumption of dark green leafy vegetables has been shown in clinical studies to reduce the risk of ARMD.

Enhanced chlorophyll and carotenoid levels could also improve yield in crop plants. Lutein, like other xanthophylls such as zeaxanthin and violaxanthin, is an essential component in the protection of the plant against the damaging effects of excessive light. Specifically, lutein contributes, directly or indirectly, to the rapid rise of non-photochemical quenching in plants exposed to high light. Crop plants engineered to contain higher levels of lutein could therefore have improved photo-protection, leading to less oxidative damage and better growth under high light (e.g., during long summer days, or at higher altitudes or lower latitudes than those at which a non-transformed plant would survive). Additionally, elevated chlorophyll levels increases photosynthetic capacity.

Leaf morphology: changes in leaf shape. Presently disclosed transcription factors produce marked and diverse effects on leaf development and shape. The transcription factors include G211, G353, G674, G736, G1063, G1146, G1357, G1452, G1494, G1543, G1863, G2143, G2144, and their equivalogs. At early stages of growth, transgenic seedlings have developed narrow, upward pointing leaves with long petioles, possibly indicating a disruption in circadian-clock controlled processes or nyctinastic movements. Other transcription factor genes can be used to alter leaf shape in a significant manner from wild type, some of which may find use in ornamental applications.

Leaf morphology: altered leaf size. Large leaves, such as those produced in plants overexpressing G189,G1451,G2430 and their functional equivalogs, generally increase plant biomass. This provides benefit for crops where the vegetative portion of the plant is the marketable portion.

Leaf morphology: light green and variegated leaves. Transcription factor genes such as G635, G1494, G2144 and their equivalogs that provide an altered appearance may positively affect a plant's value to the ornamental horticulture industry.

Leaf morphology: glossy leaves. Transcription factor genes such as G30, G1792, G2583 and their equivalogs that induce the formation of glossy leaves generally do so by elevating levels of epidermal wax. Thus, the genes could be used to engineer changes in the composition and amount of leaf surface components, including waxes. The ability to manipulate wax composition, amount, or distribution could modify plant tolerance to drought and low humidity, or resistance to insects or pathogens. Additionally, wax may be a valuable commodity in some species, and altering its accumulation and/or composition could enhance yield.

Seed morphology: altered seed coloration. Presently disclosed transcription factor genes, including G1156, G2105, G2085 have also been used to modify seed color, which, along with the equivalogs of these genes, could provide added appeal to seeds or seed products.

Seed morphology: altered seed size and shape. The introduction of presently disclosed transcription factor genes into plants that increase (e.g., G450; G584; G1255; G2085; G2105; G2114) or decrease (e.g., G1040). the size of seeds may have a significant impact on yield and appearance, particularly when the product is the seed itself (e.g., in the case of grains, legumes, nuts, etc.). Seed size, in addition to seed coat integrity, thickness and permeability, seed water content and a number of other components including antioxidants and oligosaccharides, also affects affect seed longevity in storage, with larger seeds often being more desirable for prolonged storage.

Transcription factor genes that alter seed shape, including G1040, G1062, G1255 and their equivalogs may have both ornamental applications and improve or broaden the appeal of seed products.

Leaf biochemistry: increased leaf wax. Overexpression of transcription factors genes, including G975, G1792 and G2085 and their equivalogs, which results in increased leaf wax could be used to manipulate wax composition, amount, or distribution. These transcription factors can improve yield in those plants and crops from which wax is a valuable product. The genes may also be used to modify plant tolerance to drought and/or low humidity or resistance to insects, as well as plant appearance (glossy leaves). The effect of increased wax deposition on leaves of a plant like may improve water use efficiency. Manipulation of these genes may reduce the wax coating on sunflower seeds; this wax fouls the oil extraction system during sunflower seed processing for oil. For the latter purpose or any other where wax reduction is valuable, antisense or cosuppression of the transcription factor genes in a tissue-specific manner would be valuable.

Leaf biochemistry: leaf prenyl lipids, including tocopherol. Prenyl lipids play a role in anchoring proteins in membranes or membranous organelles. Thus modifying the prenyl lipid content of seeds and leaves could affect membrane integrity and function. One important group of prenyl lipids, the tocopherols, have both anti-oxidant and vitamin E activity. A number of presently disclosed transcription factor genes, including G214, G652, G748, G987, G1543, and G2509, have been shown to modify the tocopherol composition of leaves in plants, and these genes and their equivalogs may thus be used to alter prenyl lipid content of leaves.

Leaf biochemistry: increased leaf insoluble sugars. Overexpression of a number of presently disclosed transcription factors, including G211, resulted in plants with altered leaf insoluble sugar content. This transcription factor and its equivalogs that alter plant cell wall composition have several potential applications including altering food digestibility, plant tensile strength, wood quality, pathogen resistance and in pulp production. In particular, hemicellulose is not desirable in paper pulps because of its lack of strength compared with cellulose. Thus modulating the amounts of cellulose vs. hemicellulose in the plant cell wall is desirable for the paper/lumber industry. Increasing the insoluble carbohydrate content in various fruits, vegetables, and other edible consumer products will result in enhanced fiber content. Increased fiber content would not only provide health benefits in food products, but might also increase digestibility of forage crops. In addition, the hemicellulose and pectin content of fruits and berries affects the quality of jam and catsup made from them. Changes in hemicellulose and pectin content could result in a superior consumer product.

Leaf biochemistry: increased leaf anthoc anin. Several presently disclosed transcription factor genes may be used to alter anthocyanin production in numerous plant species. Expression of presently disclosed transcription factor genes that increase flavonoid production in plants, including anthocyanins and condensed tannins, may be used to alter in pigment production for horticultural purposes, and possibly increasing stress resistance. G362, G663, G1482 and G1888 or their equivalogs, for example, could be used to alter anthocyanin production or accumulation. A number of flavonoids have been shown to have antimicrobial activity and could be used to engineer pathogen resistance. Several flavonoid compounds have health promoting effects such as inhibition of tumor growth, prevention of bone loss and prevention of the oxidation of lipids. Increased levels of condensed tannins, in forage legumes would be an important agronomic trait because they prevent pasture bloat by collapsing protein foams within the rumen. For a review on the utilities of flavonoids and their derivatives, refer to Dixon et al. (1999) Trends Plant Sci. 4: 394-400.

Leaf and seed biochemistry: altered fatty acid content. A number of the presently disclosed transcription factor genes have been shown to alter the fatty acid composition in plants, and seeds and leaves in particular. This modification suggests several utilities, including improving the nutritional value of seeds or whole plants. Dietary fatty acids ratios have been shown to have an effect on, for example, bone integrity and remodeling (see, for example, Weiler (2000) Pediatr. Res. 47:5692-697). The ratio of dietary fatty acids may alter the precursor pools of long-chain polyunsaturated fatty acids that serve as precursors for prostaglandin synthesis. In mammalian connective tissue, prostaglandins serve as important signals regulating the balance between resorption and formation in bone and cartilage. Thus dietary fatty acid ratios altered in seeds may affect the etiology and outcome of bone loss.

Transcription factors that reduce leaf fatty acids, for example, 16:3 fatty acids, may be used to control thylakoid membrane development, including proplastid to chloroplast development. The genes that encode these transcription factors might thus be useful for controlling the transition from proplastid to chromoplast in fruits and vegetables. It may also be desirable to change the expression of these genes to prevent cotyledon greening in Brassica napus or B. campestris to avoid green oil due to early frost.

A number of transcription factor genes are involved in mediating an aspect of the regulatory response to temperature. These genes may be used to alter the expression of desaturases that lead to production of 18:3 and 16:3 fatty acids, the balance of which affects membrane fluidity and mitigates damage to cell membranes and photosynthetic structures at high and low temperatures.

Seed biochemistry: modified seed oil and fatty acid content. The composition of seeds, particularly with respect to seed oil amounts and/or composition, is very important for the nutritional and caloric value and production of various food and feed products. Several of the presently disclosed transcription factor genes in seed lipid saturation that alter seed oil content could be used to improve the heat stability of oils or to improve the nutritional quality of seed oil, by, for example, reducing the number of calories in seed by decreasing oil or fatty acid content (e.g., G180; G192; G241; G1229; G1323; G1543), increasing the number of calories in animal feeds by increasing oil or fatty acid content (e.g. G162; G291; G427; G590; G598; G629, G715; G849; G1198, G1471; G1526; G1640; G1646, G1750; G1777; G1793; G1838; G1902; G1946; G1948; G2123; G2138; G2830), altering seed oil content (G504; G509; G519; G561; G567; G892; G961; G974; G1143; G1226; G1451; G1478; G1496; G1672; G1677; G1765; G2509; G2343), or altering the ratio of saturated to unsaturated lipids comprising the oils (e.g. G869; G1417; G2192).

Seed biochemistry: modified seed protein content. As with seed oils, the composition of seeds, particularly with respect to protein amounts and/or composition, is very important for the nutritional value and production of various food and feed products. A number of the presently disclosed transcription factor genes modify the protein concentrations in seeds, including G162; G226; G1323; G1419; G1818, which increase seed protein, G427; G1777; G1903; G1946, which decrease seed protein, and G162; G241; G509; G567; G597; G849; G892; G988; G1478; G1634; G1637; G1652; G1677; G1820; G1958; G2509; G2117; G2509, which alter seed protein content, would provide nutritional benefits, and may be used to prolong storage, increase seed pest or disease resistance, or modify germination rates.

Seed biochemistry: seed prenyl lipids. Prenyl lipids play a role in anchoring proteins in membranes or membranous organelles. Thus, modifying the prenyl lipid content of seeds and leaves could affect membrane integrity and function. A number of presently disclosed transcription factor genes have been shown to modify the tocopherol composition of plants. α-Tocopherol is better known as vitamin E. Tocopherols such as α- and γ-tocopherol both have anti-oxidant activity.

Seed biochemistry: seed glucosinolates. A number of glucosinolates have been shown to have anti-cancer activity; thus, increasing the levels or composition of these compounds by introducing several of the presently disclosed transcription factors, including G484 and G2340, can have a beneficial effect on human diet.

Glucosinolates are undesirable components of the oilseeds used in animal feed since they produce toxic effects. Low-glucosinolate varieties of canola, for example, have been developed to combat this problem. Glucosinolates form part of a plant's natural defense against insects. Modification of glucosinolate composition or quantity by introducing transcription factors that affect these characteristics can therefore afford increased protection from herbivores. Furthermore, in edible crops, tissue specific promoters can be used to ensure that these compounds accumulate specifically in tissues, such as the epidermis, which are not taken for consumption.

Seed biochemistry: increased seed anthocyanin. Several presently disclosed transcription factor genes may be used to alter anthocyanin production in the seeds of plants. As with leaf anthocyanins, expression of presently disclosed transcription factor genes that increase flavonoid (anthocyanins and condensed tannins) production in seeds, including G663 and its equivalogs, may be used to alter in pigment production for horticultural purposes, and possibly increasing stress resistance, antimicrobial activity and health promoting effects such as inhibition of tumor growth, prevention of bone loss and prevention of the oxidation of lipids.

Leaf and seed biochemistry: production of seed and leaf phytosterols: Presently disclosed transcription factor genes that modify levels of phytosterols in plants may have at least two utilities. First, phytosterols are an important source of precursors for the manufacture of human steroid hormones. Thus, regulation of transcription factor expression or activity could lead to elevated levels of important human steroid precursors for steroid semi-synthesis. For example, transcription factors that cause elevated levels of campesterol in leaves, or sitosterols and stigmasterols in seed crops, would be useful for this purpose. Phytosterols and their hydrogenated derivatives phytostanols also have proven cholesterol-lowering properties, and transcription factor genes that modify the expression of these compounds in plants would thus provide health benefits.

Root biochemistry: increased root anthocyanin. Presently disclosed transcription factor genes, including G663, may be used to alter anthocyanin production in the root of plants. As described above for seed anthocyanins, expression of presently disclosed transcription factor genes that increase flavonoid (anthocyanins and condensed tannins) production in seeds, including G663 and its equivalogs, may be used to alter in pigment production for horticultural purposes, and possibly increasing stress resistance, antimicrobial activity and health promoting effects such as inhibition of tumor growth, prevention of bone loss and prevention of the oxidation of lipids.

Light response/shade avoidance: altered cotyledon, hypocotyl, petiole development, altered leaf orientation, constitutive photomorphogenesis, photomorphogenesis in low light. Presently disclosed transcription factor genes, including G183; G354; G1322; G11331; G1488; G1494; G11794; G2144; and G2555, that modify a plant's response to light may be useful for modifying plant growth or development, for example, photomorphogenesis in poor light, or accelerating flowering time in response to various light intensities, quality or duration to which a non-transformed plant would not similarly respond. Examples of such responses that have been demonstrated include leaf number and arrangement, and early flower bud appearances. Elimination of shading responses may lead to increased planting densities with subsequent yield enhancement. As these genes may also alter plant architecture, they may find use in the ornamental horticulture industry.

Pigment: increased anthocyanin level in various plant organs and tissues. In addition to seed, leaves and roots, as mentioned above, several presently disclosed transcription factor genes can be used to alter anthocyanin levels in one or more tissues. The potential utilities of these genes include alterations in pigment production for horticultural purposes, and possibly increasing stress resistance, antimicrobial activity and health promoting effects such as inhibition of tumor growth, prevention of bone loss and prevention of the oxidation of lipids.

Miscellaneous biochemistry: diterpenes in leaves and other plant parts. Depending on the plant species, varying amounts of diverse secondary biochemicals (often lipophilic terpenes) are produced and exuded or volatilized by trichomes. These exotic secondary biochemicals, which are relatively easy to extract because they are on the surface of the leaf, have been widely used in such products as flavors and aromas, drugs, pesticides and cosmetics. Thus, the overexpression of genes that are used to produce diterpenes in plants may be accomplished by introducing transcription factor genes that induce said overexpression. One class of secondary metabolites, the diterpenes, can effect several biological systems such as tumor progression, prostaglandin synthesis and tissue inflammation. In addition, diterpenes can act as insect pheromones, termite allomones, and can exhibit neurotoxic, cytotoxic and antimitotic activities. As a result of this functional diversity, diterpenes have been the target of research several pharmaceutical ventures. In most cases where the metabolic pathways are impossible to engineer, increasing trichome density or size on leaves may be the only way to increase plant productivity.

Miscellaneous biochemistry: production of miscellaneous secondary metabolites. Microarray data suggests that flux through the aromatic amino acid biosynthetic pathways and primary and secondary metabolite biosynthetic pathways are up-regulated. Presently disclosed transcription factors have been shown to be involved in regulating alkaloid biosynthesis, in part by up-regulating the enzymes indole-3-glycerol phosphatase and strictosidine synthase. Phenylalanine ammonia lyase, chalcone synthase and trans-cinnamate mono-oxygenase are also induced, and are involved in phenylpropenoid biosynthesis.

Antisense and Co-Suppression

In addition to expression of the nucleic acids of the invention as gene replacement or plant phenotype modification nucleic acids, the nucleic acids are also useful for sense and anti-sense suppression of expression, e.g., to down-regulate expression of a nucleic acid of the invention, e.g., as a further mechanism for modulating plant phenotype. That is, the nucleic acids of the invention, or subsequences or anti-sense sequences thereof, can be used to block expression of naturally occurring homologous nucleic acids. A variety of sense and anti-sense technologies are known in the art, e.g., as set forth in Lichtenstein and Nellen (1997) Antisense Technology: A Practical Approach IRL Press at Oxford University Press, Oxford, U.K. Antisense regulation is also described in Crowley et al. (1985) Cell 43: 633-641; Rosenberg et al. (1985) Nature 313: 703-706; Preiss et al. (1985) Nature 313: 27-32; Melton (1985) Proc. Natl. Acad. Sci. 82: 144-148; Izant and Weintraub (1985) Science 229: 345-352; and Kim and Wold (1985) Cell 42: 129-00 138. Additional methods for antisense regulation are known in the art. Antisense regulation has been used to reduce or inhibit expression of plant genes in, for example in European Patent Publication No. 271988. Antisense RNA may be used to reduce gene expression to produce a visible or biochemical phenotypic change in a plant (Smith et al. (1988) Nature, 334: 724-726; Smith et al. (1990) Plant Mol. Biol. 14: 369-379). In general, sense or anti-sense sequences are introduced into a cell, where they are optionally amplified, e.g., by transcription. Such sequences include both simple oligonucleotide sequences and catalytic sequences such as ribozymes.

For example, a reduction or elimination of expression (i.e., a “knock-out”) of a transcription factor or transcription factor homolog polypeptide in a transgenic plant, e.g., to modify a plant trait, can be obtained by introducing an antisense construct corresponding to the polypeptide of interest as a cDNA. For antisense suppression, the transcription factor or homolog cDNA is arranged in reverse orientation (with respect to the coding sequence) relative to the promoter sequence in the expression vector. The introduced sequence need not be the full length cDNA or gene, and need not be identical to the cDNA or gene found in the plant type to be transformed. Typically, the antisense sequence need only be capable of hybridizing to the target gene or RNA of interest. Thus, where the introduced sequence is of shorter length, a higher degree of homology to the endogenous transcription factor sequence will be needed for effective antisense suppression. While antisense sequences of various lengths can be utilized, preferably, the introduced antisense sequence in the vector will be at least 30 nucleotides in length, and improved antisense suppression will typically be observed as the length of the antisense sequence increases. Preferably, the length of the antisense sequence in the vector will be greater than 100 nucleotides. Transcription of an antisense construct as described results in the production of RNA molecules that are the reverse complement of mRNA molecules transcribed from the endogenous transcription factor gene in the plant cell.

Suppression of endogenous transcription factor gene expression can also be achieved using a ribozyme. Ribozymes are RNA molecules that possess highly specific endoribonuclease activity. The production and use of ribozymes are disclosed in U.S. Pat. No. 4,987,071 and U.S. Pat. No. 5,543,508. Synthetic ribozyme sequences including antisense RNAs can be used to confer RNA cleaving activity on the antisense RNA, such that endogenous mRNA molecules that hybridize to the antisense RNA are cleaved, which in turn leads to an enhanced antisense inhibition of endogenous gene expression.

Vectors in which RNA encoded by a transcription factor or transcription factor homolog cDNA is over-expressed can also be used to obtain co-suppression of a corresponding endogenous gene, e.g., in the manner described in U.S. Pat. No. 5,231,020 to Jorgensen. Such co-suppression (also termed sense suppression) does not require that the entire transcription factor cDNA be introduced into the plant cells, nor does it require that the introduced sequence be exactly identical to the endogenous transcription factor gene of interest. However, as with antisense suppression, the suppressive efficiency will be enhanced as specificity of hybridization is increased, e.g., as the introduced sequence is lengthened, and/or as the sequence similarity between the introduced sequence and the endogenous transcription factor gene is increased.

Vectors expressing an untranslatable form of the transcription factor mRNA, e.g., sequences comprising one or more stop codon, or nonsense mutation) can also be used to suppress expression of an endogenous transcription factor, thereby reducing or eliminating its activity and modifying one or more traits. Methods for producing such constructs are described in U.S. Pat. No. 5,583,021. Preferably, such constructs are made by introducing a premature stop codon into the transcription factor gene. Alternatively, a plant trait can be modified by gene silencing using double-strand RNA (Sharp (1999) Genes and Development 13: 139-141). Another method for abolishing the expression of a gene is by insertion mutagenesis using the T-DNA of Agrobacterium tumefaciens. After generating the insertion mutants, the mutants can be screened to identify those containing the insertion in a transcription factor or transcription factor homolog gene. Plants containing a single transgene insertion event at the desired gene can be crossed to generate homozygous plants for the mutation. Such methods are well known to those of skill in the art (See for example Koncz et al. (1992) Methods in Arabidopsis Research, World Scientific Publishing Co. Pte. Ltd., River Edge, N.J.).

Alternatively, a plant phenotype can be altered by eliminating an endogenous gene, such as a transcription factor or transcription factor homolog, e.g., by homologous recombination (Kempin et al. (1997) Nature 389: 802-803).

A plant trait can also be modified by using the Cre-lox system (for example, as described in U.S. Pat. No. 5,658,772). A plant genome can be modified to include first and second lox sites that are then contacted with a Cre recombinase. If the lox sites are in the same orientation, the intervening DNA sequence between the two sites is excised. If the lox sites are in the opposite orientation, the intervening sequence is inverted.

The polynucleotides and polypeptides of this invention can also be expressed in a plant in the absence of an expression cassette by manipulating the activity or expression level of the endogenous gene by other means, such as, for example, by ectopically expressing a gene by T-DNA activation tagging (Ichikawa et al. (1997) Nature 390 698-701; Kakimoto et al. (1996) Science 274: 982-985). This method entails transforming a plant with a gene tag containing multiple transcriptional enhancers and once the tag has inserted into the genome, expression of a flanking gene coding sequence becomes deregulated. In another example, the transcriptional machinery in a plant can be modified so as to increase transcription levels of a polynucleotide of the invention (See, e.g., PCT Publications WO 96/06166 and WO 98/53057 which describe the modification of the DNA-binding specificity of zinc finger proteins by changing particular amino acids in the DNA-binding motif).

The transgenic plant can also include the machinery necessary for expressing or altering the activity of a polypeptide encoded by an endogenous gene, for example, by altering the phosphorylation state of the polypeptide to maintain it in an activated state.

Transgenic plants (or plant cells, or plant explants, or plant tissues) incorporating the polynucleotides of the invention and/or expressing the polypeptides of the invention can be produced by a variety of well established techniques as described above. Following construction of a vector, most typically an expression cassette, including a polynucleotide, e.g., encoding a transcription factor or transcription factor homolog, of the invention, standard techniques can be used to introduce the polynucleotide into a plant, a plant cell, a plant explant or a plant tissue of interest. Optionally, the plant cell, explant or tissue can be regenerated to produce a transgenic plant.

The plant can be any higher plant, including gymnosperms, monocotyledonous and dicotyledenous plants. Suitable protocols are available for Leguminosae (alfalfa, soybean, clover, etc.), Umbelliferae (carrot, celery, parsnip), Cruciferae (cabbage, radish, rapeseed, broccoli, etc.), Curcurbitaceae (melons and cucumber), Gramineae (wheat, corn, rice, barley, millet, etc.), Solanaceae (potato, tomato, tobacco, peppers, etc.), and various other crops. See protocols described in Ammirato et al., Eds., (1984) Handbook of Plant Cell Culture—Crop Species, Macmillan Publ. Co., New York, N.Y.; Shimamoto et al. (1989) Nature 338: 274-276; Fromm et al. (1990) Bio/Technol. 8: 833-839; and Vasil et al. (1990) Bio/Technol. 8: 429-434.

Transformation and regeneration of both monocotyledonous and dicotyledonous plant cells is now routine, and the selection of the most appropriate transformation technique will be determined by the practitioner. The choice of method will vary with the type of plant to be transformed; those skilled in the art will recognize the suitability of particular methods for given plant types. Suitable methods can include, but are not limited to: electroporation of plant protoplasts; liposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium tumefaciens mediated transformation. Transformation means introducing a nucleotide sequence into a plant in a manner to cause stable or transient expression of the sequence.

Successful examples of the modification of plant characteristics by transformation with cloned sequences which serve to illustrate the current knowledge in this field of technology, and which are herein incorporated by reference, include: U.S. Pat. Nos. 5,571,706; 5,677,175; 5,510,471; 5,750,386; 5,597,945; 5,589,615; 5,750,871; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,610,042.

Following transformation, plants are preferably selected using a dominant selectable marker incorporated into the transformation vector. Typically, such a marker will confer antibiotic or herbicide resistance on the transformed plants, and selection of transformants can be accomplished by exposing the plants to appropriate concentrations of the antibiotic or herbicide.

After transformed plants are selected and grown to maturity, those plants showing a modified trait are identified. The modified trait can be any of those traits described above. Additionally, to confirm that the modified trait is due to changes in expression levels or activity of the polypeptide or polynucleotide of the invention can be determined by analyzing mRNA expression using Northern blots, RT-PCR or microarrays, or protein expression using immunoblots or Western blots or gel shift assays.

Integrated Systems—Sequence Identity

Additionally, the present invention may be an integrated system, computer or computer readable medium that comprises an instruction set for determining the identity of one or more sequences in a database. In addition, the instruction set can be used to generate or identify sequences that meet any specified criteria. Furthermore, the instruction set may be used to associate or link certain functional benefits, such improved characteristics, with one or more identified sequence.

For example, the instruction set can include, e.g., a sequence comparison or other alignment program, e.g., an available program such as, for example, the Wisconsin Package Version 10.0, such as BLAST, FASTA, PILEUP, FINDPATTERNS or the like (GCG, Madison, Wis.). Public sequence databases such as GenBank, EMBL, Swiss-Prot and PIR or private sequence databases such as PHYTOSEQ sequence database (Incyte Genomics, Palo Alto, Calif.) can be searched.

Alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2: 482-489, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48: 443-453, by the search for similarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85: 2444-2448, by computerized implementations of these algorithms. After alignment, sequence comparisons between two (or more) polynucleotides or polypeptides are typically performed by comparing sequences of the two sequences over a comparison window to identify and compare local regions of sequence similarity. The comparison window can be a segment of at least about 20 contiguous positions, usually about 50 to about 200, more usually about 100 to about 150 contiguous positions. A description of the method is provided in Ausubel et al. supra.

A variety of methods for determining sequence relationships can be used, including manual alignment and computer assisted sequence alignment and analysis. This later approach is a preferred approach in the present invention, due to the increased throughput afforded by computer assisted methods. As noted above, a variety of computer programs for performing sequence alignment are available, or can be produced by one of skill.

One example algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410. Software for performing BLAST analyses is publicly available, e.g., through the National Library of Medicine's National Center for Biotechnology Information (ncbi.nlm.nih; see at world wide web (www) National Institutes of Health U.S. government (gov) website). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al. supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. 89: 10915-10919). Unless otherwise indicated, “sequence identity” here refers to the % sequence identity generated from a tblastx using the NCBI version of the algorithm at the default settings using gapped alignments with the filter “off” (see, for example, NIH NLM NCBI website at ncbi.nlm.nih, supra).

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g. Karlin and Altschul (1993) Proc. Natl. Acad. Sci. 90: 5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence (and, therefore, in this context, homologous) if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, or less than about 0.01, and or even less than about 0.001. An additional example of a useful sequence alignment algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. The program can align, e.g., up to 300 sequences of a maximum length of 5,000 letters.

The integrated system, or computer typically includes a user input interface allowing a user to selectively view one or more sequence records corresponding to the one or more character strings, as well as an instruction set which aligns the one or more character strings with each other or with an additional character string to identify one or more region of sequence similarity. The system may include a link of one or more character strings with a particular phenotype or gene function. Typically, the system includes a user readable output element that displays an alignment produced by the alignment instruction set.

The methods of this invention can be implemented in a localized or distributed computing environment. In a distributed environment, the methods may implemented on a single computer comprising multiple processors or on a multiplicity of computers. The computers can be linked, e.g. through a common bus, but more preferably the computer(s) are nodes on a network. The network can be a generalized or a dedicated local or wide-area network and, in certain preferred embodiments, the computers may be components of an intra-net or an internet.

Thus, the invention provides methods for identifying a sequence similar or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an inter or intra net) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions.

Any sequence herein can be entered into the database, before or after querying the database. This provides for both expansion of the database and, if done before the querying step, for insertion of control sequences into the database. The control sequences can be detected by the query to ensure the general integrity of both the database and the query. As noted, the query can be performed using a web browser based interface. For example, the database can be a centralized public database such as those noted herein, and the querying can be done from a remote terminal or computer across an internet or intranet.

Any sequence herein can be used to identify a similar, homologous, paralogous, or orthologous sequence in another plant. This provides means for identifying endogenous sequences in other plants that may be useful to alter a trait of progeny plants, which results from crossing two plants of different strain. For example, sequences that encode an ortholog of any of the sequences herein that naturally occur in a plant with a desired trait can be identified using the sequences disclosed herein. The plant is then crossed with a second plant of the same species but which does not have the desired trait to produce progeny which can then be used in further crossing experiments to produce the desired trait in the second plant. Therefore the resulting progeny plant contains no transgenes; expression of the endogenous sequence may also be regulated by treatment with a particular chemical or other means, such as EMR. Some examples of such compounds well known in the art include: ethylene; cytokinins; phenolic compounds, which stimulate the transcription of the genes needed for infection; specific monosaccharides and acidic environments which potentiate vir gene induction; acidic polysaccharides which induce one or more chromosomal genes; and opines; other mechanisms include light or dark treatment (for a review of examples of such treatments, see, Winans (1992) Microbiol. Rev. 56: 12-31; Eyal et al. (1992) Plant Mol. Biol. 19: 589-599; Chrispeels et al. (2000) Plant Mol. Biol. 42: 279-290; Piazza et al. (2002) Plant Physiol. 128: 1077-1086).

Table 7 lists sequences discovered to be orthologous to a number of representative transcription factors of the present invention. The column headings include the transcription factors listed by SEQ ID NO; corresponding Gene ID (GID) numbers; the species from which the orthologs to the transcription factors are derived; the type of sequence (i.e., DNA or protein) discovered to be orthologous to the transcription factors; and the SEQ ID NO of the orthologs, the latter corresponding to the ortholog SEQ ID NOs listed in the Sequence Listing.

TABLE 7 Orthologs of Representative Arabidopsis Transcription Factor Genes SEQ ID NO: of Nucleotide SEQ ID NO: GID NO of Encoding of Ortholog Sequence type Orthologous Orthologous or Nucleotide used for Arabidopsis Arabidopsis Encoding Ortholog Species from Which determination Transcription Transcription Ortholog GID NO Ortholog is Derived (DNA or Protein) Factor Factor 459 Glycine max DNA G8 1 460 Glycine max DNA G8 1 461 Glycine max DNA G8 1 462 Glycine max DNA G8 1 463 Oryza sativa DNA G8 1 464 Zea mays DNA G8 1 465 Zea mays DNA G8 1 466 Zea mays DNA G8 1 467 Oryza sativa PRT G8 1 468 Glycine max DNA G19 3 469 Glycine max DNA G19 3 470 Glycine max DNA G19 3 471 Glycinemax DNA G19 3 472 Oryza sativa DNA G19 3 473 Oryza sativa DNA G19 3 474 Oryza sativa DNA G19 3 475 Zea mays DNA G19 3 476 Zea mays DNA G19 3 477 Glycine max DNA G22 5 478 Glycine max DNA G22 5 479 Glycine max DNA G24 7 480 Glycine max DNA G24 7 481 Glycine max DNA G24 7 482 Glycine max DNA G24 7 483 Glycine max DNA G24 7 484 Glycine max DNA G24 7 485 Glycine max DNA G24 7 486 Oryza sativa DNA G24 7 487 Zea mays DNA G24 7 488 Oryza sativa PRT G24 7 489 Oryza sativa PRT G24 7 490 Oryza sativa PRT G24 7 491 Glycine max DNA G28 9 492 Glycine max DNA G28 9 493 Glycine max DNA G28 9 494 Glycine max DNA G28 9 495 Glycine max DNA G28 9 496 Glycine max DNA G28 9 497 Glycine max DNA G28 9 498 Glycine max DNA G28 9 499 Oryza sativa DNA G28 9 500 Zea mays DNA G28 9 501 Oryza sativa PRT G28 9 502 Oryza sativa PRT G28 9 503 Mesembryanthemum PRT G28 9 crystallinum 504 Glycine max DNA G47, G2133 11, 407 505 Oryza sativa PRT G47, G2133 11, 407 506 Glycine max DNA G157, G859, 15, 165, 349, G1842, G1843 351 507 Glycine max DNA G175, G877 19, 173 508 Oryza sativa DNA G175, G877 19, 173 509 Zea mays DNA G175, G877 19, 173 510 Zea mays DNA G175, G877 19, 173 511 Zea mays DNA G175, G877 19, 173 512 Oryza sativa PRT G175, G877 19, 173 513 Oryza sativa PRT G175, G877 19, 173 514 Oryza sativa PRT G175, G877 19, 173 515 Nicotiana tabacum PRT G175, G877 19, 173 516 Glycine max DNA G180 21 517 Glycine max DNA G180 21 518 Oryza sativa DNA G180 21 519 Zea mays DNA G180 21 520 Solanum tuberosum DNA G180 21 521 Oryza sativa PRT G180 21 522 Capsella rubella PRT G183 23 523 Glycine max DNA G188 25 524 Zea mays DNA G188 25 525 Oryza sativa PRT G188 25 526 Oryza sativa PRT G188 25 527 Glycine max DNA G189 27 528 Nicotiana tabacum PRT G189 27 529 Glycine max DNA G192 29 530 Oryza sativa PRT G192 29 531 Glycine max DNA G196 31 532 Zea mays DNA G196 31 533 Zea mays DNA G196 31 534 Oryza sativa PRT G196 31 535 Oryza sativa PRT G196 31 536 Oryza sativa PRT G196 31 537 Oryza sativa PRT G196 31 538 Glycine max DNA G211 33 539 Oryza sativa DNA G211 33 540 Oryza sativa PRT G211 33 541 Glycine max DNA G214, G680 35, 145 542 Glycine max DNA G214, G680 35, 145 543 Glycine max DNA G214, G680 35, 145 544 Glycine max DNA G214, G680 35, 145 545 Oryza sativa DNA G214, G680 35, 145 546 Oryza sativa DNA G214, G680 35, 145 547 Zea mays DNA G214, G680 35, 145 548 Zea mays DNA G214, G680 35, 145 549 Zea mays DNA G214, G680 35, 145 550 Glycine max DNA G226, G682 37, 147 551 Glycine max DNA G226 37 552 Glycine max DNA G226, G682 37, 147 553 Glycine max DNA G226, G682 37, 147 554 Glycine max DNA G226, G682 37, 147 555 Oryza sativa DNA G226, G682 37, 147 556 Zea mays DNA G226, G682 37, 147 557 Zea mays DNA G226, G682 37, 147 558 Oryza sativa PRT G226, G682 37, 147 559 Oryza sativa PRT G226, G682 37, 147 560 Glycine max DNA G241 39 561 Glycine max DNA G241 39 562 Glycine max DNA G241 39 563 Oryza sativa DNA G241 39 564 Zea mays DNA G241 39 565 Zea mays DNA G241 39 566 Zea mays DNA G241 39 567 Zea mays DNA G241 39 568 Zea mays DNA G241 39 569 Nicotiana tabacum PRT G241 39 570 Glycine max DNA G254 43 571 Glycine max DNA G256 45 572 Glycine max DNA G256 45 573 Glycine max DNA G256 45 574 Glycine max DNA G256 45 575 Glycine max DNA G256 45 576 Glycine max DNA G256 45 577 Glycine max DNA G256 45 578 Oryza sativa DNA G256 45 579 Zea mays DNA G256 45 580 Zea mays DNA G256 45 581 Zea mays DNA G256 45 582 Zea mays DNA G256 45 583 Zea mays DNA G256 45 584 Zea mays DNA G256 45 585 G3500 Lycopersicon DNA G256 45 esculentum 586 G3501 Lycopersicon DNA G256 45 esculentum 587 G3385 Oryza sativa PRT G256 45 588 G3386 Oryza sativa PRT G256 45 589 Oryza sativa PRT G256 45 590 G3384 Oryza sativa PRT G256 45 591 Oryza sativa PRT G256 45 592 G3502 Oryza sativa japonica PRT G256 45 593 G3500 Lycopersicon PRT G256 45 esculentum 594 G3501 Lycopersicon PRT G256 45 esculentum 595 Oryza sativa DNA G278 47 596 Zea mays DNA G278 47 597 Oryza sativa PRT G278 47 598 Glycine max DNA G312 53 599 Zea mays DNA G312 53 600 Euphorbia esula DNA G312 53 601 Glycine max DNA G325 55 602 Glycine max DNA G343 57 603 Glycine max DNA G343 57 604 Glycine max DNA G343 57 605 Oryza sativa DNA G343 57 606 Oryza sativa DNA G343 57 607 Oryza sativa PRT G343 57 608 Oryza sativa PRT G343 57 609 Oryza sativa PRT G343 57 610 Glycine max DNA G353, G354 59, 61 611 Glycine max DNA G353, G354 59, 61 612 Glycine max DNA G353, G354 59, 61 613 Oryza sativa DNA G353, G354 59, 61 614 Zea mays DNA G353, G354 59, 61 615 Zea mays DNA G353, G354 59, 61 616 Zea mays DNA G353, G354 59, 61 617 Zea mays DNA G353, G354 59, 61 618 Zea mays DNA G353, G354 59, 61 619 Zea mays DNA G353, G354 59, 61 620 Zea mays DNA G353, G354 59, 61 621 Oryza sativa PRT G353, G354 59, 61 622 Oryza sativa PRT G353, G354 59, 61 623 Oryza sativa PRT G353, G354 59, 61 624 Oryza sativa PRT G353, G354 59, 61 625 Oryza sativa PRT G353, G354 59, 61 626 Oryza sativa PRT G353, G354 59, 61 627 Glycine max DNA G361, G362 63, 65 628 Glycine max DNA G361, G362 63, 65 629 Glycine max DNA G361 63 630 Glycine max DNA G361, G362 63, 65 631 Glycine max DNA G361, G362 63, 65 632 Oryza sativa DNA G361, G362 63, 65 633 Zea mays DNA G361, G362 63, 65 634 Zea mays DNA G361, G362 63, 65 635 Oryza sativa PRT G361, G362 63, 65 636 Oryza sativa PRT G361, G362 63, 65 637 Oryza sativa PRT G361, G362 63, 65 638 Oryza sativa PRT G361, G362 63, 65 639 Oryza sativa PRT G361, G362 63, 65 640 Glycine max DNA G390, G391, 69, 71, 77 G438 641 Glycine max DNA G390, G391, 69, 71, 77 G438 642 Glycine max DNA G390, G391, 69, 71, 77 G438 643 Glycine max DNA G390, G391, 69, 71, 77 G438 644 Glycine max DNA G390, G391, 69, 71, 77 G438 645 Glycine max DNA G390, G391, 69, 71, 77 G438 646 Glycine max DNA G390, G391, 69, 71, 77 G438 647 Glycine max DNA G390, G391 69, 71 648 Glycine max DNA G390, G391, 69, 71, 77 G438 649 Glycine max DNA G390, G391, 69, 71, 77 G438 650 Oryza sativa DNA G390 69 651 Oryza sativa DNA G390, G438 69, 77 652 Zea mays DNA G390, G391, 69, 71, 77 G438 653 Zea mays DNA G390, G391, 69, 71, 77 G438 654 Zea mays DNA G390, G391, 69, 71, 77 G438 655 Zea mays DNA G390, G391 69, 71 656 Zea mays DNA G390, G391, 69, 71, 77 G438 657 Zea mays DNA G390, G391, 69, 71, 77 G438 658 Zea mays DNA G390, G391, 69, 71, 77 G438 659 Zea mays DNA G390, G391, 69, 71, 77 G438 660 Zea mays DNA G390, G391, 69, 71, 77 G438 661 Zea mays DNA G390, G391, 69, 71, 77 G438 662 Zea mays DNA G390, G391, 69, 71, 77 G438 663 Lycopersicon DNA G390, G391, 69, 71, 77 esculentum G438 664 Oryza sativa DNA G391, G438 71, 77 665 Oryza sativa PRT G390, G391, 69, 71, 77 G438 666 Oryza sativa PRT G390, G391, 69, 71, 77 G438 667 Oryza sativa PRT G390, G391, 69, 71, 77 G438 668 Oryza sativa PRT G390, G391, 69, 71, 77 G438 669 Physcomitrella PRT G391 71 patens 670 Glycine max DNA G409 73 671 Glycine max DNA G409 73 672 Glycine max DNA G409 73 673 Glycine max DNA G409 73 674 Glycine max DNA G409 73 675 Glycine max DNA G409 73 676 Glycine max DNA G409 73 677 Glycine max DNA G409 73 678 Oryza sativa DNA G409 73 679 Oryza sativa DNA G409 73 680 Oryza sativa DNA G409 73 681 Zea mays DNA G409 73 682 Zea mays DNA G409 73 683 Zea mays DNA G409 73 684 Zea mays DNA G409 73 685 Zea mays DNA G409 73 686 Zea mays DNA G409 73 687 Zea mays DNA G409 73 688 Glycine max DNA G427 75 689 Glycine max DNA G427 75 690 Glycine max DNA G427 75 691 Glycine max DNA G427 75 692 Glycine max DNA G427 75 693 Glycine max DNA G427 75 694 Glycine max DNA G427 75 695 Glycine max DNA G427 75 696 Glycine max DNA G427 75 697 Glycine max DNA G427 75 698 Oryza sativa DNA G427 75 699 Zea mays DNA G427 75 700 Zea mays DNA G427 75 701 Zea mays DNA G427 75 702 Zea mays DNA G427 75 703 Zea mays DNA G427 75 704 Zea mays DNA G427 75 705 Zea mays DNA G427 75 706 Zea mays DNA G427 75 707 Zea mays DNA G427 75 708 Oryza sativa PRT G427 75 709 Oryza sativa PRT G427 75 710 Oryza sativa PRT G427 75 711 Malus x domestica PRT G427 75 712 Nicotiana tabacum PRT G427 75 713 Lycopersicon PRT G427 75 esculentum 714 Glycine max DNA G438 77 715 Oryza sativa DNA G438 77 716 Oryza sativa DNA G438 77 717 Oryza sativa DNA G438 77 718 Oryza sativa DNA G438 77 719 Zea mays DNA G438 77 720 Physcomitrella PRT G438 77 patens 721 Oryza sativa PRT G438 77 722 Glycine max DNA G450 79 723 Glycine max DNA G450 79 724 Glycine max DNA G450 79 725 Glycine max DNA G450 79 726 Glycine max DNA G450 79 727 Glycine max DNA G450 79 728 Glycine max DNA G450 79 729 Glycine max DNA G450 79 730 Glycine max DNA G450 79 731 Oryza sativa DNA G450 79 732 Oryza sativa DNA G450 79 733 Zea mays DNA G450 79 734 Zea mays DNA G450 79 735 Zea mays DNA G450 79 736 Oryza sativa PRT G450 79 737 Oryza sativa PRT G450 79 738 Oryza sativa PRT G450 79 739 Oryza sativa PRT G450 79 740 Oryza sativa DNA G464 81 741 Zea mays DNA G464 81 742 Oryza sativa PRT G464 81 743 Glycine max DNA G470 83 744 Oryza sativa DNA G470 83 745 Oryza sativa DNA G470 83 746 Glycine max DNA G481, G482 87, 89 747 Glycine max DNA G481, G482 87, 89 748 Glycine max DNA G481, G482 87, 89 749 Glycine max DNA G481, G482 87, 89 750 Glycine max DNA G481, G482 87, 89 751 Glycine max DNA G481, G482 87, 89 752 Glycine max DNA G481, G482 87, 89 753 Glycine max DNA G481, G482 87, 89 754 Glycine max DNA G481 87 755 Glycine max DNA G481 87 756 Oryza sativa DNA G481 87 757 Oryza sativa DNA G481, G482 87, 89 758 Zea mays DNA G481 87 759 Zea mays DNA G481, G482 87, 89 760 Zea mays DNA G481, G482 87, 89 761 Zea mays DNA G481, G482 87, 89 762 Zea mays DNA G481, G482 87, 89 763 Zea mays DNA G481, G482 87, 89 764 Zea mays DNA G481, G482 87, 89 765 Zea mays DNA G481, G482 87, 89 766 Zea mays DNA G481, G482 87, 89 767 Zea mays DNA G481, G482 87, 89 768 Gossypium arboreum DNA G481, G482 87, 89 769 Glycine max DNA G481, G482 87, 89 770 Gossypium hirsutum DNA G481, G482 87, 89 771 Lycopersicon DNA G481, G482 87, 89 esculentum 772 Lycopersicon DNA G481, G482 87, 89 esculentum 773 Medicago truncatula DNA G481, G482 87, 89 774 Lycopersicon DNA G481, G482 87, 89 esculentum 775 Solanum tuberosum DNA G481, G482 87, 89 776 Triticum aestivum DNA G481, G482 87, 89 777 Hordeum vulgare DNA G481, G482 87, 89 778 Triticum DNA G481, G482 87, 89 monococcum 779 Glycine max DNA G482 89 780 Oryza sativa PRT G481, G482 87, 89 781 Oryza sativa PRT G481, G482 87, 89 782 Oryza sativa PRT G481, G482 87, 89 783 Oryza sativa PRT G481, G482 87, 89 784 Oryza sativa PRT G481, G482 87, 89 785 Zea mays PRT G481, G482 87, 89 786 Zea mays PRT G481, G482 87, 89 787 Oryza sativa PRT G481, G482 87, 89 788 Oryza sativa PRT G481, G482 87, 89 789 Oryza sativa PRT G481, G482 87, 89 790 Oryza sativa PRT G481, G482 87, 89 791 Oryza sativa PRT G481, G482 87, 89 792 Oryza sativa PRT G481, G482 87, 89 793 Oryza sativa PRT G481, G482 87, 89 794 Oryza sativa PRT G481, G482 87, 89 795 Oryza sativa PRT G481, G482 87, 89 796 Oryza sativa PRT G481, G482 87, 89 797 Glycine max PRT G481, G482 87, 89 798 Glycine max PRT G481, G482 87, 89 799 Glycine max PRT G481, G482 87, 89 800 Glycine max PRT G481, G482 87,89 801 Glycine max PRT G481, G482 87, 89 802 Glycine max PRT G481, G482 87, 89 803 Glycine max PRT G481, G482 87, 89 804 Zea mays PRT G481, G482 87, 89 805 Zea mays PRT G481, G482 87, 89 806 Zea mays PRT G481, G482 87, 89 807 Zea mays PRT G481, G482 87, 89 808 Glycine max DNA G484 91 809 Glycine max DNA G484 91 810 Glycine max DNA G484 91 811 Glycine max DNA G484 91 812 Glycine max DNA G484 91 813 Glycine max DNA G484 91 814 Glycine max DNA G484 91 815 Glycine max DNA G484 91 816 Glycine max DNA G484 91 817 Glycine max DNA G484 91 818 Oryza sativa DNA G484 91 819 Zea mays DNA G484 91 820 Zea mays DNA G484 91 821 Zea mays DNA G484 91 822 Zea mays DNA G484 91 823 Zea mays DNA G484 91 824 Oryza sativa PRT G484 91 825 Glycine max DNA G489 93 826 Glycine max DNA G489 93 827 Glycine max DNA G489 93 828 Glycine max DNA G489 93 829 Glycine max DNA G489 93 830 Glycine max DNA G489 93 831 Glycine max DNA G489 93 832 Oryza sativa DNA G489 93 833 Oryza sativa DNA G489 93 834 Zea mays DNA G489 93 835 Oryza sativa PRT G489 93 836 Oryza sativa PRT G489 93 837 Oryza sativa PRT G489 93 838 Glycine max DNA G504 97 839 Glycine max DNA G504 97 840 Glycine max DNA G504 97 841 Glycine max DNA G504 97 842 Glycine max DNA G504 97 843 Glycine max DNA G504 97 844 Glycine max DNA G504 97 845 Oryza sativa DNA G504 97 846 Oryza sativa DNA G504 97 847 Zea mays DNA G504 97 848 Zea mays DNA G504 97 849 Zea mays DNA G504 97 850 Zea mays DNA G504 97 851 Oryza sativa PRT G504 97 852 Oryza sativa PRT G504 97 853 Oryza sativa PRT G504 97 854 Oryza sativa PRT G504 97 855 Lycopersicon DNA G509 99 esculentum 856 Glycine max DNA G509 99 857 Glycine max DNA G509 99 858 Glycine max DNA G509 99 859 Oryza sativa DNA G509 99 860 Oryza sativa DNA G509 99 861 Zea mays DNA G509 99 862 Zea mays DNA G509 99 863 Zea mays DNA G509 99 864 Zea mays DNA G509 99 865 Oryza sativa PRT G509 99 866 Oryza sativa PRT G509 99 867 Oryza sativa PRT G509 99 868 Glycine max DNA G519 101 869 Glycine max DNA G519 101 870 Glycine max DNA G519 101 871 Glycine max DNA G519 101 872 Glycine max DNA G519 101 873 Glycine max DNA G519 101 874 Glycine max DNA G519 101 875 Glycine max DNA G519 101 876 Glycine max DNA G519 101 877 Oryza sativa DNA G519 101 878 Oryza sativa DNA G519 101 879 Oryza sativa DNA G519 101 880 Zea mays DNA G519 101 881 Zea mays DNA G519 101 882 Zea mays DNA G519 101 883 Zea mays DNA G519 101 884 Zea mays DNA G519 101 885 Zea mays DNA G519 101 886 Zea mays DNA G519 101 887 Zea mays DNA G519 101 888 Zea mays DNA G519 101 889 Zea mays DNA G519 101 890 Oryza sativa PRT G519 101 891 Oryza sativa PRT G519 101 892 Glycine max DNA G545 103 893 Glycine max DNA G545 103 894 Glycine max DNA G545 103 895 Glycine max DNA G545 103 896 Glycine max DNA G545 103 897 Glycine max DNA G545 103 898 Glycine max DNA G545 103 899 Oryza sativa DNA G545 103 900 Zea mays DNA G545 103 901 Zea mays DNA G545 103 902 Zea mays DNA G545 103 903 Oryza sativa PRT G545 103 904 Oryza sativa PRT G545 103 905 Oryza sativa PRT G545 103 906 Oryza sativa PRT G545 103 907 Datisca glomerata PRT G545 103 908 Oryza sativa DNA G546 105 909 Zea mays DNA G561 107 910 Sinapis alba PRT G561 107 911 Raphanus sativus PRT G561 107 912 Brassica napus PRT G561 107 913 Brassica napus PRT G561 107 914 Glycine max DNA G562 109 915 Glycine max DNA G562 109 916 Glycine max DNA G562 109 917 Glycine max DNA G562 109 918 Glycine max DNA G562 109 919 Zea mays DNA G562 109 920 Zea mays DNA G562 109 921 Zea mays DNA G562 109 922 Oryza sativa PRT G562 109 923 Oryza sativa PRT G562 109 924 Glycine max DNA G567 111 925 Oryza sativa DNA G567 111 926 Oryza sativa PRT G567 111 927 Glycine max DNA G568 113 928 Glycine max DNA G568 113 929 Oryza sativa DNA G568 113 930 Oryza sativa DNA G568 113 931 Oryza sativa DNA G568 113 932 Zea mays DNA G568 113 933 Oryza sativa PRT G568 113 934 Populus balsamifera PRT G568 113 subsp. trichocarpa x Populus deltoides 935 Glycine max DNA G584 115 936 Glycine max DNA G584 115 937 Glycine max DNA G584 115 938 Glycine max DNA G584 115 939 Glycine max DNA G584 115 940 Zea mays DNA G584 115 941 Zea mays DNA G584 115 942 Zea mays DNA G584 115 943 Oryza sativa PRT G584 115 944 Glycine max DNA G585 117 945 Glycine max DNA G585 117 946 Glycine max DNA G585 117 947 Glycine max DNA G585 117 948 Oryza sativa DNA G585 117 949 Zea mays DNA G585 117 950 Zea mays DNA G585 117 951 Zea mays DNA G585 117 952 Zea mays DNA G585 117 953 Oryza sativa PRT G585 117 954 Oryza sativa PRT G585 117 955 Oryza sativa PRT G585 117 956 Oryza sativa PRT G585 117 957 Oryza sativa PRT G585 117 958 Oryza sativa PRT G585 117 959 Gossypium hirsutum PRT G585 117 960 Antirrhinum majus PRT G585 117 961 Glycine max DNA G590 119 962 Glycine max DNA G590 119 963 Glycine max DNA G590 119 964 Oryza sativa DNA G590 119 965 Zea mays DNA G590 119 966 Oryza sativa PRT G590 119 967 Oryza sativa PRT G590 119 968 Oryza sativa DNA G597 123 969 Oryza sativa DNA G597 123 970 Oryza sativa DNA G597 123 971 Zea mays DNA G597 123 972 Zea mays DNA G597 123 973 Zea mays DNA G597 123 974 Zea mays DNA G597 123 975 Zea mays DNA G597 123 976 Zea mays DNA G597 123 977 Zea mays DNA G597 123 978 Zea mays DNA G597 123 979 Zea mays DNA G597 123 980 Zea mays DNA G597 123 981 Oryza sativa DNA G634 127 982 Oryza sativa DNA G634 127 983 Oryza sativa DNA G634 127 984 Zea mays DNA G634 127 985 Zea mays DNA G634 127 986 Zea mays DNA G634 127 987 Oryza sativa PRT G634 127 988 Oryza sativa PRT G634 127 989 Glycine max DNA G635 129 990 Glycine max DNA G635 129 991 Oryza sativa DNA G635 129 992 Oryza sativa DNA G635 129 993 Zea mays DNA G635 129 994 Oryza sativa PRT G635 129 995 Glycine max DNA G636 131 996 Glycine max DNA G636 131 997 Glycine max DNA G636 131 998 Glycine max DNA G636 131 999 Glycine max DNA G636 131 1000 Glycine max DNA G636 131 1001 Glycine max DNA G636 131 1002 Glycine max DNA G636 131 1003 Oryza sativa DNA G636 131 1004 Oryza sativa DNA G636 131 1005 Oryza sativa DNA G636 131 1006 Oryza sativa DNA G636 131 1007 Zea mays DNA G636 131 1008 Zea mays DNA G636 131 1009 Zea mays DNA G636 131 1010 Zea mays DNA G636 131 1011 Pisum sativum PRT G636 131 1012 Glycine max DNA G638 133 1013 Glycine max DNA G638 133 1014 Glycine max DNA G638 133 1015 Glycine max DNA G638 133 1016 Medicago truncatula DNA G638 133 1017 Glycine max DNA G652 135 1018 Glycine max DNA G652 135 1019 Glycine max DNA G652 135 1020 Glycine max DNA G652 135 1021 Glycine max DNA G652 135 1022 Glycine max DNA G652 135 1023 Glycine max DNA G652 135 1024 Glycine max DNA G652 135 1025 Oryza sativa DNA G652 135 1026 Oryza sativa DNA G652 135 1027 Oryza sativa DNA G652 135 1028 Zea mays DNA G652 135 1029 Zea mays DNA G652 135 1030 Zea mays DNA G652 135 1031 Zea mays DNA G652 135 1032 Zea mays DNA G652 135 1033 Zea mays DNA G652 135 1034 Zea mays DNA G652 135 1035 Oryza sativa PRT G652 135 1036 Oryza sativa PRT G652 135 1037 Oryza sativa PRT G652 135 1038 Oryza sativa PRT G652 135 1039 Oryza sativa PRT G652 135 1040 Oryza sativa PRT G652 135 1041 Oryza sativa PRT G652 135 1042 Oryza sativa PRT G652 135 1043 Glycine max DNA G663 137 1044 Glycine max DNA G664 139 1045 Glycine max DNA G664 139 1046 Glycine max DNA G664 139 1047 Glycine max DNA G664 139 1048 Glycine max DNA G664 139 1049 Glycine max DNA G664 139 1050 Glycine max DNA G664 139 1051 Oryza sativa DNA G664 139 1052 Oryza sativa DNA G664 139 1053 Oryza sativa DNA G664 139 1054 Oryza sativa DNA G664 139 1055 Zea mays DNA G664 139 1056 Zea mays DNA G664 139 1057 Zea mays DNA G664 139 1058 Zea mays DNA G664 139 1059 Zea mays DNA G664 139 1060 Zea mays DNA G664 139 1061 Zea mays DNA G664 139 1062 Zea mays DNA G664 139 1063 G3509 Lycopersicon DNA G664 139 esculentum 1064 G3506 Oryza sativa PRT G664 139 1065 G3504 Oryza sativa PRT G664 139 1066 Oryza sativa PRT G664 139 1067 Oryza sativa PRT G664 139 1068 G3503 Oryza sativa indica PRT G664 139 1069 G3505 Oryza sativa japonica PRT G664 139 1070 G3507 Oryza sativa japonica PRT G664 139 1071 G3508 Oryza sativa japonica PRT G664 139 1072 G3509 Lycopersicon PRT G664 139 esculentum 1073 Hordeum vulgare PRT G664 139 subsp. vulgare 1074 Oryza sativa DNA G680 145 1075 Zea mays DNA G680 145 1076 Glycine max DNA G682 147 1077 Hordeum vulgare DNA G682 147 subsp. vulgare 1078 Populus tremula x DNA G682 147 Populus tremuloides 1079 Triticum aestivum DNA G682 147 1080 Gossypium arboreum DNA G682 147 1081 Oryza sativa PRT G682 147 1082 Oryza sativa PRT G682 147 1083 Glycine max PRT G682 147 1084 Glycine max PRT G682 147 1085 Glycine max PRT G682 147 1086 Glycine max PRT G682 147 1087 Glycine max PRT G682 147 1088 Glycine max PRT G682 147 1089 Zea mays PRT G682 147 1090 Zea mays PRT G682 147 1091 Glycine max DNA G715, G1646 149, 313 1092 Glycine max DNA G715, G1646 149, 313 1093 Glycine max DNA G715, G1646 149, 313 1094 Oryza sativa DNA G715, G1646 149, 313 1095 Oryza sativa DNA G715, G1646 149, 313 1096 Zea mays DNA G715, G1646 149, 313 1097 Zea mays DNA G715, G1646 149, 313 1098 Zea mays DNA G715, G1646 149, 313 1099 Zea mays DNA G715, G1646 149, 313 1100 Zea mays DNA G715, G1646 149, 313 1101 Zea mays DNA G715, G1646 149, 313 1102 Zea mays DNA G715, G1646 149, 313 1103 Zea mays DNA G715, G1646 149, 313 1104 Zea mays DNA G715, G1646 149, 313 1105 Oryza sativa PRT G715, G1646 149, 313 1106 Oryza sativa PRT G715, G1646 149, 313 1107 Oryza sativa PRT G715, G1646 149, 313 1108 Oryza sativa PRT G715, G1646 149, 313 1109 Oryza sativa PRT G715, G1646 149, 313 1110 Oryza sativa PRT G715, G1646 149, 313 1111 Glycine max DNA G720 151 1112 Glycine max DNA G720 151 1113 Glycine max DNA G720 151 1114 Glycine max DNA G720 151 1115 Medicago truncatula DNA G720 151 1116 Lycopersicon DNA G720 151 esculentum 1117 Lycopersicon DNA G720 151 esculentum 1118 Lycopersicon DNA G720 151 esculentum 1119 Solanum tuberosum DNA G720 151 1120 Glycine max DNA G736 153 1121 Glycine max DNA G736 153 1122 Oryza sativa PRT G736 153 1123 Glycine max DNA G748 155 1124 Glycine max DNA G748 155 1125 Glycine max DNA G748 155 1126 Oryza sativa DNA G748 155 1127 Oryza sativa DNA G748 155 1128 Zea mays DNA G748 155 1129 Oryza sativa PRT G748 155 1130 Oryza sativa PRT G748 155 1131 Oryza sativa PRT G748 155 1132 Oryza sativa PRT G748 155 1133 Cucurbita maxima PRT G748 155 1134 Glycine max DNA G789, G1494 159, 291 1135 Glycine max DNA G789, G1494 159, 291 1136 Oryza sativa DNA G789 159 1137 Oryza sativa DNA G789, G1494 159, 291 1138 Zea mays DNA G789, G1494 159, 291 1139 Oryza sativa PRT G789, G1494 159, 291 1140 Oryza sativa PRT G789, G1494 159, 291 1141 Oryza sativa PRT G789, G1494 159, 291 1142 Glycine max DNA G801 161 1143 Glycine max DNA G801 161 1144 Zea mays DNA G801 161 1145 Glycine max DNA G849 163 1146 Glycine max DNA G849 163 1147 Glycine max DNA G849 163 1148 Glycine max DNA G849 163 1149 Glycine max DNA G849 163 1150 Glycine max DNA G849 163 1151 Zea mays DNA G849 163 1152 Zea mays DNA G849 163 1153 Zea mays DNA G849 163 1154 Glycine max DNA G864 167 1155 Glycine max DNA G864 167 1156 Zea mays DNA G864 167 1157 Oryza sativa PRT G864 167 1158 Oryza sativa PRT G864 167 1159 Glycine max DNA G867, G1930 169, 369 1160 Glycine max DNA G867, G1930 169, 369 1161 Glycine max DNA G867, G1930 169, 369 1162 Glycine max DNA G867, G1930 169, 369 1163 Glycine max DNA G867, G1930 169, 369 1164 Glycine max DNA G867 169 1165 Oryza sativa DNA G867 169 1166 Oryza sativa DNA G867, G1930 169, 369 1167 Zea mays DNA G867, G1930 169, 369 1168 Zea mays DNA G867, G1930 169, 369 1169 Zea mays DNA G867, G1930 169, 369 1170 Zea mays DNA G867, G1930 169, 369 1171 Glycine max DNA G867, G1930 169, 369 1172 Mesembryanthemum DNA G867, G1930 169, 369 crystallinum 1173 Lycopersicon DNA G867, G1930 169, 369 esculentum 1174 Solanum tuberosum DNA G867, G1930 169, 369 1175 Hordeum vulgare DNA G867, G1930 169, 369 1176 Oryza sativa PRT G867, G1930 169, 369 1177 Oryza sativa PRT G867, G1930 169, 369 1178 Oryza sativa PRT G867, G1930 169, 369 1179 Oryza sativa PRT G867, G1930 169, 369 1180 Oryza sativa PRT G867, G1930 169, 369 1181 Oryza sativa PRT G867, G1930 169, 369 1182 Glycine max PRT G867, G1930 169, 369 1183 Glycine max PRT G867, G1930 169, 369 1184 Glycine max PRT G867, G1930 169, 369 1185 Zea mays PRT G867, G1930 169, 369 1186 Zea mays PRT G867, G1930 169, 369 1187 Glycine max DNA G869 171 1188 Glycine max DNA G869 171 1189 Oryza sativa DNA G869 171 1190 Zea mays DNA G869 171 1191 Oryza sativa PRT G869 171 1192 Oryza sativa DNA G877 173 1193 Glycine max DNA G881 175 1194 Oryza sativa DNA G881 175 1195 Oryza sativa DNA G881 175 1196 Zea mays DNA G881 175 1197 Zea mays DNA G881 175 1198 Zea mays DNA G881 175 1199 Zea mays DNA G881 175 1200 Oryza sativa PRT G881 175 1201 Oryza sativa PRT G892 177 1202 Mentha x piperita DNA G896 179 1203 Glycine max DNA G910 181 1204 Glycine max DNA G912 185 1205 Glycine max DNA G912 185 1206 Glycine max DNA G912 185 1207 Glycine max DNA G912 185 1208 Glycine max DNA G912 185 1209 Glycine max DNA G912 185 1210 Glycine max DNA G912 185 1211 Oryza sativa DNA G912 185 1212 Oryza sativa DNA G912, G913 185, 187 1213 Zea mays DNA G912 185 1214 Zea mays DNA G912 185 1215 Zea mays DNA G912, G913 185, 187 1216 Zea mays DNA G912 185 1217 Zea mays DNA G912 185 1218 Brassica napus DNA G912, G913 185, 187 1219 Solanum tuberosum DNA G912 185 1220 Descurainia sophia DNA G912 185 1221 Oryza sativa PRT G912 185 1222 Oryza sativa PRT G912, G913 185, 187 1223 Oryza sativa PRT G912, G913 185, 187 1224 Oryza sativa PRT G912 185 1225 Brassica napus PRT G912 185 1226 Nicotiana tabacum PRT G912 185 1227 Oryza sativa PRT G912 185 1228 Oryza sativa PRT G912 185 1229 Oryza sativa PRT G912 185 1230 Oryza sativa PRT G912 185 1231 Oryza sativa PRT G912 185 1232 Oryza sativa PRT G912 185 1233 Oryza sativa PRT G912 185 1234 Oryza sativa PRT G912 185 1235 Oryza sativa PRT G912 185 1236 Oryza sativa PRT G912 185 1237 Glycine max PRT G912 185 1238 Glycine max PRT G912 185 1239 Glycine max PRT G912 185 1240 Glycine max PRT G912 185 1241 Glycine max PRT G912 185 1242 Glycine max PRT G912 185 1243 Glycine max PRT G912 185 1244 Zea mays PRT G912 185 1245 Zea mays PRT G912 185 1246 Zea mays PRT G912 185 1247 Zea mays PRT G912 185 1248 Zea mays PRT G912 185 1249 Glycine max DNA G922 189 1250 Glycine max DNA G922 189 1251 Glycine max DNA G922 189 1252 Oryza sativa DNA G922 189 1253 Oryza sativa DNA G922 189 1254 Oryza sativa PRT G922 189 1255 Oryza sativa PRT G922 189 1256 Oryza sativa PRT G922 189 1257 Oryza sativa PRT G922 189 1258 Glycine max DNA G926 191 1259 Glycine max DNA G926 191 1260 Oryza sativa DNA G926 191 1261 Oryza sativa DNA G926 191 1262 Zea mays DNA G926 191 1263 Brassica napus PRT G926 191 1264 Glycine max DNA G961 193 1265 Glycine max DNA G961 193 1266 Oryza sativa DNA G961 193 1267 Zea mays DNA G961 193 1268 Zea mays DNA G961 193 1269 Zea mays DNA G961 193 1270 Oryza sativa PRT G961 193 1271 Glycine max DNA G974 197 1272 Glycine max DNA G974 197 1273 Glycine max DNA G974 197 1274 Glycine max DNA G974 197 1275 Glycine max DNA G974 197 1276 Glycine max DNA G974 197 1277 Oryza sativa DNA G974 197 1278 Zea mays DNA G974 197 1279 Zea mays DNA G974 197 1280 Zea mays DNA G974 197 1281 Zea mays DNA G974 197 1282 Lycopersicon DNA G974 197 esculentum 1283 Glycine max DNA G974 197 1284 Solanum tuberosum DNA G974 197 1285 Poplar xylem DNA G974 197 1286 Medicago truncatula DNA G974 197 1287 Sorghum bicolor DNA G974 197 1288 Oryza sativa PRT G974 197 1289 Oryza sativa PRT G974 197 1290 Oryza sativa PRT G974 197 1291 Atriplex hortensis PRT G974 197 1292 Glycine max DNA G975, G2583 199, 449 1293 Glycine max DNA G975, G2583 199, 449 1294 Glycine max DNA G975, G2583 199, 449 1295 Glycine max DNA G975, G2583 199, 449 1296 Glycine max DNA G975, G2583 199, 449 1297 Oryza sativa DNA G975 199 1298 Oryza sativa DNA G975, G2583 199, 449 1299 Zea mays DNA G975, G2583 199, 449 1300 Zea mays DNA G975, G2583 199, 449 1301 Brassica rapa DNA G975, G2583 199, 449 1302 Oryza sativa PRT G975, G2583 199, 449 1303 Glycine max DNA G979 201 1304 Glycine max DNA G979 201 1305 Glycine max DNA G979 201 1306 Oryza sativa DNA G979 201 1307 Zea mays DNA G979 201 1308 Zea mays DNA G979 201 1309 Zea mays DNA G979 201 1310 Oryza sativa PRT G979 201 1311 Oryza sativa PRT G979 201 1312 Oryza sativa PRT G979 201 1313 Oryza sativa PRT G979 201 1314 Oryza sativa PRT G979 201 1315 Glycine max DNA G987 203 1316 Glycine max DNA G987 203 1317 Glycine max DNA G987 203 1318 Glycine max DNA G987 203 1319 Glycine max DNA G987 203 1320 Glycine max DNA G987 203 1321 Oryza sativa DNA G987 203 1322 Oryza sativa DNA G987 203 1323 Zea mays DNA G987 203 1324 Oryza sativa PRT G987 203 1325 Oryza sativa PRT G988 205 1326 Oryza sativa PRT G988 205 1327 Capsella rubella PRT G988 205 1328 Glycine max DNA G1040 207 1329 Glycine max DNA G1040 207 1330 Glycine max DNA G1040 207 1331 Glycine max DNA G1040 207 1332 Glycine max DNA G1040 207 1333 Zea mays DNA G1040 207 1334 Zea mays DNA G1040 207 1335 Zea mays DNA G1040 207 1336 Zea mays DNA G1040 207 1337 Zea mays DNA G1040 207 1338 Oryza sativa PRT G1040 207 1339 Oryza sativa PRT G1040 207 1340 Glycine max DNA G1047 209 1341 Zea mays DNA G1047 209 1342 Oryza sativa PRT G1047 209 1343 Oryza sativa PRT G1047 209 1344 Glycine max DNA G1051, G1052 211, 213 1345 Glycine max DNA G1051, G1052 211, 213 1346 Glycine max DNA G1051, G1052 211, 213 1347 Glycine max DNA G1051, G1052 211, 213 1348 Glycine max DNA G1051, G1052 211, 213 1349 Glycine max DNA G1051, G1052 211, 213 1350 Glycine max DNA G1051, G1052 211, 213 1351 Oryza sativa DNA G1051, G1052 211, 213 1352 Zea mays DNA G1051, G1052 211, 213 1353 Zea mays DNA G1051, G1052 211, 213 1354 Zea mays DNA G1051, G1052 211, 213 1355 Zea mays DNA G1051, G1052 211, 213 1356 Zea mays DNA G1051, G1052 211, 213 1357 Zea mays DNA G1051, G1052 211, 213 1358 Zea mays DNA G1051, G1052 211, 213 1359 Oryza sativa DNA G1052 213 1360 Zea mays DNA G1052 213 1361 Zea mays DNA G1052 213 1362 Oryza sativa PRT G1051, G1052 211, 213 1363 Oryza sativa PRT G1051, G1052 211, 213 1364 Oryza sativa PRT G1051, G1052 211, 213 1365 Glycine max DNA G1062 215 1366 Glycine max DNA G1062 215 1367 Glycine max DNA G1062 215 1368 Glycine max DNA G1062 215 1369 Oryza sativa DNA G1062 215 1370 Oryza sativa DNA G1062 215 1371 Zea mays DNA G1062 215 1372 Zea mays DNA G1062 215 1373 Zea mays DNA G1062 215 1374 Zea mays DNA G1062 215 1375 Zea mays DNA G1062 215 1376 Medicago truncatula DNA G1062 215 1377 Lycopersicon DNA G1062 215 esculentum 1378 Oryza sativa PRT G1062 215 1379 Glycine max DNA G1063, G2143 217, 413 1380 Glycine max DNA G1063, G2143 217, 413 1381 Glycine max DNA G1063, G2143 217, 413 1382 Glycine max DNA G1063, G2143 217, 413 1383 Glycine max DNA G1063, G2143 217, 413 1384 Lycopersicon DNA G1063, G2143 217, 413 esculentum 1385 Glycine max DNA G1064 219 1386 Glycine max DNA G1064 219 1387 Glycine max DNA G1064 219 1388 Zea mays DNA G1064 219 1389 Zea mays DNA G1064 219 1390 Lycopersicon DNA G1064 219 esculentum 1391 Oryza sativa PRT G1064 219 1392 Gossypium hirsutum PRT G1064 219 1393 Glycine max DNA G1069 221 1394 Glycine max DNA G1069 221 1395 Oryza sativa PRT G1069, G1073 221, 223 1396 Zea mays DNA G1069 221 1397 Lotus japonicus DNA G1069 221 1398 Lycopersicon DNA G1073 223 esculentum 1399 Oryza sativa PRT G1073 223 1400 Oryza sativa PRT G1073 223 1401 Oryza sativa PRT G1073 223 1402 Oryza sativa PRT G1073 223 1403 Oryza sativa PRT G1073 223 1404 Oryza sativa PRT G1073 223 1405 Oryza sativa PRT G1073 223 1406 Oryza sativa PRT G1073 223 1407 Oryza sativa PRT G1073 223 1408 Oryza sativa PRT G1073 223 1409 Oryza sativa PRT G1073 223 1410 Oryza sativa PRT G1073 223 1411 Glycine max PRT G1073 223 1412 Glycine max PRT G1073 223 1413 Glycine max PRT G1073 223 1414 Glycine max PRT G1073 223 1415 Glycine max PRT G1073 223 1416 Glycine max PRT G1073 223 1417 Glycine max PRT G1073 223 1418 Zea mays PRT G1073 223 1419 Glycine max DNA G1075 225 1420 Glycine max DNA G1075 225 1421 Glycine max DNA G1075 225 1422 Glycine max DNA G1075 225 1423 Glycine max DNA G1075 225 1424 Oryza sativa DNA G1075 225 1425 Oryza sativa DNA G1075 225 1426 Oryza sativa DNA G1075 225 1427 Oryza sativa DNA G1089 229 1428 Zea mays DNA G1089 229 1429 Zea mays DNA G1089 229 1430 Zea mays DNA G1089 229 1431 Zea mays DNA G1089 229 1432 Zea mays DNA G1089 229 1433 Oryza sativa PRT G1089 229 1434 Glycine max DNA G1134, G2555 231, 445 1435 Glycine max DNA G1134, G2555 231, 445 1436 Oryza sativa DNA G1134, G2555 231, 445 1437 Glycine max DNA G1140 233 1438 Glycine max DNA G1140 233 1439 Glycine max DNA G1140 233 1440 Glycine max DNA G1140 233 1441 Glycine max DNA G1140 233 1442 Glycine max DNA G1140 233 1443 Oryza sativa DNA G1140 233 1444 Zea mays DNA G1140 233 1445 Zea mays DNA G1140 233 1446 Zea mays DNA G1140 233 1447 Zea mays DNA G1140 233 1448 Zea mays DNA G1140 233 1449 Zea mays DNA G1140 233 1450 Zea mays DNA G1140 233 1451 Zea mays DNA G1140 233 1452 Zea mays DNA G1140 233 1453 Oryza sativa PRT G1140 233 1454 Ipomoea batatas PRT G1140 233 1455 Zea mays DNA G1146 237 1456 Zea mays DNA G1146 237 1457 Oryza sativa PRT G1146 237 1458 Oryza sativa PRT G1146 237 1459 Oryza sativa PRT G1146 237 1460 Glycine max DNA G1196 239 1461 Glycine max DNA G1196 239 1462 Glycine max DNA G1196 239 1463 Oryza sativa DNA G1196 239 1464 Zea mays DNA G1196 239 1465 Zea mays DNA G1196 239 1466 Oryza sativa PRT G1196 239 1467 Oryza sativa PRT G1196 239 1468 Glycine max DNA G1198 241 1469 Glycine max DNA G1198 241 1470 Glycine max DNA G1198 241 1471 Glycine max DNA G1198 241 1472 Glycine max DNA G1198 241 1473 Glycine max DNA G1198 241 1474 Glycine max DNA G1198 241 1475 Glycine max DNA G1198 241 1476 Oryza sativa DNA G1198 241 1477 Oryza sativa DNA G1198 241 1478 Oryza sativa DNA G1198 241 1479 Oryza sativa DNA G1198 241 1480 Oryza sativa DNA G1198 241 1481 Zea mays DNA G1198 241 1482 Zea mays DNA G1198 241 1483 Zea mays DNA G1198 241 1484 Zea mays DNA G1198 241 1485 Zea mays DNA G1198 241 1486 Zea mays DNA G1198 241 1487 Zea mays DNA G1198 241 1488 Zea mays DNA G1198 241 1489 Zea mays DNA G1198 241 1490 Zea mays DNA G1198 241 1491 Nicotiana tabacum DNA G1198 241 1492 Oryza sativa PRT G1198 241 1493 Oryza sativa PRT G1198 241 1494 Oryza sativa PRT G1198 241 1495 Oryza sativa PRT G1198 241 1496 Oryza sativa PRT G1198 241 1497 Oryza sativa PRT G1198 241 1498 Oryza sativa PRT G1198 241 1499 Zea mays DNA G1225 243 1500 Oryza sativa PRT G1225 243 1501 Oryza sativa PRT G1226 245 1502 Glycine max DNA G1229 247 1503 Oryza sativa PRT G1229 247 1504 Oryza sativa PRT G1229 247 1505 Glycine max DNA G1255 249 1506 Glycine max DNA G1255 249 1507 Glycine max DNA G1255 249 1508 Glycine max DNA G1255 249 1509 Glycine max DNA G1255 249 1510 Glycine max DNA G1255 249 1511 Glycine max DNA G1255 249 1512 Oryza sativa DNA G1255 249 1513 Oryza sativa DNA G1255 249 1514 Oryza sativa DNA G1255 249 1515 Oryza sativa DNA G1255 249 1516 Zea mays DNA G1255 249 1517 Zea mays DNA G1255 249 1518 Zea mays DNA G1255 249 1519 Zea mays DNA G1255 249 1520 Zea mays DNA G1255 249 1521 Zea mays DNA G1255 249 1522 Oryza sativa PRT G1255 249 1523 Glycine max DNA G1266 251 1524 Glycine max DNA G1266 251 1525 Glycine max DNA G1266 251 1526 Glycine max DNA G1266 251 1527 Oryza sativa DNA G1266 251 1528 Nicotiana tabacum PRT G1266 251 1529 Oryza sativa DNA G1275 253 1530 Zea mays DNA G1275 253 1531 Zea mays DNA G1275 253 1532 Zea mays DNA G1275 253 1533 Oryza sativa PRT G1275 253 1534 Oryza sativa PRT G1275 253 1535 Oryza sativa PRT G1275 253 1536 Glycine max DNA G1322 257 1537 Glycine max DNA G1322 257 1538 Glycine max DNA G1322 257 1539 Oryza sativa DNA G1322 257 1540 Oryza sativa PRT G1322 257 1541 Oryza sativa PRT G1322 257 1542 Zea mays DNA G1323 259 1543 Zea mays DNA G1323 259 1544 Glycine max DNA G1330 261 1545 Glycine max DNA G1330 261 1546 Glycine max DNA G1330 261 1547 Glycine max DNA G1330 261 1548 Glycine max DNA G1330 261 1549 Glycine max DNA G1330 261 1550 Glycine max DNA G1330 261 1551 Oryza sativa DNA G1330 261 1552 Oryza sativa DNA G1330 261 1553 Oryza sativa DNA G1330 261 1554 Oryza sativa DNA G1330 261 1555 Zea mays DNA G1330 261 1556 Zea mays DNA G1330 261 1557 Zea mays DNA G1330 261 1558 Zea mays DNA G1330 261 1559 Zea mays DNA G1330 261 1560 Zea mays DNA G1330 261 1561 Zea mays DNA G1330 261 1562 Lycopersicon DNA G1330 261 esculentum 1563 Oryza sativa PRT G1330 261 1564 Oryza sativa PRT G1330 261 1565 Oryza sativa PRT G1330 261 1566 Oryza sativa PRT G1330 261 1567 Glycine max DNA G1331 263 1568 Glycine max DNA G1331 263 1569 Oryza sativa DNA G1331 263 1570 Zea mays DNA G1331 263 1571 Zea mays DNA G1331 263 1572 Oryza sativa PRT G1331 263 1573 Glycine max DNA G1363 267 1574 Oryza sativa DNA G1363 267 1575 Oryza sativa DNA G1363 267 1576 Oryza sativa DNA G1363 267 1577 Oryza sativa DNA G1363 267 1578 Zea mays DNA G1363 267 1579 Zea mays DNA G1363 267 1580 Zea mays DNA G1363 267 1581 Zea mays DNA G1363 267 1582 Zea mays DNA G1363 267 1583 Oryza sativa PRT G1363 267 1584 Oryza sativa PRT G1363 267 1585 Oryza sativa PRT G1363 267 1586 Oryza sativa PRT G1363 267 1587 Glycine max DNA G1411, G2509 269, 439 1588 Glycine max DNA G1411, G2509 269, 439 1589 Glycine max DNA G1411, G2509 269, 439 1590 Glycine max DNA G1411, G2509 269, 439 1591 Zea mays DNA G1411, G2509 269, 439 1592 Glycine max DNA G1417 271 1593 Oryza sativa PRT G1417 271 1594 Oryza sativa PRT G1417 271 1595 Glycine max DNA G1419 273 1596 Glycine max DNA G1449 275 1597 Glycine max DNA G1449 275 1598 Oryza sativa DNA G1449 275 1599 Oryza sativa DNA G1449 275 1600 Zea mays DNA G1449 275 1601 Zea mays DNA G1449 275 1602 Zea mays DNA G1449 275 1603 Zea mays DNA G1449 275 1604 Glycine max DNA G1451 277 1605 Glycine max DNA G1451 277 1606 Oryza sativa DNA G1451 277 1607 Oryza sativa DNA G1451 277 1608 Oryza sativa DNA G1451 277 1609 Zea mays DNA G1451 277 1610 Zea mays DNA G1451 277 1611 Zea mays DNA G1451 277 1612 Zea mays DNA G1451 277 1613 Medicago truncatula DNA G1451 277 1614 Solanum tuberosum DNA G1451 277 1615 Zea mays DNA G1451 277 1616 Sorghum DNA G1451 277 propinquum 1617 Glycine max DNA G1451 277 1618 Sorghum bicolor DNA G1451 277 1619 Hordeum vulgare DNA G1451 277 1620 Lycopersicon DNA G1451 277 esculentum 1621 Oryza sativa PRT G1451 277 1622 Oryza sativa PRT G1451 277 1623 Oryza sativa PRT G1451 277 1624 Oryza sativa PRT G1451 277 1625 Glycine max DNA G1452 279 1626 Glycine max DNA G1478 285 1627 Glycine max DNA G1478 285 1628 Glycine max DNA G1478 285 1629 Zea mays DNA G1478 285 1630 Glycine max DNA G1482 287 1631 Glycine max DNA G1482 287 1632 Glycine max DNA G1482 287 1633 Glycine max DNA G1482 287 1634 Glycine max DNA G1482 287 1635 Oryza sativa DNA G1482 287 1636 Oryza sativa DNA G1482 287 1637 Oryza sativa DNA G1482 287 1638 Oryza sativa DNA G1482 287 1639 Zea mays DNA G1482 287 1640 Zea mays DNA G1482 287 1641 Zea mays DNA G1482 287 1642 Zea mays DNA G1482 287 1643 Zea mays DNA G1482 287 1644 Zea mays DNA G1482 287 1645 Oryza sativa PRT G1482 287 1646 Oryza sativa PRT G1482 287 1647 Glycine max DNA G1488 289 1648 Glycine max DNA G1488 289 1649 Glycine max DNA G1488 289 1650 Oryza sativa DNA G1488 289 1651 Oryza sativa DNA G1488 289 1652 Zea mays DNA G1488 289 1653 Zea mays DNA G1488 289 1654 Zea mays DNA G1488 289 1655 Oryza sativa PRT G1488 289 1656 Oryza sativa PRT G1488 289 1657 Oryza sativa PRT G1488 289 1658 Oryza sativa PRT G1499 295 1659 Brassica rapa subsp. DNA G1499 295 pekinensis 1660 Glycine max DNA G1519 297 1661 Oryza sativa DNA G1519 297 1662 Zea mays DNA G1519 297 1663 Zea mays DNA G1519 297 1664 Lycopersicon DNA G1519 297 esculentum 1665 Glycine max DNA G1526 2199 1666 Oryza sativa DNA G1526 299 1667 Oryza sativa DNA G1526 299 1668 Zea mays DNA G1526 299 1669 Glycine max DNA G1540 301 1670 Oryza sativa PRT G1540 301 1671 Glycine max DNA G1543 303 1672 Oryza sativa DNA G1543 303 1673 Zea mays DNA G1543 303 1674 Oryza sativa PRT G1543 303 1675 Zea mays DNA G1637 307 1676 Zea mays DNA G1637 307 1677 Zea mays DNA G1637 307 1678 Glycine max DNA G1640 309 1679 Glycine max DNA G1640 309 1680 Glycine max DNA G1640 309 1681 Oryza sativa PRT G1640 309 1682 Zea mays DNA G1645 311 1683 Zea mays DNA G1645 311 1684 Zea mays DNA G1645 311 1685 Lycopersicon DNA G1645 311 esculentum 1686 Medicago truncatula DNA G1645 311 1687 Oryza sativa PRT G1645 311 1688 Oryza sativa DNA G1646 313 1689 Oryza sativa DNA G1646 313 1690 Glycine max DNA G1652 315 1691 Glycine max DNA G1652 315 1692 Glycine max DNA G1652 315 1693 Glycine max DNA G1652 315 1694 Glycine max DNA G1652 315 1695 Glycine max DNA G1652 315 1696 Glycine max DNA G1652 315 1697 Glycine max DNA G1652 315 1698 Oryza sativa DNA G1652 315 1699 Zea mays DNA G1652 315 1700 Zea mays DNA G1652 315 1701 Oryza sativa PRT G1652 315 1702 Oryza sativa PRT G1652 315 1703 Oryza sativa PRT G1652 315 1704 Oryza sativa PRT G1652 315 1705 Oryza sativa PRT G1652 315 1706 Glycine max DNA G1672 317 1707 Oryza sativa DNA G1672 317 1708 Zea mays DNA G1672 317 1709 Zea mays DNA G1672 317 1710 Oryza sativa PRT G1672 317 1711 Oryza sativa PRT G1672 317 1712 Oryza sativa PRT G1672 317 1713 Oryza sativa PRT G1672 317 1714 Glycine max DNA G1750 323 1715 Glycine max DNA G1750 323 1716 Glycine max DNA G1750 323 1717 Glycine max DNA G1750 323 1718 Oryza sativa DNA G1750 323 1719 Zea mays DNA G1750 323 1720 Zea mays DNA G1750 323 1721 Glycine max DNA G1756 325 1722 Medicago truncatula DNA G1765 327 1723 Glycine max DNA G1777 329 1724 Oryza sativa DNA G1777 329 1725 Zea mays DNA G1777 329 1726 Zea mays DNA G1777 329 1727 Oryza sativa PRT G1777 329 1728 Glycine max DNA G1792 331 1729 Glycine max DNA G1792 331 1730 Glycine max DNA G1792 331 1731 Glycine max DNA G1792 331 1732 Glycine max DNA G1792 331 1733 Zea mays DNA G1792 331 1734 Lycopersicon DNA G1792 331 esculentum 1735 G3380 Oryza sativa PRT G1792 331 1736 G3381 Oryza sativa indica PRT G1792 331 1737 G3383 Oryza sativa japonica PRT G1792 331 1738 Glycine max DNA G1793 333 1739 Oryza sativa DNA G1793 333 1740 Zea mays DNA G1793 333 1741 Zea mays DNA G1793 333 1742 Zea mays DNA G1793 333 1743 Oryza sativa PRT G1793 333 1744 Glycine max DNA G1794 335 1745 Glycine max DNA G1794 335 1746 Glycine max DNA G1794 335 1747 Glycine max DNA G1794 335 1748 Glycine max DNA G1794 335 1749 Glycine max DNA G1794 335 1750 Glycine max DNA G1794 335 1751 Zea mays DNA G1794 335 1752 Zea mays DNA G1794 335 1753 Zea mays DNA G1794 335 1754 Oryza sativa PRT G1794 335 1755 Oryza sativa PRT G1794 335 1756 Oryza sativa PRT G1794 335 1757 Glycine max DNA G1804 337 1758 Glycine max DNA G1804 337 1759 Glycine max DNA G1804 337 1760 Oryza sativa DNA G1804 337 1761 Oryza sativa PRT G1804 337 1762 Helianthus annuus PRT G1804 337 1763 Glycine max DNA G1838 345 1764 Glycine max DNA G1838 345 1765 Oryza sativa PRT G1838 345 1766 Glycine max DNA G1841 347 1767 Glycine max DNA G1841 347 1768 Oryza sativa DNA G1841 347 1769 Oryza sativa PRT G1841 347 1770 Solanum tuberosum DNA G1852 353 1771 Gossypium arboreum DNA G1852 353 1772 Medicago truncatula DNA G1852 353 1773 Glycine max DNA G1852 353 1774 Lycopersicon DNA G1852 353 esculentum 1775 Pinus taeda DNA G1852 353 1776 Lotus japonicus DNA G1852 353 1777 Gossypium hirsutum DNA G1852 353 1778 Solanum tuberosum DNA G1863 355 1779 Medicago truncatula DNA G1863 355 1780 Lycopersicon DNA G1863 355 esculentum 1781 Oryza sativa PRT G1863 355 1782 Glycine max DNA G1880 357 1783 Glycine max DNA G1880 357 1784 Medicago truncatula DNA G1880 357 1785 Oryza sativa PRT G1880 357 1786 Glycine max DNA G1902 361 1787 Glycine max DNA G1902 361 1788 Glycine max DNA G1902 361 1789 Zea mays DNA G1902 361 1790 Oryza sativa PRT G1902 361 1791 Glycine max DNA G1927 367 1792 Oryza sativa DNA G1927 367 1793 Zea mays DNA G1927 367 1794 Lycopersicon DNA G1927 367 esculentum 1795 Oryza sativa DNA G1930 369 1796 Glycine max DNA G1944 373 1797 Glycine max DNA G1944 373 1798 Zea mays DNA G1944 373 1799 Glycine max DNA G1944 373 1800 Glycine max DNA G1944 373 1801 Glycine max DNA G1946 375 1802 Glycine max DNA G1946 375 1803 Zea mays DNA G1946 375 1804 Zea mays DNA G1946 375 1805 Oryza sativa PRT G1946 375 1806 Glycine max DNA G1948 379 1807 Glycine max DNA G1948 379 1808 Oryza sativa DNA G1948 379 1809 Oryza sativa DNA G1948 379 1810 Zea mays DNA G1948 379 1811 Zea mays DNA G1948 379 1812 Zea mays DNA G1948 379 1813 Oryza sativa PRT G1948 379 1814 Glycine max DNA G1950 381 1815 Glycine max DNA G1950 381 1816 Glycine max DNA G1950 381 1817 Glycine max DNA G1950 381 1818 Glycine max DNA G1950 381 1819 Glycine max DNA G1950 381 1820 Oryza sativa DNA G1950 381 1821 Oryza sativa DNA G1950 381 1822 Oryza sativa DNA G1950 381 1823 Oryza sativa DNA G1950 381 1824 Oryza sativa DNA G1950 381 1825 Oryza sativa DNA G1950 381 1826 Oryza sativa DNA G1950 381 1827 Oryza sativa DNA G1950 381 1828 Oryza sativa DNA G1950 381 1829 Zea mays DNA G1950 381 1830 Zea mays DNA G1950 381 1831 Zea mays DNA G1950 381 1832 Zea mays DNA G1950 381 1833 Zea mays DNA G1950 381 1834 Zea mays DNA G1950 381 1835 Zea mays DNA G1950 381 1836 Zea mays DNA G1950 381 1837 Zea mays DNA G1950 381 1838 Oryza sativa PRT G1950 381 1839 Oryza sativa PRT G1950 381 1840 Oryza sativa PRT G1950 381 1841 Oryza sativa PRT G1950 381 1842 Oryza sativa PRT G1950 381 1843 Oryza sativa PRT G1950 381 1844 Oryza sativa PRT G1950 381 1845 Oryza sativa PRT G1950 381 1846 Oryza sativa PRT G1950 381 1847 Glycine max DNA G1958 383 1848 Glycine max DNA G1958 383 1849 Glycine max DNA G1958 383 1850 Glycine max DNA G1958 383 1851 Glycine max DNA G1958 383 1852 Oryza sativa DNA G1958 383 1853 Oryza sativa DNA G1958 383 1854 Zea mays DNA G1958 383 1855 Zea mays DNA G1958 383 1856 Zea mays DNA G1958 383 1857 Nicotiana tabacum PRT G1958 383 1858 Glycine max DNA G2007 385 1859 Glycine max DNA G2007 385 1860 Zea mays DNA G2007 385 1861 Zea mays DNA G2007 385 1862 Zea mays DNA G2007 385 1863 Oryza sativa PRT G2007 385 1864 Glycine max DNA G2010, G2347 387, 431 1865 Oryza sativa DNA G2010, G2347 387, 431 1866 Zea mays DNA G2010 387 1867 Zea mays DNA G2010, G2347 387, 431 1868 Glycine max DNA G2059 391 1869 Glycine max DNA G2085 393 1870 Glycine max DNA G2085 393 1871 Glycine max DNA G2085 393 1872 Glycine max DNA G2085 393 1873 Zea mays DNA G2085 393 1874 Oryza sativa PRT G2085 393 1875 Oryza sativa PRT G2105 395 1876 Glycine max DNA G2110 397 1877 Oryza sativa DNA G2114 399 1878 Oryza sativa DNA G2114 399 1879 Zea mays DNA G2114 399 1880 Zea mays DNA G2114 399 1881 Oryza sativa DNA G2117 401 1882 Medicago truncatula DNA G2130 405 1883 Oryza sativa PRT G2130 405 1884 Oryza sativa PRT G2130 405 1885 Glycine max DNA G2140 411 1886 Glycine max DNA G2140 411 1887 Glycine max DNA G2140 411 1888 Glycine max DNA G2140 411 1889 Glycine max DNA G2140 411 1890 Glycine max DNA G2140 411 1891 Oryza sativa DNA G2140 411 1892 Oryza sativa DNA G2140 411 1893 Oryza sativa DNA G2140 411 1894 Oryza sativa DNA G2140 411 1895 Zea mays DNA G2140 411 1896 Lycopersicon DNA G2140 411 esculentum 1897 Oryza sativa PRT G2140 411 1898 Oryza sativa PRT G2140 411 1899 Oryza sativa PRT G2140 411 1900 Oryza sativa PRT G2140 411 1901 Oryza sativa PRT G2140 411 1902 Glycine max DNA G2143 413 1903 Glycine max DNA G2143 413 1904 Glycine max DNA G2144 415 1905 Glycine max DNA G2144 415 1906 Zea mays DNA G2144 415 1907 Zea mays DNA G2144 415 1908 Medicago truncatula DNA G2155 419 1909 Medicago truncatula DNA G2155 419 1910 Glycine max DNA G2155 419 1911 Oryza sativa PRT G2192 421 1912 Oryza sativa PRT G2295 423 1913 Glycine max DNA G2340 425 1914 Glycine max DNA G2343 427 1915 Glycine max DNA G2343 427 1916 Glycine max DNA G2343 427 1917 Lycopersicon PRT G2343 427 esculentum 1918 Oryza sativa PRT G2379 433 1919 Oryza sativa PRT G2379 433 1920 Oryza sativa PRT G2379 433 1921 Glycine max DNA G2505 437 1922 Zea mays DNA G2505 437 1923 Glycine max DNA G2520 443 1924 Glycine max DNA G2520 443 1925 Oryza sativa DNA G2520 443 1926 Zea mays DNA G2520 443 1927 Zea mays DNA G2520 443 1928 Zea mays DNA G2520 443 1929 Oryza sativa PRT G2520 443 1930 Oryza sativa PRT G2520 443 1931 Glycine max DNA G2557 447 1932 Glycine max DNA G2557 447 1933 Glycine max DNA G2557 447 1934 Zea mays DNA G2557 447 1935 Zea mays DNA G2557 447 1936 Glycine max DNA G2557 447 1937 Oryza sativa PRT G2557 447 1938 Oryza sativa PRT G2557 447 1939 Oryza sativa PRT G2557 447 1940 Glycine max DNA G2719 453 1941 Zea mays DNA G2719 453 1942 Oryza sativa PRT G2719 453 1943 Oryza sativa PRT G2719 453 1944 Glycine max DNA G2789 455 1945 Medicago truncatula DNA G2789 455 1946 Glycine max DNA G2830 457

Table 8 lists a summary of homologous sequences identified using BLAST (tblastx program). The first column shows the polynucleotide sequence identifier (SEQ ID NO), the second column shows the corresponding cDNA identifier (Gene ID), the third column shows the orthologous or homologous polynucleotide GenBank Accession Number (Test Sequence ID), the fourth column shows the calculated probability value that the sequence identity is due to chance (Smallest Sum Probability), the fifth column shows the plant species from which the test sequence was isolated (Test Sequence Species), and the sixth column shows the orthologous or homologous test sequence GenBank annotation (Test Sequence GenBank Annotation).

TABLE 8 Summary of representative sequences that are homologous to presently-disclosed transcription factors Smallest Polynucleotide Sum Test Sequence GenBank SEQ ID NO: GID Test Sequence ID Probability Test Sequence Species Annotation 1 G8 AF134116 2.00E−92 Hyacinthus orientalis APETALA2 protein homolog HAP2 (HAP2) 1 G8 AF132002 6.00E−86 Petunia x hybrida PHAP2B protein (Ap2B) mRNA, complete cds. 1 G8 AF332215 8.00E−84 Malus x domestica transcription factor AHAP2 (AHAP2) mRNA, 1 G8 CA783794 3.00E−83 Glycine max sat57d09.y1 Gm-c1056 Glycine max cDNA clone SOY 1 G8 AY069953 7.00E−82 Hordeum vulgare APETALA2-like protein (AP2L1) mRNA, complet 1 G8 AF253971 5.00E−81 Picea abies APETALA2-related transcription factor 2 (AP2L2) 1 G8 AF048900 2.00E−80 Zea mays indeterminate spikelet 1 (ids1) mRNA, complete cds 1 G8 AF325506 4.00E−80 Pisum sativum APETAL2-like protein mRNA, complete cds. 1 G8 BG321674 6.00E−79 Descurainia sophia Ds01_06a02_A Ds01_AAFC_ECORC_cold stress 1 G8 BQ120583 3.00E−78 Solanum tuberosum EST606159 mixed potato tissues Solanum tu 1 G8 gi24059986 1.30E−91 Oryza sativa (japonica putative indetermi cultivar-group) 1 G8 gi5360996 8.70E−88 Hyacinthus orientalis APETALA2 protein homolog HAP2. 1 G8 gi5081555 4.50E−86 Petunia x hybrida PHAP2A protein. 1 G8 gi2944040 5.80E−84 Zea mays indeterminate spikelet 1. 1 G8 gi21717332 9.30E−82 Malus x domestica transcription factor AHAP2. 1 G8 gi11181612 7.50E−78 Picea abies APETALA2-related transcription factor 2. 1 G8 gi13173164 1.60E−77 Pisum sativum APETAL2-like protein. 1 G8 gi18476518 2.60E−70 Hordeum vulgare APETALA2-like protein. 1 G8 gi21069051 1.40E−34 Brassica napus AP2/EREBP transcription factor BABY BOOM1. 1 G8 gi21304225 8.60E−33 Oryza sativa aintegumenta-like protein. 3 G19 BG321358 1.00E−101 Descurainia sophia Ds01_07d03_R Ds01_AAFC_ECORC_cold stress 3 G19 BH444831 1.00E−77 Brassica oleracea BOHPW42TR BOHP Brassica oleracea genomic 3 G19 BM412184 2.00E−43 Lycopersicon EST586511 tomato breaker esculentum fruit Lyco 3 G19 BU837697 3.00E−43 Populus tremula x T104G02 Populus apica Populus tremuloides 3 G19 CA784650 6.00E−43 Glycine max sat87a10.y1 Gm-c1062 Glycine max cDNA clone SOY 3 G19 BU819833 3.00E−41 Populus tremula UA48BPB07 Populus tremula cambium cDNA libr 3 G19 BU870388 4.00E−41 Populus balsamifera Q011H05 Populus flow subsp. trichocarpa 3 G19 CA797119 1.00E−38 Theobroma cacao Cac_BL_4204 Cac_BL (Bean and Leaf from Amel 3 G19 BI436183 2.00E−38 Solanum tuberosum EST538944 cSTE Solanum tuberosum cDNA clo 3 G19 BQ989448 2.00E−36 Lactuca sativa QGF17L05.yg.ab1 QG_EFGHJ lettuce serriola La 3 G19 gi10798644 5.70E−36 Nicotiana tabacum AP2 domain-containing transcription fac 3 G19 gi6176534 2.40E−35 Oryza sativa EREBP-like protein. 3 G19 gi1688233 7.50E−34 Solanum tuberosum DNA binding protein homolog. 3 G19 gi22074046 1.50E−33 Lycopersicon transcription factor JERF1. esculentum 3 G19 gi18496063 4.90E−33 Fagus sylvatica ethylene responsive element binding prote 3 G19 gi20805105 2.10E−32 Oryza sativa (japonica contains ESTs AU06 cultivar-group) 3 G19 gi24940524 2.30E−31 Triticum aestivum ethylene response element binding prote 3 G19 gi18266198 2.30E−31 Narcissus AP-2 domain containing pseudonarcissus protein. 3 G19 gi3264767 1.30E−30 Prunus armeniaca AP2 domain containing protein. 3 G19 gi24817250 4.00E−28 Cicer arietinum transcription factor EREBP- like protein. 5 G22 AB016264 9.00E−48 Nicotiana sylvestris nserf2 gene for ethylene- responsive el 5 G22 TOBBY4A 1.00E−47 Nicotiana tabacum mRNA for ERF1, complete cds. 5 G22 AP004533 4.00E−47 Lotus japonicus genomic DNA, chromosome 3, clone: LjT14G02, 5 G22 LEU89255 6.00E−47 Lycopersicon DNA-binding protein Pti4 esculentum mRNA, comp 5 G22 BQ517082 6.00E−46 Solanum tuberosum EST624497 Generation of a set of potato c 5 G22 BE449392 1.00E−45 Lycopersicon hirsutum EST356151 L. hirsutum trichome, Corne 5 G22 AF245119 5.00E−45 Mesembryanthemum AP2-related transcription crystallinum fac 5 G22 BQ165291 7.00E−45 Medicago truncatula EST611160 KVKC Medicago truncatula cDNA 5 G22 AW618245 8.00E−38 Lycopersicon pennellii EST314295 L. pennellii trichome, Cor 5 G22 BG444654 2.00E−36 Gossypium arboreum GA_Ea0025B11f Gossypium arboreum 7-10 d 5 G22 gi1208495 6.10E−48 Nicotiana tabacum ERF1. 5 G22 gi3342211 3.30E−47 Lycopersicon Pti4. esculentum 5 G22 gi8809571 8.90E−47 Nicotiana sylvestris ethylene-responsive element binding 5 G22 gi17385636 2.70E−36 Matricaria chamomilla ethylene-responsive element binding 5 G22 gi8980313 2.50E−33 Catharanthus roseus AP2-domain DNA-binding protein. 5 G22 gi7528276 8.60E−33 Mesembryanthemum AP2-related transcription f crystallinum 5 G22 gi21304712 3.10E−28 Glycine max ethylene-responsive element binding protein 1 5 G22 gi14140141 1.50E−26 Oryza sativa putative AP2-related transcription factor. 5 G22 gi15623863 1.30E−22 Oryza sativa (japonica contains EST˜hypot cultivar-group) 5 G22 gi4099914 3.10E−21 Stylosanthes hamata ethylene-responsive element binding p 7 G24 BZ026790 7.00E−71 Brassica oleracea oeh27a09.b1 B. oleracea002 Brassica olerac 7 G24 BM985484 4.00E−52 Thellungiella halophila 10_C12_T Ath Thellungiella halophil 7 G24 BQ405872 3.00E−45 Gossypium arboreum GA_Ed0088A03f Gossypium arboreum 7-10 d 7 G24 BG543187 3.00E−44 Brassica rapa subsp. E0677 Chinese cabbage pekinensis etiol 7 G24 AW981184 7.00E−42 Medicago truncatula EST392378 DSIL Medicago truncatula cDNA 7 G24 BQ704289 9.00E−41 Brassica napus Bn01_04f19_A 7 G24 BG321374 9.00E−40 Descurainia sophia Ds01_06d08_R Ds01_AAFC_ECORC_cold stress 7 G24 OSIG00036 4.00E−37 Oryza sativa chromosome 4 clone H0721B11, *** SEQUENCING I 7 G24 AAAA01024762 4.00E−37 Oryza sativa (indica ( ) scaffold024762 cultivar-group) 7 G24 BQ586795 6.00E−37 Beta vulgaris E012390-024-012-J13-SP6 MPIZ-ADIS-024-leaf Be 7 G24 gi5091503 9.60E−34 Oryza sativa EST AU055776(S20048) corresponds to a region 7 G24 gi20161239 6.40E−21 Oryza sativa (japonica hypothetical prote cultivar-group) 7 G24 gi8980313 2.20E−20 Catharanthus roseus AP2-domain DNA-binding protein. 7 G24 gi4099921 2.80E−20 Stylosanthes hamata EREBP-3 homolog. 7 G24 gi10798644 5.70E−20 Nicotiana tabacum AP2 domain-containing transcription fac 7 G24 gi8571476 1.70E−18 Atriplex hortensis apetala2 domain-containing protein. 7 G24 gi8809573 2.10E−18 Nicotiana sylvestris ethylene-responsive element binding 7 G24 gi21908034 2.20E−18 Zea mays DRE binding factor 2. 7 G24 gi17352283 9.60E−18 Brassica napus CBF-like protein. 7 G24 gi3342211 4.70E−17 Lycopersicon Pti4. esculentum 9 G28 AF245119 2.00E−72 Mesembryanthemum AP2-related transcription crystallinum fac 9 G28 BQ165291 1.00E−68 Medicago truncatula EST611160 KVKC Medicago truncatula cDNA 9 G28 AB016264 1.00E−57 Nicotiana sylvestris nserf2 gene for ethylene- responsive el 9 G28 TOBBY4D 2.00E−57 Nicotiana tabacum Tobacco mRNA for EREBP-2, complete cds. 9 G28 BQ047502 2.00E−57 Solanum tuberosum EST596620 P. infestans- challenged potato 9 G28 LEU89255 2.00E−56 Lycopersicon DNA-binding protein Pti4 esculentum mRNA, comp 9 G28 BH454277 2.00E−54 Brassica oleracea BOGSI45TR BOGS Brassica oleracea genomic 9 G28 BE449392 1.00E−53 Lycopersicon hirsutum EST356151 L. hirsutum trichome, Corne 9 G28 AB035270 2.00E−50 Matricaria chamomilla McEREBP1 mRNA for ethylene-responsive 9 G28 AW233956 5.00E−50 Glycine max sf32e02.y1 Gm-c1028 Glycine max cDNA clone GENO 9 G28 gi7528276 6.10E−71 Mesembryanthemum AP2-related transcription f crystallinum 9 G28 gi8809571 3.30E−56 Nicotiana sylvestris ethylene-responsive element binding 9 G28 gi3342211 4.20E−56 Lycopersicon Pti4. esculentum 9 G28 gi1208498 8.70E−56 Nicotiana tabacum EREBP-2. 9 G28 gi14140141 4.20E−49 Oryza sativa putative AP2-related transcription factor. 9 G28 gi17385636 3.00E−46 Matricaria chamomilla ethylene-responsive element binding 9 G28 gi21304712 2.90E−31 Glycine max ethylene-responsive element binding protein 1 9 G28 gi15623863 5.60E−29 Oryza sativa (japonica contains EST˜hypot cultivar-group) 9 G28 gi8980313 1.20E−26 Catharanthus roseus AP2-domain DNA-binding protein. 9 G28 gi4099921 3.10E−21 Stylosanthes hamata EREBP-3 homolog. 11 G47 BG543936 1.00E−60 Brassica rapa subsp. E1686 Chinese cabbage pekinensis etiol 11 G47 BH420519 3.00E−43 Brassica oleracea BOGUH88TF BOGU Brassica oleracea genomic 11 G47 AU292603 3.00E−30 Zinnia elegans AU292603 zinnia cultured mesophyll cell equa 11 G47 BE320193 1.00E−24 Medicago truncatula NF024B04RT1F1029 Developing root Medica 11 G47 AAAA01000718 1.00E−22 Oryza sativa (indica ( ) scaffold000718 cultivar-group) 11 G47 AP003379 2.00E−22 Oryza sativa chromosome 1 clone P0408G07, *** SEQUENCING IN 11 G47 AC124836 8.00E−21 Oryza sativa (japonica ( ) chromosome 5 clo cultivar-group) 11 G47 BZ403609 2.00E−20 Zea mays OGABN17TM ZM_0.7_1.5_KB Zea mays genomic clone ZMM 11 G47 BM112772 6.00E−17 Solanum tuberosum EST560308 potato roots Solanum tuberosum 11 G47 BQ698717 1.00E−16 Pinus taeda NXPV_148_C06_F NXPV (Nsf Xylem Planings wood Ve 11 G47 gi20161239 6.90E−24 Oryza sativa (japonica hypothetical prote cultivar-group) 11 G47 gi14140155 6.80E−17 Oryza sativa putative AP2 domain transcription factor. 11 G47 gi21908034 7.00E−15 Zea mays DRE binding factor 2. 11 G47 gi20303011 1.90E−14 Brassica napus CBF-like protein CBF5. 11 G47 gi8571476 3.00E−14 Atriplex hortensis apetala2 domain-containing protein. 11 G47 gi8980313 2.10E−13 Catharanthus roseus AP2-domain DNA-binding protein. 11 G47 gi19071243 4.40E−13 Hordeum vulgare CRT/DRE binding factor 1. 11 G47 gi18650662 5.60E−13 Lycopersicon ethylene response factor 1. esculentum 11 G47 gi17385636 1.20E−12 Matricaria chamomilla ethylene-responsive element binding 11 G47 gi1208498 1.50E−12 Nicotiana tabacum EREBP-2. 13 G156 AF335242 4.00E−45 Petunia x hybrida MADS-box transcription factor FBP24 (FBP2 13 G156 AMA307056 2.00E−41 Antirrhinum majus mRNA for putative MADS- domain transcript 13 G156 BF276751 1.00E−35 Gossypium arboreum GA_Eb0030I08f Gossypium arboreum 7-10 d 13 G156 AB071380 2.00E−35 Lilium regale LRGLOB mRNA for MADS-box transcription factor 13 G156 ZMA271208 2.00E−34 Zea mays mRNA for putative MADS- domain transcription facto 13 G156 AI899235 1.00E−33 Lycopersicon EST268678 tomato ovary, esculentum TAMU Lycope 13 G156 GGN132219 8.00E−33 Gnetum gnemon mRNA for putative MADS domain transcription 13 G156 BQ753907 2.00E−32 Hordeum vulgare subsp. EBca01_SQ002_D17_R vulgare carpel, p 13 G156 AF134114 1.00E−31 Hyacinthus orientalis PISTILLATA protein homolog HPI1 (HPI1 13 G156 AB094985 1.00E−30 Orchis italica OrcPI mRNA for PI/GLO- like protein, complete 13 G156 gi13384062 8.50E−42 Petunia x hybrida MADS-box transcription factor FBP24. 13 G156 gi19578307 2.00E−40 Antirrhinum majus putative MADS-domain transcription fact 13 G156 gi20513262 1.30E−36 Lilium regale MADS-box transcription factor. 13 G156 gi18076209 2.70E−36 Zea mays putative MADS-domain transcription factor. 13 G156 gi5019464 1.40E−34 Gnetum gnemon putative MADS domain transcription factor G 13 G156 gi3114586 7.10E−34 Eucalyptus grandis MADS box protein. 13 G156 gi4885036 9.00E−34 Hyacinthus orientalis PISTILLATA protein homolog HPI2. 13 G156 gi24421111 1.60E−31 Orchis italica PI/GLO-like protein. 13 G156 gi2961437 2.30E−31 Oryza sativa MADS box protein. 13 G156 gi16549070 3.40E−31 Magnolia praecocissima putative MADS-domain transcription 15 G157 AY036888 1.00E−63 Brassica napus MADS-box protein (FLC1) mRNA, complete cds. 15 G157 BG596731 1.00E−37 Solanum tuberosum EST495409 cSTS Solanum tuberosum cDNA clo 15 G157 BG544805 1.00E−37 Brassica rapa subsp. E2809 Chinese cabbage pekinensis etiol 15 G157 AW219962 4.00E−37 Lycopersicon EST302445 tomato root esculentum during/after 15 G157 BM436799 5.00E−36 Vitis vinifera VVA010B05 53181 An expressed sequence tag da 15 G157 BU875165 1.00E−31 Populus balsamifera V003A12 Populus flow subsp. trichocarpa 15 G157 BQ868455 2.00E−31 Lactuca sativa QGD14A13.yg.ab1 QG_ABCDI lettuce salinas Lac 15 G157 BI957545 1.00E−30 Hordeum vulgare HVSMEn0010B09f Hordeum vulgare rachis EST1 15 G157 BJ213269 3.00E−30 Triticum aestivum BJ213269 Y. Ogihara unpublished cDNA libr 15 G157 BU887610 3.00E−30 Populus tremula x R064B01 Populus root Populus tremuloides 15 G157 gi17933450 4.90E−62 Brassica napus MADS-box protein. 15 G157 gi9367313 2.60E−31 Hordeum vulgare MADS-box protein 8. 15 G157 gi16874557 5.50E−31 Antirrhinum majus MADS-box transcription factor DEFH28. 15 G157 gi1483232 7.00E−31 Betula pendula MADS5 protein. 15 G157 gi4204234 1.40E−30 Lolium temulentum MADS-box protein 2. 15 G157 gi7592642 1.40E−30 Oryza sativa AP1-like MADS box protein. 15 G157 gi12002141 1.80E−30 Zea mays MADS box protein 3. 15 G157 gi21070923 1.80E−30 Oryza sativa (japonica AP1-like MADS-box cultivar-group) 15 G157 gi13384068 8.00E−30 Petunia x hybrida MADS-box transcription factor FBP29. 15 G157 gi6469345 1.30E−29 Brassica rapa subsp. DNA-binding protein. pekinensis 17 G162 BZ073323 6.00E−44 Brassica oleracea 1kf66e08.b1 B. oleracea002 Brassica olerac 17 G162 BQ403135 3.00E−33 Gossypium arboreum GA_Ed0054C07f Gossypium arboreum 7-10 d 17 G162 AC122160 2.00E−27 Medicago truncatula clone mth2-23d6, WORKING DRAFT SEQUENCE 17 G162 CRU91416 2.00E−18 Ceratopteris richardii CMADS2 mRNA, complete cds. 17 G162 AP005789 3.00E−18 Oryza sativa (japonica ( ) chromosome 9 clo cultivar-group) 17 G162 AAAA01007138 3.00E−18 Oryza sativa (indica ( ) scaffold007138 cultivar-group) 17 G162 AP003627 8.00E−18 Oryza sativa genomic DNA, chromosome 1, PAC clone: P0459B04, 17 G162 BZ415846 1.00E−16 Zea mays if60b04.g1 WGS-ZmaysF (DH5a methyl filtered) Zea m 17 G162 CA733624 3.00E−16 Triticum aestivum w1p1c.pk005.p15 w1p1c Triticum aestivum c 17 G162 AF035379 4.00E−16 Lolium temulentum MADS-box protein 2 (MADS2) mRNA, alternat 17 G162 gi3253149 1.30E−20 Ceratopteris richardii CMADS2. 17 G162 gi15290141 2.80E−20 Oryza sativa hypothetical protein. 17 G162 gi6580943 2.40E−19 Picea abies MADS-box transcription factor. 17 G162 gi5019431 4.90E−19 Gnetum gnemon putative MADS domain transcription factor G 17 G162 gi1206005 4.90E−19 Pinus radiata putative MADS-box family transcription fact 17 G162 gi1702951 4.90E−19 Pinus resinosa MADS-box family transcription factor. 17 G162 gi887392 8.00E−19 Brassica oleracea BOAP1. 17 G162 gi21396799 1.60E−18 Lycopodium annotinum MADS-box gene 4 protein. 17 G162 gi20219014 3.40E−18 Lycopersicon MADS-box transcription esculentum factor MAD 17 G162 gi7672991 3.60E−18 Canavalia lineata MADS-box transcription factor. 19 G175 AB063576 1.00E−108 Nicotiana tabacum NtWRKY-9 mRNA for WRKY DNA-binding protei 19 G175 LES303343 1.00E−103 Lycopersicon mRNA for hypothetical esculentum protein (ORF 19 G175 BZ005522 2.00E−74 Brassica oleracea oej73d10.b1 B. oleracea002 Brassica olerac 19 G175 IPBSPF1P 3.00E−71 Ipomoea batatas Sweet potato mRNA for SPF1 protein, complet 19 G175 AX192162 3.00E−68 Glycine max Sequence 9 from Patent WO0149840. 19 G175 AX192164 1.00E−66 Triticum aestivum Sequence 11 from Patent WO0149840. 19 G175 AF439274 5.00E−65 Retama raetam WRKY-like drought- induced protein (WRK) mRNA, 19 G175 OSJN00012 5.00E−64 Oryza sativa chromosome 4 clone OSJNBa0089K21, *** SEQUENC 19 G175 CUSSLDB 6.00E−63 Cucumis sativus SPF1-like DNA-binding protein mRNA, complet 19 G175 PCU48831 7.00E−63 Petroselinum crispum DNA-binding protein WRKY1 mRNA, comple 19 G175 gi13620227 8.20E−108 Lycopersicon hypothetical protein. esculentum 19 G175 gi14530687 2.00E−89 Nicotiana tabacum WRKY DNA-binding protein. 19 G175 gi1076685 2.10E−74 Ipomoea batatas SPF1 protein - sweet potato. 19 G175 gi18158619 1.10E−69 Retama raetam WRKY-like drought- induced protein. 19 G175 gi7484759 5.90E−68 Cucumis sativus SP8 binding protein homolog - cucumber. 19 G175 gi5917653 7.80E−64 Petroselinum crispum zinc-finger type transcription facto 19 G175 gi14587365 2.40E−63 Oryza sativa putative DNA-binding protein ABF1. 19 G175 gi4894965 9.90E−61 Avena sativa DNA-binding protein WRKY1. 19 G175 gi1159877 2.40E−60 Avena fatua DNA-binding protein. 19 G175 gi16588566 7.30E−52 Solanum dulcamara thermal hysteresis protein STHP-64. 21 G180 BU896559 7.00E−66 Populus tremula x X042D08 Populus wood Populus tremuloides 21 G180 CA800201 2.00E−58 Glycine max sat79d02.y1 Gm-c1062 Glycine max cDNA clone SOY 21 G180 BQ507128 8.00E−55 Solanum tuberosum EST614543 Generation of a set of potato c 21 G180 BJ322852 1.00E−39 Triticum aestivum BJ322852 Y. Ogihara unpublished cDNA libr 21 G180 BQ293390 8.00E−39 Zea mays 1091013C10.x2 1091 - Immature ear with common ESTs 21 G180 BM370440 9.00E−30 Hordeum vulgare EBro08_SQ004_D21_RIGF Barley EBro08 librar 21 G180 AF140554 3.00E−28 Avena sativa DNA-binding protein WRKY1 (wrky1) mRNA, comple 21 G180 BI210061 1.00E−27 Lycopersicon EST528101 cTOS esculentum Lycopersicon esculen 21 G180 AFABF1 4.00E−27 Avena fatua A. fatua mRNA for DNA- binding protein (clone ABF 21 G180 BQ864325 2.00E−26 Lactuca sativa QGC26J22.yg.ab1 QG_ABCDI lettuce salinas Lac 21 G180 gi14140117 9.60E−50 Oryza sativa WRKY-like DNA-binding protein. 21 G180 gi24745606 1.10E−31 Solanum tuberosum WRKY-type DNA binding protein. 21 G180 gi4894965 1.90E−29 Avena sativa DNA-binding protein WRKY1. 21 G180 gi1159877 3.50E−29 Avena fatua DNA-binding protein. 21 G180 gi20161004 5.60E−29 Oryza sativa (japonica hypothetical prote cultivar-group) 21 G180 gi1431872 7.30E−29 Petroselinum crispum WRKY1. 21 G180 gi5360683 6.90E−28 Nicotiana tabacum NtWRKY1. 21 G180 gi13620227 3.50E−27 Lycopersicon hypothetical protein. esculentum 21 G180 gi3420906 5.30E−27 Pimpinella brachycarpa zinc finger protein; WRKY1. 21 G180 gi1076685 1.20E−26 Ipomoea batatas SPF1 protein - sweet potato. 23 G183 CRU303349 3.00E−54 Capsella rubella ORF1, ORF2, ORF3, ORF4, ORF5 and ORF6 (pa 23 G183 AB063576 5.00E−33 Nicotiana tabacum NtWRKY-9 mRNA for WRKY DNA-binding protei 23 G183 LES303343 3.00E−32 Lycopersicon mRNA for hypothetical esculentum protein (ORF 23 G183 IPBSPF1P 2.00E−29 Ipomoea batatas Sweet potato mRNA for SPF1 protein, complet 23 G183 BM408205 2.00E−29 Solanum tuberosum EST582532 potato roots Solanum tuberosum 23 G183 BI128063 5.00E−29 Populus tremula x G070P32Y Populus camb Populus tremuloides 23 G183 BU043758 1.00E−28 Prunus persica PP_LEa0017B09f Peach developing fruit mesoca 23 G183 AX192162 4.00E−28 Glycine max Sequence 9 from Patent WO0149840. 23 G183 BG442954 5.00E−28 Gossypium arboreum GA_Ea0018P14f Gossypium arboreum 7-10 d 23 G183 AF080595 2.00E−27 Pimpinella brachycarpa zinc finger protein (ZFPl) mRNA, com 23 G183 gi13620168 1.30E−86 Capsella rubella hypothetical protein. 23 G183 gi13620227 2.60E−52 Lycopersicon hypothetical protein. esculentum 23 G183 gi6174838 1.10E−37 Nicotiana tabacum transcription factor NtWRKY4. 23 G183 gi1076685 1.70E−35 Ipomoea batatas SPF1 protein - sweet potato. 23 G183 gi7484759 9.20E−29 Cucumis sativus SP8 binding protein homolog - cucumber. 23 G183 gi1159877 9.50E−29 Avena fatua DNA-binding protein. 23 G183 gi14587365 8.00E−28 Oryza sativa putative DNA-binding protein ABF1. 23 G183 gi3420906 1.10E−27 Pimpinella brachycarpa zinc finger protein; WRKY1. 23 G183 gi5917653 1.00E−26 Petroselinum crispum zinc-finger type transcription facto 23 G183 gi4894965 2.30E−26 Avena sativa DNA-binding protein WRKY1. 25 G188 AW596933 6.00E−43 Glycine max sj84f07.y1 Gm-c1034 Glycine max cDNA clone GENO 25 G188 BI923414 2.00E−40 Lycopersicon EST543319 tomato callus esculentum Lycopersico 25 G188 AV423663 3.00E−40 Lotus japonicus AV423663 Lotus japonicus young plants (two- 25 G188 BM112869 6.00E−39 Solanum tuberosum EST560405 potato roots Solanum tuberosum 25 G188 AP003951 6.00E−39 Oryza sativa chromosome 6 clone OJ1288_C01, *** SEQUENCING 25 G188 AP004683 9.00E−39 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 25 G188 AAAA01011017 9.00E−39 Oryza sativa (indica ( ) scaffold011017 cultivar-group) 25 G188 BU837263 6.00E−38 Populus tremula x T096G05 Populus apica Populus tremuloides 25 G188 AW447931 4.00E−34 Triticum aestivum BRY_1082 BRY Triticum aestivum cDNA clone 25 G188 BQ763996 2.00E−32 Hordeum vulgare subsp. EBro03_SQ006_A04_R vulgare root, 3 w 25 G188 gi12039364 4.00E−37 Oryza sativa putative DNA-binding protein. 25 G188 gi4322940 4.70E−21 Nicotiana tabacum DNA-binding protein 2. 25 G188 gi4894963 5.00E−20 Avena sativa DNA-binding protein WRKY3. 25 G188 gi1432056 7.80E−20 Petroselinum crispum WRKY3. 25 G188 gi11993901 3.10E−18 Dactylis glomerata somatic embryogenesis related protein. 25 G188 gi22830985 1.10E−17 Oryza sativa (japonica WRKY transcription cultivar-group) 25 G188 gi7484759 1.40E−16 Cucumis sativus SP8 binding protein homolog - cucumber. 25 G188 gi1159879 2.70E−15 Avena fatua DNA-binding protein. 25 G188 gi23305051 8.00E−15 Oryza sativa (indica WRKY transcription f cultivar-group) 25 G188 gi9187622 2.70E−14 Solanum tuberosum WRKY DNA binding protein. 27 G189 AB041520 2.00E−67 Nicotiana tabacum mRNA for WRKY transcription factor Nt-Sub 27 G189 PCU56834 2.00E−64 Petroselinum crispum DNA binding protein WRKY3 mRNA, comple 27 G189 AF140553 6.00E−55 Avena sativa DNA-binding protein WRKY3 (wrky3) mRNA, comple 27 G189 BI469529 1.00E−54 Glycine max sah61a11.y1 Gm-c1049 Glycine max cDNA clone GEN 27 G189 AY108689 5.00E−54 Zea mays PCO134907 mRNA sequence. 27 G189 AAAA01014145 7.00E−54 Oryza sativa (indica ( ) scaffold014145 cultivar-group) 27 G189 BI209749 2.00E−53 Lycopersicon EST527789 cTOS esculentum Lycopersicon esculen 27 G189 BU046845 4.00E−53 Prunus persica PP_LEa0027O15f Peach developing fruit mesoca 27 G189 AP004648 4.00E−51 Oryza sativa (japonica ( ) chromosome 8 clo cultivar-group) 27 G189 OSJN00198 6.00E−48 Oryza sativa chromosome 4 clone OSJNBb0015N08, *** SEQUENC 27 G189 gi4894963 1.00E−54 Avena sativa DNA-binding protein WRKY3. 27 G189 gi10798760 1.70E−50 Nicotiana tabacum WRKY transcription factor Nt-SubD48. 27 G189 gi1432056 1.60E−49 Petroselinum crispum WRKY3. 27 G189 gi11993901 5.80E−43 Dactylis glomerata somatic embryogenesis related protein. 27 G189 gi15289829 5.60E−25 Oryza sativa contains ESTs D24303(R1701), C26098 (C11628)˜u 27 G189 gi1076685 1.60E−21 Ipomoea batatas SPF1 protein-sweet potato. 27 G189 gi1159877 6.50E−21 Avena fatua DNA-binding protein. 27 G189 gi18158619 5.10E−20 Retama raetam WRKY-like drought- induced protein. 27 G189 gi3420906 9.80E−20 Pimpinella brachycarpa zinc finger protein; WRKY1. 27 G189 gi23305051 4.50E−19 Oryza sativa (indica WRKY transcription f cultivar-group) 29 G192 BH471182 3.00E−62 Brassica oleracea BOHES67TF BOHE Brassica oleracea genomic 29 G192 BI923235 2.00E−49 Lycopersicon EST543139 tomato callus esculentum Lycopersico 29 G192 AW596933 3.00E−47 Glycine max sj84f07.y1 Gm-c1034 Glycine max cDNA clone GENO 29 G192 AV423663 2.00E−46 Lotus japonicus AV423663 Lotus japonicus young plants (two- 29 G192 BM112869 1.00E−41 Solanum tuberosum EST560405 potato roots Solanum tuberosum 29 G192 BU837263 8.00E−39 Populus tremula x T096G05 Populus apica Populus tremuloides 29 G192 AAAA01003718 6.00E−34 Oryza sativa (indica ( ) scaffold003718 cultivar-group) 29 G192 AC018727 6.00E−34 Oryza sativa chromosome 10 clone OSJNBa0056G17, *** SEQUENC 29 G192 AP004683 1.00E−33 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 29 G192 AW447931 1.00E−32 Triticum aestivum BRY_1082 BRY Triticum aestivum cDNA clone 29 G192 gi12039364 1.90E−35 Oryza sativa putative DNA-binding protein. 29 G192 gi1432056 2.00E−24 Petroselinum crispum WRKY3. 29 G192 gi4894963 8.80E−24 Avena sativa DNA-binding protein WRKY3. 29 G192 gi4760596 1.80E−23 Nicotiana tabacum DNA-binding protein NtWRKY3. 29 G192 gi11993901 4.30E−20 Dactylis glomerata somatic embryogenesis related protein. 29 G192 gi21644680 1.60E−17 Oryza sativa (japonica hypothetical prote cultivar-group) 29 G192 gi23305051 5.00E−17 Oryza sativa (indica WRKY transcription f cultivar-group) 29 G192 gi1076685 1.90E−15 Ipomoea batatas SPF 1 protein - sweet potato. 29 G192 gi7484759 2.30E−15 Cucumis sativus SP8 binding protein homolog - cucumber. 29 G192 gi3420906 5.10E−15 Pimpinella brachycarpa zinc finger protein; WRKY1. 31 G196 BH944961 9.00E−69 Brassica oleracea obu81g06.g1 B. oleracea002 Brassica olerac 31 G196 AAAA01003718 1.00E−46 Oryza sativa (indica ( ) scaffold003718 cultivar-group) 31 G196 AC018727 1.00E−46 Oryza sativa chromosome 10 clone OSJNBa0056G17, *** SEQUENC 31 G196 BI923235 6.00E−40 Lycopersicon EST543139 tomato callus esculentum Lycopersico 31 G196 BM113882 4.00E−38 Solanum tuberosum EST561418 potato roots Solanum tuberosum 31 G196 AW596933 1.00E−35 Glycine max sj84f07.y1 Gm-c1034 Glycine max cDNA clone GENO 31 G196 AV423663 2.00E−34 Lotus japonicus AV423663 Lotus japonicus young plants (two- 31 G196 BG647709 3.00E−34 Medicago truncatula EST509328 HOGA Medicago truncatula cDNA 31 G196 BQ855766 3.00E−33 Lactuca sativa QGB27K18.yg.ab1 QG_ABCDI lettuce salinas Lac 31 G196 BU837263 5.00E−32 Populus tremula x T096G05 Populus apica Populus tremuloides 31 G196 gi12039364 3.30E−51 Oryza sativa putative DNA-binding protein. 31 G196 gi4894963 2.40E−27 Avena sativa DNA-binding protein WRKY3. 31 G196 gi10798760 7.00E−26 Nicotiana tabacum WRKY transcription factor Nt-SubD48. 31 G196 gi1432056 6.20E−25 Petroselinum crispum WRKY3. 31 G196 gi11993901 3.00E−20 Dactylis glomerata somatic embryogenesis related protein. 31 G196 gi20160973 3.50E−20 Oryza sativa (japonica hypothetical prote cultivar-group) 31 G196 gi23305051 1.10E−14 Oryza sativa (indica WRKY transcription f cultivar-group) 31 G196 gi9187622 1.40E−14 Solanum tuberosum WRKY DNA binding protein. 31 G196 gi1076685 2.50E−14 Ipomoea batatas SPF1 protein - sweet potato. 31 G196 gi13620227 5.50E−14 Lycopersicon hypothetical protein. esculentum 33 G211 BG441912 6.00E−70 Gossypium arboreum GA_Ea0015B19f Gossypium arboreum 7-10 d 33 G211 AF336278 1.00E−69 Gossypium hirsutum BNLGHi233 (bnlghi6233) mRNA, complete cd 33 G211 BU837990 3.00E−66 Populus tremula x T108C04 Populus apica Populus tremuloides 33 G211 D88620 2.00E−57 Oryza sativa mRNA for OSMYB4, complete cds. 33 G211 AW186273 6.00E−54 Glycine max se65f12.y1 Gm-c1019 Glycine max cDNA clone GENO 33 G211 PMU39448 1.00E−52 Picea mariana MYB-like transcriptional factor MBF1 mRNA, co 33 G211 AAAA01005841 1.00E−52 Oryza sativa (indica ( ) scaffold005841 cultivar-group) 33 G211 BI674748 7.00E−52 Zea mays 949066G11.y2 949 - Juvenile leaf and shoot cDNA fr 33 G211 AW775893 2.00E−51 Medicago truncatula EST334958 DSIL Medicago truncatula cDNA 33 G211 HVMYB2 2.00E−51 Hordeum vulgare H. vulgare myb2 mRNA. 33 G211 gi13346178 1.50E−67 Gossypium hirsutum BNLGHi233. 33 G211 gi22535556 1.10E−53 Oryza sativa (japonica myb-related protei cultivar-group) 33 G211 gi2605623 1.10E−53 Oryza sativa OSMYB4. 33 G211 gi1101770 5.70E−52 Picea mariana MYB-like transcriptional factor MBF 1. 33 G211 gi82310 2.00E−51 Antirrhinum majus myb protein 330 - garden snapdragon. 33 G211 gi127582 4.00E−51 Zea mays MYB-RELATED PROTEIN ZM38. 33 G211 gi19055 1.10E−50 Hordeum vulgare MybHv5. 33 G211 gi22795039 1.10E−50 Populus x canescens putative MYB transcription factor. 33 G211 gi1167484 3.60E−50 Lycopersicon transcription factor. esculentum 33 G211 gi20563 3.70E−50 Petunia x hybrida protein 1. 35 G214 PVU420902 1.00E−111 Phaseolus vulgaris mRNA for LHY protein. 35 G214 BU868664 6.00E−60 Populus balsamifera M118F07 Populus flow subsp. trichocarpa 35 G214 BE331563 2.00E−50 Glycine max sp15d08.y1 Gm-c1042 Glycine max cDNA clone GENO 35 G214 BH935194 1.00E−49 Brassica oleracea ode18e05.g1 B. oleracea002 Brassica olerac 35 G214 AAAA01009649 4.00E−49 Oryza sativa (indica ( ) scaffold009649 cultivar-group) 35 G214 AP004460 5.00E−48 Oryza sativa (japonica ( ) chromosome 8 clo cultivar-group) 35 G214 AW979367 2.00E−46 Lycopersicon EST310415 tomato root esculentum deficiency, C 35 G214 BM322287 5.00E−46 Sorghum bicolor PIC1_2_F02.b1_A002 Pathogen-infected compat 35 G214 AY103618 4.00E−45 Zea mays PCO118792 mRNA sequence. 35 G214 BG524104 3.00E−44 Stevia rebaudiana 38-82 Stevia field grown leaf cDNA Stevia 35 G214 gi21213868 7.60E−57 Phaseolus vulgaris LHY protein. 35 G214 gi15528628 2.40E−23 Oryza sativa hypothetical protein˜similar to Oryza sativa 35 G214 gi12406993 1.20E−06 Hordeum vulgare MCB1 protein. 35 G214 gi20067661 1.40E−06 Zea mays one repeat myb transcriptional factor. 35 G214 gi18874263 3.70E−06 Antirrhinum majus MYB-like transcription factor DIVARICAT 35 G214 gi24850305 1.00E−05 Oryza sativa (japonica transcription fact cultivar-group) 35 G214 gi12005328 3.00E−05 Hevea brasiliensis unknown. 35 G214 gi6688529 6.80E−05 Lycopersicon I-box binding factor. esculentum 35 G214 gi19911579 7.10E−05 Glycine max syringolide-induced protein 1-3-1B. 35 G214 gi7677132 0.0025 Secale cereale c-myb-likc transcription factor. 37 G226 BU872107 2.00E−21 Populus balsamifera Q039C07 Populus flow subsp. trichocarpa 37 G226 BU831849 2.00E−21 Populus tremula x T026E01 Populus apica Populus tremuloides 37 G226 BM437313 9.00E−21 Vitis vinifera VVA017F06_54121 An expressed sequence tag da 37 G226 BI699876 1.00E−19 Glycine max sag49b09.y1 Gm-c1081 Glycine max cDNA clone GEN 37 G226 AL750151 4.00E−16 Pinus pinaster AL750151 AS Pinus pinaster cDNA clone AS06C1 37 G226 CA744013 2.00E−12 Triticum aestivum wrils.pk006.m22 wrils Triticum aestivum c 37 G226 BH961028 3.00E−12 Brassica oleracea odj30d06.g1 B. oleracea002 Brassica olerac 37 G226 BJ472717 8.00E−12 Hordeum vulgare subsp. BJ472717 K. Sato vulgare unpublished 37 G226 BF617445 8.00E−12 Hordeum vulgare HVSMEc0017G08f Hordeum vulgare seedling sho 37 G226 CA762299 2.00E−11 Oryza sativa (indica BR060003B10F03.ab1 IRR cultivar-group) 37 G226 gi9954118 2.20E−11 Solanum tuberosum tuber-specific and sucrose- responsive e 37 G226 gi14269333 2.50E−10 Gossypium raimondii myb-like transcription factor Myb 3. 37 G226 gi14269335 2.50E−10 Gossypium herbaceum myb-like transcription factor Myb 3. 37 G226 gi14269337 2.50E−10 Gossypium hirsutum myb-like transcription factor Myb 3. 37 G226 gi23476297 2.50E−10 Gossypioides kirkii myb-like transcription factor 3. 37 G226 gi15082210 8.50E−10 Fragaria x ananassa transcription factor MYB1. 37 G226 gi19072770 8.50E−10 Oryza sativa typical P-type R2R3 Myb protein. 37 G226 gi15042108 1.40E−09 Zea mays subsp. CI protein. parviglumis 37 G226 gi15042124 1.40E−09 Zea luxurians CI protein. 37 G226 gi20514371 1.40E−09 Cucumis sativus werewolf. 39 G241 AB028650 3.00E−69 Nicotiana tabacum mRNA for myb-related transcription factor 39 G241 PHMYBPH22 3.00E−68 Petunia x hybrida P. Hybrida myb.Ph2 gene encoding protein 39 G241 LETHM18GE 1.00E−65 Lycopersicon L. esculentum mRNA for esculentum myb-related 39 G241 AB073017 2.00E−63 Vitis labrusca x Vitis VlmybB1-2 gene for myb- vinifera rela 39 G241 OSMYB1202 5.00E−63 Oryza sativa O. sativa mRNA for myb factor, 1202 bp. 39 G241 AB029162 2.00E−62 Glycine max gene for GmMYB293, complete cds. 39 G241 BQ514539 1.00E−61 Solanum tuberosum EST621954 Generation of a set of potato c 39 G241 AW981167 5.00E−61 Medicago truncatula EST392361 DSIL Medicago truncatula cDNA 39 G241 BJ312394 4.00E−60 Triticum aestivum BJ312394 Y. Ogihara unpublished cDNA libr 39 6241 BM816803 2.00E−59 Hordeum vulgare HC114B11_SK.ab1 HC Hordeum vulgare cDNA clo 39 G241 gi6552361 1.50E−67 Nicotiana tabacum myb-related transcription factor LBM2. 39 G241 gi20561 8.30E−67 Petunia x hybrida protein 2. 39 G241 gi1370140 3.70E−64 Lycopersicon myb-related transcription esculentum factor. 39 G241 gi6492385 3.80E−62 Glycine max GmMYB29A2. 39 G241 gi1946265 2.70E−61 Oryza sativa myb. 39 G241 gi22266675 9.70E−57 Vitis labrusca x Vitis myb-related transcription vinifera 39 G241 gi127580 5.50E−54 Zea mays MYB-RELATED PROTEIN ZM1. 39 G241 gi11526779 9.90E−52 Zea mays subsp. P-like protein. parviglumis 39 G241 gi22795039 1.10E−48 Populus x canescens putative MYB transcription factor. 39 G241 gi13346188 1.40E−48 Gossypium hirsutum GHMYB25. 41 G248 BE642935 2.00E−25 Ceratopteris richardii Cri2_7_G20_SP6 Ceratopteris Spore Li 41 G248 AF190304 1.00E−24 Adiantum raddianum c-myb-like transcription factor (MYB3R-1 41 G248 AW040511 1.00E−24 Lycopersicon EST283471 tomato mixed esculentum elicitor, BT 41 G248 AF189786 2.00E−24 Physcomitrella patens putative c-myb-like transcription fac 41 G248 CA755789 4.00E−24 Oryza sativa (japonica BR030028000_PLATE_D1 cultivar-group) 41 G248 AB056123 2.00E−23 Nicotiana tabacum NtmybA2 mRNA for Myb, complete cds. 41 G248 AF189788 2.00E−22 Hordeum vulgare putative c-myb-like transcription factor (M 41 G248 AF236059 3.00E−22 Papaver rhoeas putative Myb-related domain (pmr) mRNA, part 41 G248 AF190302 2.00E−20 Secale cereale c-myb-like transcription factor (MYB3R-1) mR 41 G248 BH444284 1.00E−18 Brassica oleracea BOGON79TF BOGO Brassica oleracea genomic 41 G248 gi24417180 6.50E−28 Oryza sativa (japonica myb-like protein. cultivar-group) 41 G248 gi7677136 5.80E−27 Adiantum raddianum c-myb-like transcription factor. 41 G248 gi8745325 7.30E−25 Hordeum vulgare putative c-myb-like transcription factor. 41 G248 gi8745321 2.30E−24 Physcomitrella patens putative c-myb-like transcription f 41 G248 gi16326135 9.40E−23 Nicotiana tabacum Myb. 41 G248 gi7677132 1.50E−22 Secale cereale c-myb-like transcription factor. 41 G248 gi7630236 2.30E−22 Oryza sativa Similar to Arabidopsis thaliana chromosome 4 41 G248 gi7230673 7.10E−22 Papaver rhoeas putative Myb-related domain. 41 G248 gi14269337 1.50E−20 Gossypium hirsutum myb-like transcription factor Myb 3. 41 G248 gi14269333 1.60E−19 Gossypium raimondii myb-like transcription factor Myb 3. 43 G254 BU100118 4.00E−67 Triticum aestivum WHE3315_D06_H11ZS Chinese Spring wheat dr 43 G254 BI921951 1.00E−60 Lycopersicon EST541854 tomato callus esculentum Lycopersico 43 G254 AV909036 1.00E−57 Hordeum vulgare subsp. AV909036 K. Sato vulgare unpublished 43 G254 AW000459 9.00E−54 Zea mays 614016D07.y1 614 - root cDNA library from Walbot L 43 G254 BG457702 2.00E−53 Medicago truncatula NF034C07PL1F1051 Phosphate starved leaf 43 G254 BU025460 2.00E−53 Helianthus annuus QHF9I05.yg.ab1 QH_EFGHJ sunflower RHA280 43 G254 BG593097 3.00E−52 Solanum tuberosum EST491775 cSTS Solanum tuberosum cDNA clo 43 G254 BU868480 3.00E−52 Populus balsamifera M116D03 Populus flow subsp. trichocarpa 43 G254 BU815973 5.00E−52 Populus tremula x N058E04 Populus bark Populus tremuloides 43 G254 BE330818 1.00E−51 Glycine max so85g03.y1 Gm-c1041 Glycine max cDNA clone GENO 43 G254 gi15528628 1.80E−25 Oryza sativa hypothetical protein˜similar to Oryza sativa 43 G254 gi21213868 3.40E−24 Phaseolus vulgaris LHY protein. 43 G254 gi18461206 1.20E−07 Oryza sativa (japonica contains ESTs AU10 cultivar-group) 43 G254 gi12005328 1.10E−06 Hevea brasiliensis unknown. 43 G254 gi12406993 1.30E−06 Hordeum vulgare MCB1 protein. 43 G254 gi19911577 5.50E−06 Glycine max syringolide-induced protein 1-3-1A. 43 G254 gi6688529 3.90E−05 Lycopersicon I-box binding factor. esculentum 43 G254 gi18874265 3.90E−05 Antirrhinum majus MYB-like transcription factor DVL1. 43 G254 gi20067661 4.10E−05 Zea mays one repeat myb transcriptional factor. 43 G254 gi7705206 0.00072 Solanum tuberosum MybSt1. 45 G256 LETHM6 1.00E−78 Lycopersicon L. esculentum mRNA for esculentum myb-related t 45 G256 AY107969 4.00E−78 Zea mays PCO069276 mRNA sequence. 45 G256 BF270109 3.00E−76 Gossypium arboreum GA_Eb0006M14f Gossypium arboreum 7-10 d 45 G256 AW981415 5.00E−75 Medicago truncatula EST392568 DSIL Medicago truncatula cDNA 45 G256 BE342909 1.00E−72 Solanum tuberosum EST395753 potato stolon, Cornell Universi 45 G256 BQ623221 5.00E−72 Citrus sinensis USDA-FP_00312 Ridge pineapple sweet orange 45 G256 AP005636 1.00E−70 Oryza sativa (japonica ( ) chromosome 9 clo cultivar-group) 45 G256 AAAA01005623 1.00E−70 Oryza sativa (indica ( ) scaffold005623 cultivar-group) 454 G256 AC084762 8.00E−70 Oryza sativa chromosome 3 clone OSJNBa0013O08, *** SEQUENCI 45 G256 BM309647 8.00E−67 Glycine max sak65a08.y1 Gm-c1036 Glycine max cDNA clone SOY 45 G256 gi256828 1.10E−80 Antirrhinum majus Myb oncoprotein homolog {clone 306} [An 45 G256 gi1430848 8.20E−76 Lycopersicon transcription factor. esculentum 45 G256 gi18071376 6.80E−71 Oryza sativa putative transcription factor. 45 G256 gi23616974 3.60E−66 Oryza sativa (japonica contains EST C2815 cultivar-group) 45 G256 gi19072744 4.20E−65 Zea mays typical P-type R2R3 Myb protein. 45 G256 gi20563 7.30E−52 Petunia x hybrida protein 1. 45 G256 gi6552361 2.90E−50 Nicotiana tabacum myb-related transcription factor LBM2. 45 G256 gi13346188 2.30E−48 Gossypium hirsutum GHMYB25. 45 G256 gi5139802 4.70E−48 Glycine max GmMYB29A1. 45 G256 gi11526775 1.60E−47 Zea mays subsp. P2-t protein. parviglumis 47 G278 AF527176 1.0e−999 Brassica napus putative NPR1 (NPR1) mRNA, complete cds. 47 G278 BD064079 1.0e−999 Macadamia integrifolia Method for protecting plants. 47 G278 AF480488 1.00E−162 Nicotiana tabacum NPR1 mRNA, complete cds. 47 G278 AX351141 1.00E−106 Oryza sativa Sequence 15 from Patent WO0166755. 47 G278 AX041006 8.00E−97 Zea mays Sequence 1 from Patent WO0065037. 47 G278 AX351145 3.00E−95 Triticum aestivum Sequence 19 from Patent WO0166755. 47 G278 AC124609 2.00E−75 Medicago truncatula clone mth2-29b13, WORKING DRAFT SEQUENC 47 G278 AAAA01004121 6.00E−70 Oryza sativa (indica ( ) scaffold004121 cultivar-group) 47 G278 BZ056711 5.00E−67 Brassica oleracea lle49h07.b1 B. oleracea002 Brassica olerac 47 G278 BE435499 3.00E−50 Lycopersicon EST406577 tomato breaker esculentum fruit, TIG 47 G278 gi22003730 0.00E+00 Brassica napus putative NPR1. 47 G278 gi21552981 9.30E−155 Nicotiana tabacum NPR1. 47 G278 gi10934082 1.40E−128 Oryza sativa Arabidopsis thaliana regulatory protein NPR1 47 G278 gi18616499 5.00E−92 Triticum aestivum unnamed protein product. 47 G278 gi22535593 2.60E−88 Oryza sativa (japonica putative Regulator cultivar-group) 47 G278 gi11340603 3.40E−86 Zea mays unnamed protein product. 47 G278 gi17645766 0.00027 Glycine max unnamed protein product. 47 G278 gi549986 0.012 Pennisetum ciliare possible apospory- associated protein. 47 G278 gi18700703 0.14 Medicago sativa putative ankyrin-kinase. 47 G278 gi18700701 0.18 Medicago truncatula ankyrin-kinase. 49 G291 AF014375 1.00E−170 Medicago sativa putative JUN kinase activation domain bindi 49 G291 AF175964 1.00E−169 Lycopersicon JAB mRNA, complete cds. esculentum 49 G291 AF072849 1.00E−159 Oryza sativa subsp. jab1 protein (jab1) mRNA, indica comple 49 G291 AB055495 1.00E−159 Oryza sativa Jab1 mRNA for JUN- activation-domain-binding pr 49 G291 BG594615 1.00E−132 Solanum tuberosum EST493293 cSTS Solanum tuberosum cDNA clo 49 G291 BQ969736 1.00E−125 Helianthus annuus QHB39G11.yg.ab1 QH_ABCDI sunflower RHA801 49 G291 BQ871378 1.00E−123 Lactuca sativa QGI11K21.yg.ab1 QG_ABCDI lettuce salinas Lac 49 G291 BE036313 1.00E−115 Mesembryanthemum MO23B10 MO crystallinum Mesembryanthemum c 49 G291 BM066924 1.00E−113 Capsicum annuum KS07019G04 KS07 Capsicum annuum cDNA, mRNA 49 G291 BQ281547 1.00E−106 Triticum aestivum WHE3022_F07_K14ZS Wheat unstressed seedli 49 G291 gi3320379 1.80E−160 Medicago sativa putative JUN kinase activation domain bin 49 G291 gi12002865 3.00E−158 Lycopersicon JAB. esculentum 49 G291 gi17025926 4.30E−150 Oryza sativa JUN-activation-domain- binding protein homolo 49 G291 gi24636586 4.30E−150 Oryza sativa (japonica JUN-activation-dom cultivar-group) 49 G291 gi3420299 4.30E−150 Oryza sativa subsp. jab1 protein. indica 49 G291 gi13774977 0.73 Pinus mugo NADH dehydrogenase subunit 3. 49 G291 gi13774980 0.73 Pinus sylvestris NADH dehydrogenase subunit 3. 49 G291 gi13899006 0.89 Abies alba NADH dehydrogenase subunit 3. 49 G291 gi23503480 1 Glycine max heat shock protein DnaJ. 51 G303 BI677665 2.00E−40 Robinia pseudoacacia CLS342 CLS (Cambium and bark region of 51 G303 BQ995023 2.00E−38 Lactuca sativa QGF8N12.yg.ab1 QG_EFGHJ lettuce serriola Lac 51 G303 AAAA01003345 5.00E−36 Oryza sativa (indica ( ) scaffold003345 cultivar-group) 51 G303 AC121489 6.00E−36 Oryza sativa (japonica ( ) chromosome 3 clo cultivar-group) 51 G303 BE022329 6.00E−35 Glycine max sm73e05.y1 Gm-c1028 Glycine max cDNA clone GENO 51 G303 BI480474 2.00E−32 Triticum aestivum WHE2903_F02_L03ZS Wheat aluminum-stressed 51 G303 BH492255 7.00E−32 Brassica oleracea BOHLS25TR BOHL Brassica oleracea genomic 51 G303 BI128898 2.00E−30 Populus tremula x G083P21Y Populus camb Populus tremuloides 51 G303 CAR011013 1.00E−29 Cicer arietinum epicotyl EST, clone Can133. 51 G303 AW573949 4.00E−27 Medicago truncatula EST316540 GVN Medicago truncatula cDNA 51 G303 gi19920107 4.50E−43 Oryza sativa (japonica Putative helix-loo cultivar-group) 51 G303 gi3641870 4.30E−31 Cicer arietinum hypothetical protein. 51 G303 gi10998404 1.90E−09 Petunia x hybrida anthocyanin 1. 51 G303 gi18568238 2.10E−08 Zea mays regulatory protein. 51 G303 gi527661 2.90E−08 Phyllostachys acuta myc-like regulatory R gene product. 51 G303 gi1086538 6.10E−08 Oryza rufipogon transcriptional activator Rb homolog. 51 G303 gi527653 6.10E−08 Pennisetum glaucum myc-like regulatory R gene product. 51 G303 gi1086534 7.90E−08 Oryza officinalis transcriptional activator Ra homolog. 51 G303 gi1086540 1.90E−07 Oryza sativa Ra. 51 G303 gi527663 4.70E−07 Tripsacum australe myc-like regulatory R gene product. 53 G312 AAAA01008118 1.00E−137 Oryza sativa (indica ( ) scaffold008118 cultivar-group) 53 G312 BH521755 1.00E−69 Brassica oleracea BOHEY85TF BOHE Brassica oleracea genomic 53 G312 AW944694 4.00E−67 Euphorbia esula 00182 leafy spurge Lambda HybriZAP 2.1 two- 53 G312 BQ296629 3.00E−66 Glycine max san83a05.y2 Gm-c1052 Glycine max cDNA clone SOY 53 G312 BG446635 7.00E−64 Gossypium arboreum GA_Eb0036G15f Gossypium arboreum 7-10 d 53 G312 BH873477 8.00E−60 Zea mays hp45c06.b2 WGS-ZmaysF (JM107 adapted methyl filter 53 G312 BF257184 4.00E−56 Hordeum vulgare HVSMEf0012B22f Hordeum vulgare seedling roo 53 G312 AV414014 1.00E−52 Lotus japonicus AV414014 Lotus japonicus young plants (two- 53 G312 AF098674 4.00E−52 Lycopersicon lateral suppressor protein esculentum (Ls) mRN 53 G312 AB048713 2.00E−51 Pisum sativum PsSCR mRNA for SCARECROW, complete cds. 53 G312 gi13365610 1.30E−57 Pisum sativum SCARECROW. 53 G312 gi10178637 2.60E−53 Zea mays SCARECROW. 53 G312 gi13620224 1.30E−52 Lycopersicon lateral suppressor. esculentum 53 G312 gi13937306 4.80E−50 Oryza sativa gibberellin-insensitive protein OsGAI. 53 G312 gi20334379 1.80E−48 Vitis vinifera GAI-like protein 1. 53 G312 gi19571020 5.80E−48 Oryza sativa (japonica contains ESTs AU16 cultivar-group) 53 G312 gi13620166 4.20E−47 Capsella rubella hypothetical protein. 53 G312 gi13170126 1.30E−45 Brassica napus unnamed protein product. 53 G312 gi20257438 7.60E−44 Argyroxiphium GIA/RGA-li sandwicense subsp. macrocephalum 53 G312 gi20257420 9.60E−44 Dubautia arborea GIA/RGA-like gibberellin response modula 55 G325 AB001888 6.00E−41 Oryza sativa mRNA for zinc finger protein, complete cds, 55 G325 AAAA01003074 3.00E−32 Oryza sativa (indica ( ) scaffold003074 cultivar-group) 55 G325 BQ458955 2.00E−31 Hordeum vulgare HA02L20r HA Hordeum vulgare cDNA clone HA02 55 G325 AP005113 3.00E−31 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 55 G325 BJ209915 6.00E−31 Triticum aestivum BJ209915 Y. Ogihara unpublished cDNA libr 55 G325 BG644908 2.00E−30 Medicago truncatula EST506527 KV3 Medicago truncatula cDNA 55 G325 BG459023 2.00E−29 Zea mays 947052H08.y1 947 - 2 week shoot from Barkan lab Ze 55 G325 BQ121038 4.00E−29 Solanum tuberosum EST606614 mixed potato tissues Solanum tu 55 G325 AP004972 4.00E−29 Lotus japonicus genomic DNA, chromosome 3, clone: LjT41A07, 55 G325 BH926519 1.00E−28 Brassica oleracea odj42f08.b1 B. oleracea002 Brassica olerac 55 G325 gi3618320 9.80E−48 Oryza sativa zinc finger protein. 55 G325 gi3341723 1.70E−15 Raphanus sativus CONSTANS-like 1 protein. 55 G325 gi22854952 2.20E−15 Brassica nigra COL1 protein. 55 G325 gi2303683 2.00E−14 Brassica napus unnamed protein product. 55 G325 gi23495871 2.30E−13 Oryza sativa (japonica putative zinc-fing cultivar-group) 55 G325 gi4091806 3.80E−13 Malus x domestica CONSTANS-like protein 2. 55 G325 gi10946337 6.20E−13 Ipomoea nil CONSTANS-like protein. 55 G325 gi21667475 2.00E−11 Hordeum vulgare CONSTANS-like protein. 55 G325 gi4557093 1.10E−10 Pinus radiata zinc finger protein. 55 G325 gi21655154 1.20E−09 Hordeum vulgare subsp. CONSTANS-like protein vulgare CO5. 57 G343 AC069300 2.00E−50 Oryza sativa chromosome 10 clone OSJNBa0010C11, *** SEQUENC 57 G343 BU827056 4.00E−50 Populus tremula x UK127TH09 Populus api Populus tremuloides 57 G343 AAAA01001158 1.00E−47 Oryza sativa (indica ( ) scaffold001158 cultivar-group) 57 G343 BQ462644 3.00E−41 Hordeum vulgare HI01J05T HI Hordeum vulgare cDNA clone HI01 57 G343 AW235021 4.00E−41 Glycine max sf21h11.y1 Gm-c1028 Glycine max cDNA clone GENO 57 G343 BZ328210 8.00E−41 Zea mays id36b06.g1 WGS-ZmaysF (JM107 adapted methyl filter 57 G343 BH534811 1.00E−40 Brassica oleracea BOGJZ23TF BOGJ Brassica oleracea genomic 57 G343 BQ851743 2.00E−37 Lactuca sativa QGB16C22.yg.ab1 QG_ABCDI lettuce salinas Lac 57 G343 AW922818 5.00E−37 Sorghum bicolor DG1_46_F02.g1_A002 Dark Grown 1 (DG1) Sorgh 57 G343 AC132491 9.00E−37 Oryza sativa (japonica ( ) chromosome 5 clo cultivar-group) 57 G343 gi14165317 2.10E−57 Oryza sativa putative transcription factor. 57 G343 gi21902044 6.50E−45 Oryza sativa (japonica hypothetical prote cultivar-group) 57 G343 gi12711287 1.60E−31 Nicotiana tabacum GATA-1 zinc finger protein. 57 G343 gi1076609 4.40E−22 Nicotiana NTL1 protein - curled- plumbaginifolia leaved to 57 G343 gi20372847 0.34 Hordeum vulgare subsp. dof zinc finger protein. vulgare 57 G343 gi19322 0.41 Lycopersicon glycine-rich protein. esculentum 57 G343 gi21439754 0.55 Zea mays unnamed protein product. 57 G343 gi3219155 0.55 Mesembryanthemum transcription factor Vp1. crystallinum 57 G343 gi23504757 0.59 Pisum sativum nodule inception protein. 57 G343 gi21439770 0.67 Triticum aestivum unnamed protein product. 59 G353 BQ790831 5.00E−68 Brassica rapa subsp. E4675 Chinese cabbage pekinensis etiol 59 G353 BZ019752 1.00E−67 Brassica oleracea oed85c06.g1 B. oleracea002 Brassica olerac 59 G353 L46574 6.00E−40 Brassica rapa BNAF1975 Mustard flower buds Brassica rapa cD 59 G353 AB006601 7.00E−26 Petunia x hybrida mRNA for ZPT2-14, complete cds. 59 G353 BM437146 2.00E−25 Vitis vinifera VVA015A06_53787 An expressed sequence tag da 59 G353 BI422808 1.00E−24 Lycopersicon EST533474 tomato callus, esculentum TAMU Lycop 59 G353 BU867080 1.00E−24 Populus tremula x S074B01 Populus imbib Populus tremuloides 59 G353 BM527789 3.00E−23 Glycine max sal65h07.y1 Gm-c1061 Glycine max cDNA clone SOY 59 G353 BQ980246 5.00E−23 Lactuca sativa QGE10I12.yg.ab1 QG_EFGHJ lettuce serriola La 59 G353 BQ121106 2.00E−22 Solanum tuberosum EST606682 mixed potato tissues Solanum tu 59 G353 gi2346976 6.50E−28 Petunia x hybrida ZPT2-13. 59 G353 gi15623820 4.40E−25 Oryza sativa hypothetical protein. 59 G353 gi21104613 1.40E−18 Oryza sativa (japonica contains ESTs AU07 cultivar-group) 59 G353 gi485814 3.10E−13 Triticum aestivum WZF1. 59 G353 gi7228329 4.00E−12 Medicago sativa putative TFIIIA (or kruppel)-like zinc fi 59 G353 gi1763063 1.70E−11 Glycine max SCOF-1. 59 G353 gi2981169 2.60E−11 Nicotiana tabacum osmotic stress-induced zinc- finger prot 59 G353 gi4666360 1.10E−10 Datisca glomerata zinc-finger protein 1. 59 G353 gi2129892 2.30E−08 Pisum sativum probable finger protein Pszfl - garden pea. 59 G353 gi2058504 0.00018 Brassica rapa zinc-finger protein-1. 61 G354 BZ083260 5.00E−49 Brassica oleracea lle29f02.g1 B. oleracea002 Brassica olerac 61 G354 BQ790831 8.00E−45 Brassica rapa subsp. E4675 Chinese cabbage pekinensis etiol 61 G354 AB006600 6.00E−27 Petunia x hybrida mRNA for ZPT2-13, complete cds. 61 G354 L46574 1.00E−26 Brassica rapa BNAF1975 Mustard flower buds Brassica rapa cD 61 G354 BM437146 3.00E−24 Vitis vinifera VVA015A06_53787 An expressed sequence tag da 61 G354 BQ121105 6.00E−24 Solanum tuberosum EST606681 mixed potato tissues Solanum tu 61 G354 BM527789 2.00E−23 Glycine max sal65h07.y1 Gm-c1061 Glycine max cDNA clone SOY 61 G354 AI898309 2.00E−23 Lycopersicon EST267752 tomato ovary, esculentum TAMU Lycope 61 G354 BU867080 5.00E−22 Populus tremula x S074B01 Populus imbib Populus tremuloides 61 G354 BQ980246 1.00E−21 Lactuca sativa QGE10I12.yg.ab1 QG_EFGHJ lettuce serriola La 61 G354 gi2346976 5.60E−29 Petunia x hybrida ZPT2-13. 61 G354 gi15623820 1.90E−22 Oryza sativa hypothetical protein. 61 G354 gi21104613 4.00E−19 Oryza sativa (japonica contains ESTs AU07 cultivar-group) 61 G354 gi2981169 1.80E−17 Nicotiana tabacum osmotic stress-induced zinc- finger prot 61 G354 gi1763063 4.10E−16 Glycine max SCOF-1. 61 G354 gi4666360 8.90E−15 Datisca glomerata zinc-finger protein 1. 61 G354 gi2058504 1.00E−14 Brassica rapa zinc-finger protein-1. 61 G354 gi7228329 4.90E−14 Medicago sativa putative TFIIIA (or kruppel)-like zinc fi 61 G354 gi485814 3.20E−13 Triticum aestivum WZF1. 61 G354 gi2129892 1.20E−06 Pisum sativum probable finger protein Pszf1 - garden pea. 63 G361 BG135559 1.00E−24 Lycopersicon EST468451 tomato crown esculentum gall Lycoper 63 G361 AW686309 4.00E−23 Medicago truncatula NF036D10NR1F1000 Nodulated root Medicag 63 G361 BU891880 8.00E−23 Populus tremula P056E03 Populus petioles cDNA library Popul 63 G361 BU877646 2.00E−22 Populus balsamifera V037D09 Populus flow subsp. trichocarpa 63 G361 BH725134 9.00E−22 Brassica oleracea BOHWL71TF BO_2_3_KB Brassica oleracea gen 63 G361 BI426538 2.00E−21 Glycine max sag04d12.y1 Gm-c1080 Glycine max cDNA clone GEN 63 G361 AP003214 2.00E−21 Oryza sativa chromosome 1 clone OSJNBa0083M16, *** SEQUENCI 63 G361 AAAA01004859 3.00E−21 Oryza sativa (indica ( ) scaffold004859 cultivar-group) 63 G361 BU494379 1.00E−20 Lotus japonicus Ljirnpest50-154-h2 Ljirnp Lambda HybriZap t 63 G361 BQ488216 2.00E−17 Beta vulgaris 35-E8143-006-003-J02-T3 Sugar beet MPIZ-ADIS- 63 G361 gi15528588 4.00E−29 Oryza sativa hypothetical protein. 63 G361 gi18390109 2.80E−13 Sorghum bicolor putative zinc finger protein. 63 G361 gi18674684 1.50E−07 Zea ramosa unnamed protein product. 63 G361 gi14275902 6.10E−07 Petunia x hybrida lateral shoot inducing factor. 63 G361 gi21104613 0.00024 Oryza sativa (japonica contains ESTs AU07 cultivar-group) 63 G361 gi2129892 0.00062 Pisum sativum probable finger protein Pszf1 - garden pea. 63 G361 gi2058504 0.0018 Brassica rapa zinc-finger protein-1. 63 G361 gi4666360 0.018 Datisca glomerata zinc-finger protein 1. 63 G361 gi7228329 0.047 Medicago sativa putative TFIIIA (or kruppel)-like zinc fi 63 G361 gi1763063 0.084 Glycine max SCOF-1. 65 G362 BF645161 6.00E−21 Medicago truncatula NF031C06EC1F1049 Elicited cell culture 65 G362 BI206903 6.00E−21 Lycopersicon EST524943 cTOS esculentum Lycopersicon esculen 65 G362 BG047435 1.00E−18 Glycine max saa71c12.y1 Gm-c1060 Glycine max cDNA clone GEN 65 G362 BU877646 2.00E−15 Populus balsamifera V037D09 Populus flow subsp. trichocarpa 65 G362 BU891880 2.00E−15 Populus tremula P056E03 Populus petioles cDNA library Popul 65 G362 AP003214 3.00E−13 Oryza sativa chromosome 1 clone OSJNBa0083M16, *** SEQUENCI 65 G362 AAAA01004859 3.00E−13 Oryza sativa (indica ( ) scaffold004859 cultivar-group) 65 G362 BE358938 2.00E−11 Sorghum bicolor DG1_37_E12.b1_A002 Dark Grown 1 (DG1) Sorgh 65 G362 BQ488435 2.00E−11 Beta vulgaris 05-E8886-006-003-J02-T3 Sugar beet MPIZ-ADIS- 65 G362 BU494379 3.00E−11 Lotus japonicus Ljirnpest50-154-h2 Ljirnp Lambda HybriZap t 65 G362 gi15528588 2.70E−18 Oryza sativa hypothetical protein. 65 G362 gi2346984 9.00E−09 Petunia x hybrida ZPT2-9. 65 G362 gi18390109 9.90E−08 Sorghum bicolor putative zinc finger protein. 65 G362 gi21104613 0.00015 Oryza sativa (japonica contains ESTs AU07 cultivar-group) 65 G362 gi18674684 0.0028 Zea ramosa unnamed protein product. 65 G362 gi7228329 0.0029 Medicago sativa putative TFIIIA (or kruppel)-like zinc fi 65 G362 gi1763063 0.0039 Glycine max SCOF-1. 65 G362 gi485814 0.0062 Triticum aestivum WZF1. 65 G362 gi4666360 0.0072 Datisca glomerata zinc-finger protein 1. 65 G362 gi2058504 0.019 Brassica rapa zinc-finger protein-1. 67 G371 CA799489 2.00E−38 Glycine max sat34e06.y1 Gm-c1056 Glycine max cDNA clone SOY 67 G371 AF265664 2.00E−32 Solanum tuberosum resistance gene cluster, complete sequenc 67 G371 AJ497824 2.00E−31 Medicago truncatula AJ497824 MTFLOW Medicago truncatula cDN 67 G371 AY129244 4.00E−31 Populus x canescens putative RING protein (RING) mRNA, comp 67 G371 BM985575 1.00E−30 Thellungiella halophila 1_F12_T3 Ath Thellungiella halophil 67 G371 BF051105 2.00E−30 Lycopersicon EST436280 tomato esculentum developing/immatur 67 G371 BU834871 2.00E−30 Populus tremula x T066G02 Populus apica Populus tremuloides 67 G371 BM300635 5.00E−25 Mesembryanthemum MCA054H03_21640 Ice crystallinum plant Lam 67 G371 BQ586594 1.00E−24 Beta vulgaris E012388-024-012-I21-SP6 MPIZ-ADIS-024-leaf Be 67 G371 BU880207 1.00E−24 Populus balsamifera UM42TH03 Populus flo subsp. trichocarpa 67 G371 gi22795037 8.80E−24 Populus x canescens putative RING protein. 67 G371 gi15289911 2.20E−21 Oryza sativa hypothetical protein˜similar to Arabidopsis 67 G371 gi22535577 2.20E−21 Oryza sativa (japonica hypothetical prote cultivar-group) 67 G371 gi7688063 0.00026 Pisum sativum constitutively photomorphogenic 1 protein. 67 G371 gi18129286 0.0057 Pinus pinaster putative RING zinc finger protein. 67 G371 gi22775495 0.014 Arabis gemmifera similar to A. thaliana AT4g08590. 67 G371 gi15029364 0.015 Rosa hybrid cultivar photoregulatory zinc-finger protein 67 G371 gi7592844 0.025 Oryza sativa subsp. COP1. japonica 67 G371 gi25044835 0.059 Ananas comosus RING zinc finger protein. 67 G371 gi11127996 0.12 Ipomoea nil COP1. 69 G390 AB084381 1.0e−999 Zinnia elegans ZeHB-11 mRNA for homoeobox leucine-zipper pr 69 G390 AB032182 1.0e−999 Physcomitrella patens PpHB10 mRNA for homeobox protein PpHB 69 G390 AY105765 1.0e−999 Zea mays PCO144112 mRNA sequence. 69 G390 AAAA01006159 1.0e−999 Oryza sativa (indica ( ) scaffold006159 cultivar-group) 69 G390 AP003197 1.00E−177 Oryza sativa chromosome 1 clone B1015E06, *** SEQUENCING IN 69 G390 BQ857624 1.00E−106 Lactuca sativa QGB8A10.yg.ab1 QG_ABCDI lettuce salinas Lact 69 G390 BI925551 1.00E−101 Lycopersicon EST545440 tomato flower, esculentum buds 0-3 m 69 G390 AW686191 1.00E−100 Medicago truncatula NF035A10NR1F1000 Nodulated root Medicag 69 G390 CA032516 1.00E−90 Hordeum vulgare subsp. HX13F16r HX Hordeum vulgare vulgare 69 G390 BQ116871 8.00E−90 Solanum tuberosum EST602447 mixed potato tissues Solanum tu 69 G390 gi24417149 1.00E−299 Zinnia elegans homoeobox leucine-zipper protein. 69 G390 gi13384370 8.40E−280 Oryza sativa putative homeodomain- leucine zipper protein. 69 G390 gi24431605 4.10E−274 Oryza sativa (japonica Putative homeodoma cultivar-group) 69 G390 gi7209912 2.80E−244 Physcomitrella patens homeobox protein PpHB 10. 69 G390 gi3868829 4.50E−32 Ceratopteris richardii CRHB1. 69 G390 gi19070143 5.00E−22 Picea abies homeodomain protein HB2. 69 G390 gi1173622 1.10E−21 Phalaenopsis sp. homeobox protein. SM9108 69 G390 gi2147484 1.10E−21 Phalaenopsis sp. homeotic protein, ovule- specific - Phala 69 G390 gi8920427 2.30E−20 Zea mays OCL5 protein. 69 G390 gi18481701 7.70E−19 Sorghum bicolor OCL5 protein. 71 G391 AB084381 1.0e−999 Zinnia elegans ZeHB-11 mRNA for homoeobox leucine-zipper pr 71 G391 AB032182 1.0e−999 Physcomitrella patens PpHB10 mRNA for homeobox protein PpHB 71 G391 AY105765 1.0e−999 Zea mays PCO144112 mRNA sequence. 71 G391 AAAA01006159 1.00E−146 Oryza sativa (indica ( ) scaffold006159 cultivar-group) 71 G391 BQ857624 1.00E−111 Lactuca sativa QGB8A10.yg.ab1 QG_ABCDI lettuce salinas Lact 71 G391 AP003197 1.00E−106 Oryza sativa chromosome 1 clone B1015E06, *** SEQUENCING IN 71 G391 BI925551 1.00E−102 Lycopersicon EST545440 tomato flower, esculentum buds 0-3 m 71 G391 AW686191 1.00E−102 Medicago truncatula NF035A10NR1F1000 Nodulated root Medicag 71 G391 CA032516 1.00E−92 Hordeum vulgare subsp. HX13F16r HX Hordeum vulgare vulgare 71 G391 BQ116871 6.00E−91 Solanum tuberosum EST602447 mixed potato tissues Solanum tu 71 G391 gi24417149 5.3e−310 Zinnia elegans homoeobox leucine-zipper protein. 71 G391 gi13384370 3.20E−296 Oryza sativa putative homeodomain- leucine zipper protein. 71 G391 gi24431605 7.10E−283 Oryza sativa (japonica Putative homeodoma cultivar-group) 71 G391 gi7209912 4.60E−255 Physcomitrella patens homeobox protein PpHB10. 71 G391 gi3868829 6.30E−33 Ceratopteris richardii CRHB1. 71 G391 gi18481701 9.10E−24 Sorghum bicolor OCL5 protein. 71 G391 gi12002853 3.50E−23 Picea abies homeobox 1. 71 G391 gi1173622 1.20E−22 Phalaenopsis sp. homeobox protein. SM9108 71 G391 gi2147484 1.20E−22 Phalaenopsis sp. homeotic protein, ovule- specific - Phala 71 G391 gi8920427 9.30E−22 Zea mays OCL5 protein. 73 G409 BG044206 2.00E−66 Glycine max saa25c02.y1 Gm-c1059 Glycine max cDNA clone GEN 73 G409 AF443621 3.00E−66 Craterostigma homeodomain leucine plantagineum zipper prote 73 G409 AW220361 6.00E−60 Lycopersicon EST302844 tomato root esculentum during/after 73 G409 AF402606 5.00E−58 Phaseolus vulgaris homeodomain leucine zipper protein HDZ3 73 G409 AY105265 2.00E−56 Zea mays PCO062717 mRNA sequence. 73 G409 BQ165293 2.00E−51 Medicago truncatula EST611162 KVKC Medicago truncatula cDNA 73 G409 BH570275 1.00E−50 Brassica oleracea BOHAF65TF BOHA Brassica oleracea genomic 73 G409 BF620380 1.00E−48 Hordeum vulgare HVSMEc0019K 16f Hordeum vulgare seedling sho 73 G409 BF588126 2.00E−48 Sorghum propinquum FM1_38_A10.b1_A003 Floral-Induced Merist 73 G409 AF145729 5.00E−45 Oryza sativa homeodomain leucine zipper protein (hox5) mRNA 73 G409 gi18034441 4.10E−65 Craterostigma homeodomain leucine plantagineum zipper pro 73 G409 gi15148920 1.10E−57 Phaseolus vulgaris homeodomain leucine zipper protein HDZ 73 G409 gi5006855 7.20E−45 Oryza sativa homeodomain leucine zipper protein. 73 G409 gi1435021 9.00E−38 Daucus carota DNA-binding protein. 73 G409 gi6018089 1.50E−37 Glycine max homeodomain-leucine zipper protein 57. 73 G409 gi1161575 2.20E−36 Lycopersicon homeobox. esculentum 73 G409 gi11231065 1.40E−34 Zinnia elegans homeobox-leucine zipper protein. 73 G409 gi7415614 1.40E−34 Physcomitrella patens homeobox protein PpHB1. 73 G409 gi8133126 4.10E−33 Brassica rapa subsp. hb-6-like protein. pekinensis 73 G409 gi22651698 1.80E−32 Nicotiana tabacum homeodomain protein Hfi22. 75 G427 MDKNOX1 1.00E−143 Malus domestica M. domestica mRNA for knotted1-like homeobox 75 G427 AB004797 1.00E−136 Nicotiana tabacum NTH23 mRNA, complete cds. 75 G427 LEU76409 1.00E−132 Lycopersicon homeobox 1 protein esculentum (THox1) mRNA, pa 75 G427 AB043957 1.00E−118 Ceratopteris richardii mRNA for CRKNOX3, complete cds. 75 G427 AW560103 1.00E−115 Medicago truncatula EST315151 DSIR Medicago truncatula cDNA 75 G427 AB061818 1.00E−112 Oryza sativa HOS59 mRNA for KNOX family class 2 homeodomain 75 G427 BQ873924 1.00E−100 Lactuca sativa QGI2O22.yg.ab1 QG_ABCDI lettuce salinas Lact 75 G427 BNHDIBOX 9.00E−99 Brassica napus B.napus hd1 mRNA for homeodomain-containing 75 G427 AY104273 8.00E−93 Zea mays PCO147946 mRNA sequence. 75 G427 BM063854 1.00E−91 Capsicum annuum KS01060C11 KS01 Capsicum annuum cDNA, mRNA 75 G427 gi1946222 5.10E−131 Malus domestica knotted 1-like homeobox protein. 75 G427 gi3116212 3.40E−125 Nicotiana tabacum homeobox gene. 75 G427 gi4098244 8.10E−124 Lycopersicon homeobox 1 protein. esculentum 75 G427 gi1805618 3.60E−121 Oryza sativa OSH45 transcript. 75 G427 gi11463943 2.50E−113 Ceratopteris richardii CRKNOX3. 75 G427 gi1076449 1.40E−94 Brassica napus homeodomain-containing protein - rape. 75 G427 gi14348597 1.00E−93 Physcomitrella patens class 2 KNOTTED1-like protein MKN1- 75 G427 gi6016216 2.80E−43 Zea mays HOMEOBOX PROTEIN KNOTTED-1 LIKE 2. 75 G427 gi20977642 1.70E−34 Helianthus annuus knotted-1-like protein 1. 75 G427 gi3327269 6.50E−34 Ipomoea nil PKn1. 77 G438 ZEL312053 1.0e−999 Zinnia elegans mRNA for HD-Zip protein (hb1 gene). 77 G438 AB032182 1.0e−999 Physcomitrella patens PpHB10 mRNA for homeobox protein PpHB 77 G438 AY105765 1.0e−999 Zea mays PCO144112 mRNA sequence. 77 G438 AAAA01006159 1.00E−165 Oryza sativa (indica ( ) scaffold006159 cultivar-group) 77 G438 BU002601 1.00E−120 Lactuca sativa QGG31N03.yg.ab1 QG_EFGHJ lettuce serriola La 77 G438 BE035416 1.00E−106 Mesembryanthemum MO05A06 MO crystallinum Mesembryanthemum c 77 G438 BQ578798 1.00E−104 Triticum aestivum WHE0309_H06_O11ZS Wheat unstressed seedli 77 G438 BU927293 1.00E−103 Glycine max sas97g12.y1 Gm-c1036 Glycine max cDNA clone SOY 77 G438 AW696625 1.00E−102 Medicago truncatula NF109B06ST1F1048 Developing stem Medica 77 G438 BU041905 7.00E−89 Prunus persica PP_LEa0010O09f Peach developing fruit mesoca 77 G438 gi18076736 1.0e−999 Zinnia elegans HD-Zip protein. 77 G438 gi13384370 1.0e−999 Oryza sativa putative homeodomain- leucine zipper protein. 77 G438 gi24431605 3.3e−317 Oryza sativa (japonica Putative homeodoma cultivar-group) 77 G438 gi7209912 4.90E−238 Physcomitrella patens homeobox protein PpHB10. 77 G438 gi3868829 3.40E−35 Ceratopteris richardii CRHB1. 77 G438 gi18481701 4.00E−21 Sorghum bicolor OCL5 protein. 77 G438 gi1173622 8.50E−21 Phalaenopsis sp. homeobox protein. SM9108 77 G438 gi2147484 8.50E−21 Phalaenopsis sp. homeotic protein, ovule- specific - Phala 77 G438 gi12002853 1.40E−20 Picea abies homeobox 1. 77 G438 gi8920427 3.20E−20 Zea mays OCL5 protein. 79 G450 BQ155060 2.00E−84 Medicago truncatula NF075G11IR1F1088 Irradiated Medicago tr 79 G450 PTR306829 5.00E−83 Populus tremula x Populus mRNA for aux/IAA pro tremuloides 79 G450 BE053029 1.00E−81 Gossypium arboreum GA_Ea0031O18f Gossypium arboreum 7-10 d 79 G450 BI179192 1.00E−79 Solanum tuberosum EST520137 cSTE Solanum tuberosum cDNA clo 79 G450 BU006959 5.00E−78 Lactuca sativa QGH12O02.yg.ab1 QG_EFGHJ lettuce serriola La 79 G450 AF123508 8.00E−75 Nicotiana tabacum Nt-iaa28 deduced protein mRNA, complete c 79 G450 BQ623078 2.00E−72 Citrus sinensis USDA-FP_00169 Ridge pineapple sweet orange 79 G450 BI470140 7.00E−72 Glycine max sah88c10.y1 Gm-c1050 Glycine max cDNA clone GEN 79 G450 BU892057 7.00E−72 Populus tremula P058G09 Populus petioles cDNA library Popul 79 G450 AA427337 4.00E−71 Pisum sativum P482 Whero seedling lambda ZapII cDNA library 79 G450 gi20385508 4.20E−79 Populus tremula x Populus auxin-regulated pro tremuloides 79 G450 gi4887020 2.90E−73 Nicotiana tabacum Nt-iaa28 deduced protein. 79 G450 gi114734 1.10E−69 Glycine max AUXIN-INDUCED PROTEIN AUX28. 79 G450 gi22725714 2.00E−65 Mirabilis jalapa auxin-responsive protein IAA1; MjAux/IAA 79 G450 gi17976835 2.10E−61 Pinus pinaster putative auxin induced transcription facto 79 G450 gi6136832 4.20E−57 Cucumis sativus CS-IAA2. 79 G450 gi20257219 1.80E−56 Zinnia elegans auxin-regulated protein. 79 G450 gi17154533 2.10E−54 Oryza sativa putative IAA1 protein. 79 G450 gi22531416 5.30E−47 Gossypium hirsutum IAA16 protein. 79 G450 gi21104740 1.00E−43 Oryza sativa (japonica contains EST AU091 cultivar-group) 81 G464 BH998146 2.00E−50 Brassica oleracea oef97f09.g1 B. oleracea002 Brassica olerac 81 G464 BU043737 2.00E−44 Prunus persica PP_LEa0017A10f Peach 81 developing fruit mesoca 81 G464 PTR306828 5.00E−44 Populus tremula x Populus mRNA for aux/IAA pro tremuloides 81 G464 BI207567 6.00E−44 Lycopersicon EST525607 cTOS esculentum Lycopersicon esculen 81 G464 BQ592350 1.00E−35 Beta vulgaris E012681-024-020-J14-SP6 MPIZ-ADIS-024-develop 81 G464 AV933892 4.00E−35 Hordeum vulgare subsp. AV933892 K.Sato vulgare unpublished 81 G464 BQ505545 5.00E−35 Solanum tuberosum EST612960 Generation of a set of potato c 81 G464 BE364015 3.00E−34 Sorghum bicolor PI1_11_G02.b1_A002 Pathogen induced 1 (PI1) 81 G464 BI118786 3.00E−34 Oryza sativa EST174 Differentially expressed cDNA libraries 81 G464 AI725624 9.00E−32 Gossypium hirsutum BNLGHi12459 Six-day Cotton fiber Gossypi 81 G464 gi20269057 1.60E−38 Populus tremula x Populus aux/IAA protein. tremuloides 81 G464 gi17976835 5.40E−32 Pinus pinaster putative auxin induced transcription facto 81 G464 gi5139697 2.00E−30 Cucumis sativus expressed in cucumber hypocotyls. 81 G464 gi22725714 6.30E−30 Mirabilis jalapa auxin-responsive protein IAA1; MjAux/IAA 81 G464 gi17154533 1.30E−29 Oryza sativa putative IAA1 protein. 81 G464 gi20257219 4.40E−29 Zinnia elegans auxin-regulated protein. 81 G464 gi2388689 4.40E−29 Glycine max GH1 protein. 81 G464 gi16610193 1.10E−27 Nicotiana tabacum IAA9 protein. 81 G464 gi1352057 3.60E−27 Pisum sativum AUXIN-UNDUCED PROTEIN IAA4. 81 G464 gi21104740 5.80E−27 Oryza sativa (japonica contains EST AU091 cultivar-group) 83 G470 AB071293 1.0e−999 Oryza sativa OsARF2 mRNA for auxin response factor 2, parti 83 G470 OSA306306 1.0e−999 Oryza sativa (japonica Oryza sativa subsp. cultivar-group) 83 G470 AC126794 1.0e−999 Medicago truncatula clone mth2-24j7, WORKING DRAFT SEQUENCE 83 G470 AY106228 1.00E−131 Zea mays PCO137716 mRNA sequence. 83 G470 BQ578824 1.00E−118 Triticum aestivum WHE0407_B10_D19ZS Wheat etiolated seedlin 83 G470 BG045095 1.00E−108 Glycine max saa36f10.y1 Gm-c1059 Glycine max cDNA clone GEN 83 G470 CA030942 1.00E−102 Hordeum vulgare subsp. HX08J07r HX Hordeum vulgare vulgare 83 G470 BI098203 4.00E−96 Sorghum bicolor IP1_29_D05.b1_A002 Immature pannicle 1 (IP1 83 G470 BG886848 5.00E−96 Solanum tuberosum EST512699 cSTD Solanum tuberosum cDNA clo 83 G470 AI774352 7.00E−95 Lycopersicon EST255368 tomato esculentum resistant, Cornell 83 G470 gi20805236 8.60E−223 Oryza sativa (japonica auxin response fac cultivar-group) 83 G470 gi19352039 6.10E−222 Oryza sativa auxin response factor 2. 83 G470 gi24785191 7.00E−70 Nicotiana tabacum hypothetical protein. 83 G470 gi23343944 5.70E−16 Mirabilis jalapa auxin-responsive factor protein. 83 G470 gi20269053 1.70E−08 Populus tremula x Populus aux/IAA protein. tremuloides 83 G470 gi6136834 4.80E−07 Cucumis sativus CS-IAA3. 83 G470 gi287566 2.50E−06 Vigna radiata ORF. 83 G470 gi16610209 5.20E−06 Physcomitrella patens IAA/AUX protein. 83 G470 gi114733 8.60E−06 Glycine max AUXIN-INDUCED PROTEIN AUX22. 83 G470 gi18697008 4.00E−05 Zea mays unnamed protein product. 85 G477 BH981212 8.00E−48 Brassica oleracea odf77g01.b1 B. oleracea002 Brassica olerac 85 G477 BI925786 5.00E−39 Lycopersicon EST545675 tomato flower, esculentum buds 0-3 m 85 G477 BM408208 7.00E−38 Solanum tuberosum EST582535 potato roots Solanum tuberosum 85 G477 BQ874863 1.00E−30 Lactuca sativa QGI6H22.yg.ab1 QG_ABCDI lettuce salinas Lact 85 G477 AMA011622 4.00E−30 Antirrhinum majus mRNA for squamosa promoter binding 85 G477 BQ594361 4.00E−30 Beta vulgaris S015246-024-024-K10-SP6 MPIZ-ADIS-024-develop 85 G477 CA516258 1.00E−28 Capsicum annuum KS09055D03 KS09 Capsicum annuum cDNA, mRNA 85 G477 BU828403 2.00E−28 Populus tremula x Populus K022P59P Populus apic tremuloides 85 G477 BG442540 2.00E−28 Gossypium arboreum GA_Ea0017G06f Gossypium arboreum 7-10 d 85 G477 AW331087 7.00E−28 Zea mays 707047A12.x1 707 - mixed adult tissues from Walbot 85 G477 gi5931641 9.90E−32 Antirrhinum majus squamosa promoter binding protein-homol 85 G477 gi5931784 1.50E−28 Zea mays SBP-domain protein 4. 85 G477 gi8468036 4.40E−28 Oryza sativa Similar to Arabidopsis thaliana chromosome 2 85 G477 gi9087308 1.20E−14 Mitochondrion Beta orf102a. vulgaris var. altissima 85 G477 gi23630509 0.78 Triticum aestivum zinc finger protein. 85 G477 gi14597634 1 Physcomitrella patens 15_ppprotl_080_c02. 87 G481 BU238020 9.00E−71 Descurainia sophia Ds01_14a12_A Ds01_AAFC_ECORC_cold stress 87 G481 BG440251 2.00E−56 Gossypium arboreum GA_Ea0006K20f Gossypium arboreum 7-10 d 87 G481 BF071234 1.00E−54 Glycine max st06h05.y1 Gm-c1065 Glycine max cDNA clone GENO 87 G481 BQ799965 2.00E−54 Vitis vinifera EST 2134 Green Grape berries Lambda Zap II L 87 G481 BQ488908 5.00E−53 Beta vulgaris 95-E9134-006-006-M23-T3 Sugar beet MPIZ-ADIS- 87 G481 BU499457 1.00E−52 Zea mays 946175D02.y1 946 - tassel primordium prepared by S 87 G481 AI728916 2.00E−52 Gossypium hirsutum BNLGHi12022 Six-day Cotton fiber Gossypi 87 G481 BG642751 3.00E−52 Lycopersicon EST510945 tomato esculentum shoot/meristem Lyc 87 G481 BQ857127 3.00E−51 Lactuca sativa QGB6K24.yg.ab1 QG_ABCDI lettuce salinas Lact 87 G481 BE413647 6.00E−51 Triticum aestivum SCU001.E10.R990714 ITEC SCU Wheat Endospe 87 G481 gi115840 1.90E−51 Zea mays CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT A (CB 87 G481 gi20160792 2.60E−47 Oryza sativa (japonica putative CAAT-box cultivar-group) 87 G481 gi15408794 7.10E−38 Oryza sativa putative CCAAT-binding transcription factor 87 G481 gi22536010 3.20E−35 Phaseolus coccineus LEC1-like protein. 87 G481 gi16902054 1.80E−32 Vernonia galamensis CCAAT-box binding factor HAP3 B domai 87 G481 gi16902050 6.10E−32 Glycine max CCAAT-box binding factor HAP3 B domain. 87 G481 gi16902056 1.60E−31 Argemone mexicana CCAAT-box binding factor HAP3 B domain. 87 G481 gi16902058 2.20E−27 Triticum aestivum CCAAT-box binding factor HAP3 B domain. 87 G481 gi388257 0.26 Lycopersicon glycine-rich protein. esculentum 87 G481 gi18266049 0.92 Brassica oleracea myrosinase precursor. 89 G482 BQ505706 7.00E−59 Solanum tuberosum EST613121 Generation of a set of potato c 89 G482 AC122165 6.00E−57 Medicago truncatula clone mth2-32m22, WORKING DRAFT SEQUENC 89 G482 BQ104671 2.00E−55 Rosa hybrid cultivar fc0546.e Rose Petals (Fragrant Cloud) 89 G482 BI469382 4.00E−55 Glycine max sail 1b10.y1 Gm-c1053 Glycine max cDNA clone GEN 89 G482 AAAA01003638 1.00E−54 Oryza sativa (indica ( ) scaffold003638 cultivar-group) 89 G482 AP005193 1.00E−54 Oryza sativa (japonica ( ) chromosome 7 clo cultivar-group) 89 G482 BU880488 1.00E−53 Populus balsamifera UM49TG09 Populus flo subsp. trichocarpa 89 G482 BJ248969 2.00E−53 Triticum aestivum BJ248969 Y. Ogihara unpublished cDNA libr 89 G482 AC120529 4.00E−53 Oryza sativa chromosome 3 clone OSJNBa0039N21, *** SEQUENCI 89 G482 BU896236 7.00E−53 Populus tremula x Populus X037F04 Populus wood tremuloides 89 G482 gi115840 1.40E−46 Zea mays CCAAT-BINDING TRANSCRIPTION FACTOR SUBUNIT A (CB 89 G482 gi20160792 2.30E−41 Oryza sativa (japonica putative CAAT-box cultivar-group) 89 G482 gi22536010 9.00E−38 Phaseolus coccineus LEC1-like protein. 89 G482 gi15408794 1.50E−37 Oryza sativa putative CCAAT-binding transcription factor 89 G482 gi16902054 7.50E−34 Vernonia galamensis CCAAT-box binding factor HAP3 B domai 89 G482 gi16902050 5.30E−33 Glycine max CCAAT-box binding factor HAP3 B domain. 89 G482 gi16902056 4.80E−32 Argemone mexicana CCAAT-box binding factor HAP3 B domain. 89 G482 gi16902058 1.10E−30 Triticum aestivum CCAAT-box binding factor HAP3 B domain. 89 G482 gi100582 0.0018 Hordeum vulgare glycine-rich protein precursor - barley. 89 G482 gi7024451 0.0025 Citrus unshiu glycine-rich RNA-binding protein. 91 G484 BQ412047 3.00E−68 Gossypium arboreum GA_Ed0053D06r Gossypium arboreum 7-10 d 91 G484 AF464906 5.00E−67 Glycine max repressor protein (Dr1) mRNA, complete cds. 91 G484 AW719575 2.00E−64 Lotus japonicus LjNEST6a11r Lotus japonicus nodule library, 91 G484 BG648823 4.00E−64 Medicago truncatula EST510442 HOGA Medicago truncatula cDNA 91 G484 BQ593791 4.00E−64 Beta vulgaris E012763-024-026-O09-SP6 MPIZ-ADIS-024-develop 91 G484 BM436739 9.00E−64 Vitis vinifera VVA009B06_53061 An expressed sequence tag da 91 G484 BF113032 1.00E−63 Lycopersicon EST440542 tomato breaker esculentum fruit Lyco 91 G484 BG593107 7.00E−63 Solanum tuberosum EST491785 cSTS Solanum tuberosum cDNA clo 91 G484 BU014508 1.00E−61 Lactuca sativa QGJ7I14.yg.ab1 QG_EFGHJ lettuce serriola Lac 91 G484 AF464902 5.00E−59 Oryza sativa repressor protein (Dr1) mRNA, complete cds. 91 G484 gi18481628 6.70E−65 Glycine max repressor protein. 91 G484 gi18481620 4.80E−60 Oryza sativa repressor protein. 91 G484 gi18481622 2.00E−58 Triticum aestivum repressor protein. 91 G484 gi20160792 2.90E−16 Oryza sativa (japonica putative CAAT-box cultivar-group) 91 G484 gi15321716 1.30E−15 Zea mays leafy cotyledon1. 91 G484 gi22536010 1.10E−14 Phaseolus coccineus LEC1-like protein. 91 G484 gi16902054 1.50E−14 Vernonia galamensis CCAAT-box binding factor HAP3 B domai 91 G484 gi16902056 2.70E−13 Argemone mexicana CCAAT-box binding factor HAP3 B domain. 91 G484 gi18129292 1 Pinus pinaster histone H2B protein. 91 G484 gi1083950 1 Canavalia lineata subtilisin inhibitor CLSI-I - Canavalia 93 G489 BH679015 1.00E−111 Brassica oleracea BOHXO96TF BO_2_3_KB Brassica oleracea gen 93 G489 AC136503 1.00E−75 Medicago truncatula clone mth2-15n1, WORKING DRAFT SEQUENCE 93 G489 BQ118033 8.00E−73 Solanum tuberosum EST603609 mixed potato tissues Solanum tu 93 G489 BU873518 4.00E−68 Populus balsamifera Q056D09 Populus flow subsp. trichocarpa 93 G489 BI934205 2.00E−67 Lycopersicon EST554094 tomato flower, esculentum anthesis L 93 G489 BQ797616 1.00E−66 Vitis vinifera EST 6554 Ripening Grape berries Lambda Zap I 93 G489 BM064398 4.00E−63 Capsicum annuum KS01066E11 KS01 Capsicum annuum cDNA, mRNA 93 G489 BU927107 4.00E−60 Glycine max sas95f12.y1 Gm-c1036 Glycine max cDNA clone SOY 93 G489 BQ993879 6.00E−59 Lactuca sativa QGF5L12.yg.ab1 QG_EFGHJ lettuce serriola Lac 93 G489 AP004113 1.00E−58 Oryza sativa chromosome 2 clone OJ1116_A06, *** SEQUENCING 93 G489 gi5257260 6.20E−46 Oryza sativa Similar to sequence of BAC F7G19 from Arabid 93 G489 gi20804442 6.60E−19 Oryza sativa (japonica hypothetical prote cultivar-group) 93 G489 gi18481626 3.90E−09 Zea mays repressor protein. 93 G489 gi1808688 0.051 Sporobolus stapfianus hypothetical protein. 93 G489 gi8096192 0.21 Lilium longiflorum gH2A.1. 93 G489 gi2130105 0.25 Triticum aestivum histone H2A.4 - wheat. 93 G489 gi297871 0.27 Picea abies histone H2A. 93 G489 gi297887 0.31 Daucus carota glycine rich protein. 93 G489 gi15214035 0.75 Cicer arietinum HISTONE H2A. 93 G489 gi2317760 0.75 Pinus taeda H2A homolog. 95 G490 AX180963 1.00E−19 Physcomitrella patens Sequence 14 from Patent WO0145493. 95 G490 AP004836 1.00E−19 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 95 G490 AU197697 1.00E−19 Oryza sativa AU197697 Rice mature leaf Oryza sativa cDNA cl 95 G490 BJ193952 1.00E−19 Physcomitrella patens BJ193952 normalized ful subsp. patens 95 G490 AAAA01011976 1.00E−19 Oryza sativa (indica ( ) scaffold011976 cultivar-group) 95 G490 BM065544 2.00E−19 Capsicum annuum KS07004F12 KS07 Capsicum annuum cDNA, mRNA 95 G490 AL749991 2.00E−19 Pinus pinaster AL749991 AS Pinus pinaster cDNA clone AS03E0 95 G490 BG440805 3.00E−19 Gossypium arboreum GA_Ea0010D12f Gossypium arboreum 7-10 d 95 G490 BE460012 4.00E−19 Lycopersicon EST415304 tomato esculentum developing/immatur 95 G490 BJ269516 4.00E−19 Triticum aestivum BJ269516 Y. Ogihara unpublished cDNA libr 95 G490 gi5257260 7.50E−18 Oryza sativa Similar to sequence of BAC F7G19 from Arabid 95 G490 gi22138475 4.00E−13 Oryza sativa (japonica putative transcrip cultivar-group) 95 G490 gi18481626 7.00E−06 Zea mays repressor protein. 95 G490 gi16902058 0.99 Triticum aestivum CCAAT-box binding factor HAP3 B domain. 95 G490 gi16902056 1 Argemone mexicana CCAAT-box binding factor HAP3 B domain. 95 G490 gi16902050 1 Glycine max CCAAT-box binding factor HAP3 B domain. 95 G490 gi16902054 1 Vernonia galamensis CCAAT-box binding factor HAP3 B domai 97 G504 BU895066 1.00E−82 Populus tremula x X018H04 Populus wood Populus tremuloides 97 G504 BI422750 2.00E−80 Lycopersicon EST533416 tomato callus, esculentum TAMU Lycop 97 G504 AW560823 5.00E−71 Medicago truncatula EST315871 DSIR Medicago truncatula cDNA 97 G504 CA815703 1.00E−68 Vitis vinifera CA12EI204IVF_E10 Cabernet Sauvignon Leaf - C 97 G504 BQ121923 2.00E−67 Solanum tuberosum EST607499 mixed potato tissues Solanum tu 97 G504 BM092513 2.00E−66 Glycine max sah14g06.y3 Gm-c1086 Glycine max cDNA clone GEN 97 G504 BI246023 4.00E−66 Sorghum bicolor IP1_66_F11.b1_A002 Immature pannicle 1 (IP1 97 G504 BU041353 1.00E−63 Prunus persica PP_LEa0009B03f Peach developing fruit mesoca 97 G504 BU672229 2.00E−63 Triticum aestivum WHE3302_A10_A20ZS Chinese Spring wheat dr 97 G504 AF402603 4.00E−62 Phaseolus vulgaris NAC domain protein NAC2 mRNA, complete c 97 G504 gi24417196 4.20E−72 Oryza sativa (japonica contains ESTs C993 cultivar-group) 97 G504 gi15148914 2.70E−61 Phaseolus vulgaris NAC domain protein NAC2. 97 G504 gi15528779 3.50E−59 Oryza sativa development regulation gene OsNAC4. 97 G504 gi6175246 2.50E−58 Lycopersicon jasmonic acid 2. esculentum 97 G504 gi21105748 4.10E−58 Petunia x hybrida nam-like protein 10. 97 G504 gi14485513 1.60E−56 Solanum tuberosum putative NAC domain protein. 97 G504 gi4218535 2.10E−54 Triticum sp. GRAB1 protein. 97 G504 gi6732158 2.10E−54 Triticum monococcum unnamed protein product. 97 G504 gi22597158 2.90E−50 Glycine max no apical meristem-like protein. 97 G504 gi7716952 2.20E−34 Medicago truncatula NAC1. 99 G509 BG646875 2.00E−68 Medicago truncatula EST508494 HOGA Medicago truncatula cDNA 99 G509 BQ850404 2.00E−65 Lactuca sativa QGB12I10.yg.ab1 QG_ABCDI lettuce salinas Lac 99 G509 BE363054 3.00E−59 Sorghum bicolor DG1_9_D04.b1_A002 Dark Grown 1 (DG1) Sorghu 99 G509 BE434322 1.00E−56 Lycopersicon EST405400 tomato breaker esculentum fruit, TIG 99 G509 BM112823 8.00E−50 Solanum tuberosum EST560359 potato roots Solanum tuberosum 99 G509 AF402602 3.00E−49 Phaseolus vulgaris NAC domain protein NAC1 mRNA, complete c 99 G509 PHRNANAM 2.00E−48 Petunia x hybrida P.hybrida mRNA encoding NAM protein. 99 G509 BZ034968 4.00E−48 Brassica oleracea oem78a04.b1 B. oleracea002 Brassica olerac 99 G509 AV923588 3.00E−46 Hordeum vulgare subsp. AV923588 K. Sato vulgare unpublished 99 G509 BE586058 4.00E−46 Triticum aestivum Est#8pT7_C09_c9_066 KSU wheat Fusarium gr 99 G509 gi13129497 6.00E−57 Oryza sativa putative NAM (no apical meristem) protein. 99 G509 gi15148912 4.80E−50 Phaseolus vulgaris NAC domain protein NAC1. 99 G509 gi24476048 3.30E−47 Oryza sativa (japonica Putative NAM (no a cultivar-group) 99 G509 gi1279640 5.40E−47 Petunia x hybrida NAM. 99 G509 gi4218537 8.50E−42 Triticum sp. GRAB2 protein. 99 G509 gi6732156 8.50E−42 Triticum monococcum unnamed protein product. 99 G509 gi22597158 1.40E−41 Glycine max no apical meristem-like protein. 99 G509 gi14485513 1.90E−37 Solanum tuberosum putative NAC domain protein. 99 G509 gi6175246 8.40E−35 Lycoperiscon jasmonic acid 2. esculentum 99 G509 gi7716952 4.30E−32 Medicago truncatula NAC1. 101 G519 BG543276 9.00E−93 Brassica rapa subsp. E0770 Chinese cabbage pekinensis etiol 101 G519 BQ165234 2.00E−88 Medicago truncatula EST611103 KVKC Medicago truncatula cDNA 101 G519 AF509866 4.00E−85 Petunia x hybrida nam-like protein 3 (NH3) mRNA, complete c 101 G519 STU401151 9.00E−85 Solanum tuberosum mRNA for putative NAC domain protein (na 101 G519 BH476033 1.00E−80 Brassica oleracea BOHNV27TF BOHN Brassica oleracea genomic 101 G519 CA820578 2.00E−80 Glycine max sau91c12.y1 Gm-c1048 Glycine max cDNA clone SOY 101 G519 BM411425 1.00E−79 Lycopersicon EST585752 tomato breaker esculentum fruit Lyco 101 G519 BQ970677 1.00E−78 Helianthus annuus QHB42M12.yg.ab1 QH_ABCDI sunflower RHA801 101 G519 AB028185 2.00E−78 Oryza sativa mRNA for OsNAC6 protein, complete cds. 101 G519 BG441329 6.00E−78 Gossypium arboreum GA_Ea0012N05f Gossypium arboreum 7-10 d 101 G519 gi14485513 2.20E−86 Solanum tuberosum putative NAC domain protein. 101 G519 gi21105734 2.80E−86 Petunia x hybrida nam-like protein 3. 101 G519 gi13272281 1.40E−80 Oryza sativa NAC6. 101 G519 gi20161457 1.40E−80 Oryza sativa (japonica OsNAC6 protein. cultivar-group) 101 G519 gi4218535 1.40E−62 Triticum sp. GRAB1 protein. 101 G519 gi6732158 1.40E−62 Triticum monococcum unnamed protein product. 101 G519 gi6175246 1.30E−54 Lycopersicon jasmonic acid 2. esculentum 101 G519 gi15148914 4.30E−54 Phaseolus vulgaris NAC domain protein NAC2. 101 G519 gi22597158 1.70E−43 Glycine max no apical meristem-like protein. 101 G519 gi7716952 1.50E−35 Medicago truncatula NAC1. 103 G545 BH552655 9.00E−96 Brassica oleracea BOGEH82TF BOGE Brassica oleracea genomic 103 G545 BQ704580 7.00E−74 Brassica napus Bn01 02p11 A 103 G545 AF119050 5.00E−59 Datisca glomerata zinc-finger protein 1 (zfp1) mRNA, comple 103 G545 AP004523 9.00E−58 Lotus japonicus genomic DNA, chromosome 1, clone: LjT03J05, 103 G545 PETZFP4 2.00E−56 Petunia x hybrida Petunia zinc-finger protein gene. 103 G545 CA801331 4.00E−55 Glycine max sau04c04.y2 Gm-c 1062 Glycine max cDNA clone SOY 103 G545 MSY18788 1 .00E−53 Medicago sativa mRNA for putative TFIIIA (or kruppel)-like 103 G545 BG582865 2.00E−53 Medicago truncatula EST484611 GVN Medicago truncatula cDNA 103 G545 BM437679 8.00E−51 Vitis vinifera VVA023E03_54853 An expressed sequence tag da 103 G545 AF053077 8.00E−49 Nicotiana tabacum osmotic stress-induced zinc- finger protei 103 G545 gi4666360 6.00E−57 Datisca glomerata zinc-finger protein 1. 103 G545 gi7228329 2.70E−54 Medicago sativa putative TFIIIA (or kruppel)-like zinc fi 103 G545 gi1763063 9.00E−54 Glycine max SCOF-1. 103 G545 gi439487 4.70E−44 Petunia x hybrida zinc-finger DNA binding protein. 103 G545 gi2058504 1.50E−35 Brassica rapa zinc-finger protein-1. 103 G545 gi2981169 4.30E−31 Nicotiana tabacum osmotic stress-induced zinc- finger prot 103 G545 gi485814 6.50E−28 Triticum aestivum WZF1. 103 G545 gi12698882 2.90E−25 Oryza sativa zinc finger transcription factor ZF1. 103 G545 gi21104613 1.90E−14 Oryza sativa (japonica contains ESTs AU07 cultivar-group) 103 G545 gi2129892 4.70E−06 Pisum sativum probable finger protein Pszf1 - garden pea. 105 G546 BG544345 3.00E−61 Brassica rapa subsp. E2200 Chinese cabbage pekinensis etiol 105 G546 BH424854 6.00E−49 Brassica oleracea BOGML16TF BOGM Brassica oleracea genomic 105 G546 AW223952 2.00E−45 Lycopersicon EST300763 tomato fruit red esculentum ripe, TA 105 G546 BG889076 4.00E−45 Solanum tuberosum EST514927 cSTD Solanum tuberosum cDNA clo 105 G546 AC127019 3.00E−44 Medicago truncatula clone mth2-31b1, WORKTNG DRAFT SEQUENCE 105 G546 BF597949 9.00E−42 Glycine max su89e06.y1 Gm-c1055 Glycine max cDNA clone GENO 105 G546 BE033932 2.00E−40 Mesembryanthemum MG02C06 MG crystallinum Mesembryanthemum c 105 G546 OSJN00157 3.00E−37 Oryza sativa chromosome 4 clone OSJNBa0013K16, *** SEQUENC 105 G546 BI418846 3.00E−37 Lotus japonicus LjNEST36e5r Lotus japonicus nodule library 105 G546 AAAA01035793 3.00E−37 Oryza sativa (indica ( ) scaffold035793 cultivar-group) 105 G546 gi2894379 3.10E−37 Hordeum vulgare ring finger protein. 105 G546 gi12039329 9.00E−34 Oryza sativa putative ring finger protein. 105 G546 gi19571069 1.80E−25 Oryza sativa (japonica contains EST C7268 cultivar-group) 105 G546 gi17016985 3.00E−23 Cucumis melo RING-H2 zinc finger protein. 105 G546 gi21645888 5.90E−18 Zea mays ring-H2 zinc finger protein. 105 G546 gi23451086 2.10E−14 Medicago sativa RING-H2 protein. 105 G546 gi12003386 6.30E−14 Nicotiana tabacum Avr9/Cf-9 rapidly elicited protein 132. 105 G546 gi20152976 4.00E−12 Hordeum vulgare subsp. similar to A. thaliana C3H vulgare 105 G546 gi22597166 8.70E−12 Glycine max RING-H2 finger protein. 105 G546 gi1086225 3.50E−09 Lotus japonicus RING-finger protein - Lotus japonicus. 107 G561 SAY16953 1.00E−146 Sinapis alba mRNA for G-box binding factor 2A. 107 G561 BNGBBF2A 1.00E−141 Brassica napus B. napus mRNA for G-Box binding factor 2A. 107 G561 RSGBOX 1.00E−141 Raphanus sativus R. sativus mRNA for G-box binding protein. 107 G561 PVU41817 8.00E−78 Phaseolus vulgaris regulator of MAT2 (ROM2) mRNA, complete 107 G561 AF084971 7.00E−77 Catharanthus roseus G-box binding protein 1 (GBF1) mRNA, co 107 G561 SOAJ3624 2.00E−75 Spinacia oleracea mRNA for basic leucine zipper protein. 107 G561 SOYGBFB 1.00E−72 Glycine max G-box binding factor (GBF2A) mRNA, 3′ end. 107 G561 NTTAF2MR 2.00E−70 Nicotiana tabacum N. tabacum mRNA for TAF-2. 107 G561 PCCPRF1 5.00E−66 Petroselinum crispum P. crispum CPRF1 mRNA for light-inducib 107 G561 ZMU10270 6.00E−49 Zea mays G-box binding factor 1 (GBF1) mRNA, complete cds. 107 G561 gi2995462 1.00E−139 Sinapis alba G-box binding protein. 107 G561 gi1076448 2.30E−135 Brassica napus G-box binding factor 2A - rape. 107 G561 gi1033059 4.80E−135 Raphanus sativus G-Box binding protein. 107 G561 gi1155054 2.30E−58 Phaseolus vulgaris regulator of MAT2. 107 G561 gi5381311 3.50E−52 Catharanthus roseus G-box binding protein 1. 107 G561 gi2815305 4.00E−51 Spinacia oleracea basic leucine zipper protein. 107 G561 gi169959 1.20E−49 Glycine max G-box binding factor. 107 G561 gi1076623 8.00E−46 Nicotiana tabacum G-box-binding protein TAF- 2 - common to 107 G561 gi498643 1.30E−45 Zea mays G-box binding factor 1. 107 G561 gi100162 5.20E−42 Petroselinum crispum light-induced protein CPRF- 1 - parsl 109 G562 BNU27108 1.00E−160 Brassica napus transcription factor (BnGBF1) mRNA, partial 109 G562 AF084971 1.00E−102 Catharanthus roseus G-box binding protein 1 (GBF1) mRNA, co 109 G562 PVU41817 1.00E−96 Phaseolus vulgaris regulator of MAT2 (ROM2) mRNA, complete 109 G562 SOYGBFB 2.00E−94 Glycine max G-Box binding factor (GBF2A) mRNA, 3′ end. 109 G562 SOAJ3624 9.00E−94 Spinacia oleracea mRNA for basic leucine zipper protein. 109 G562 NTTAF2MR 4.00E−89 Nicotiana tabacum N. tabacum mRNA for TAF-2. 109 G562 PCCPRF1 1.00E−84 Petroselinum crispum P. crispum CPRF1 mRNA for light-inducib 109 G562 SAY16953 2.00E−81 Sinapis alba mRNA for G-box binding factor 2A. 109 G562 RSGBOX 6.00E−79 Raphanus sativus R. sativus mRNA for G-box binding protein. 109 G562 BF271790 6.00E−58 Gossypium arboreum GA_Eb0012L24f Gossypium arboreum 7-10 d 109 G562 gi1399005 2.00E−159 Brassica napus transcription factor. 109 G562 gi2995462 6.70E−81 Sinapis alba G-box binding protein. 109 G562 gi1033059 1.80E−78 Raphanus sativus G-Box binding protein. 109 G562 gi5381311 1.20E−60 Catharanthus roseus G-box binding protein 1. 109 G562 gi2815305 1.20E−60 Spinacia oleracea basic leucine zipper protein. 109 G562 gi1169081 2.20E−59 Petroselinum crispum COMMON PLANT REGULATORY FACTOR CPRF- 109 G562 gi169959 5.40E−56 Glycine max G-box binding factor. 109 G562 gi1155054 1.80E−55 Phaseolus vulgaris regulator of MAT2. 109 G562 gi498643 2.10E−52 Zea mays G-box binding factor 1. 109 G562 gi1076624 1.30E−47 Nicotiana tabacum G-box-binding protein TAF- 3 - common to 111 G567 PCCPRF2 1.00E−55 Petroselinum crispum P. crispum CPRF2 mRNA for DNA-binding p 111 G567 AY061648 8.00E−53 Nicotiana tabacum bZIP transcription factor (BZI-1) mRNA, c 111 G567 BH590739 2.00E−48 Brassica oleracea BOHCB55TR BOHC Brassica oleracea genomic 111 G567 GMGHBF1 2.00E−47 Glycine max G. max mRNA for G/HBF-1. 111 G567 RICBZIPPA 2.00E−44 Oryza sativa mRNA for bZIP protein, complete cds. 111 G567 MZEBZIP 2.00E−43 Zea mays opaque2 heterodimerizing protein 2 mRNA, complete 111 G567 BU041142 3.00E−43 Prunus persica PP_LEa0008G18f Peach developing fruit mesoca 111 G567 BG645542 4.00E−42 Medicago truncatula EST507161 KV3 Medicago truncatula cDNA 111 G567 AJ487392 4.00E−41 Solanum tuberosum AJ487392 Solanum tuberosum cv. Provita So 111 G567 AW647973 9.00E−41 Lycopersicon EST326427 tomato esculentum germinating seedli 111 G567 gi1806261 1.60E−49 Petroselinum crispum DNA-binding protein; bZIP type. 111 G567 gi1783305 1.80E−46 Oryza sativa bZIP protein. 111 G567 gi16797791 8.20E−44 Nicotiana tabacum bZIP transcription factor. 111 G567 gi168428 8.20E−44 Zea mays opaque2 heterodimerizing protein 2. 111 G567 gi1905785 2.20E−43 Glycine max G/HBF-1. 111 G567 gi1869928 9.70E−41 Hordeum vulgare blz-1 protein. 111 G567 gi463212 4.40E−34 Coix lacryma-jobi opaque 2. 111 G567 gi1362178 1.00E−32 Sorghum bicolor opaque-2 protein - sorghum. 111 G567 gi21435101 2.90E−32 Pennisetum glaucum opaque-2-like protein. 111 G567 gi1654099 2.30E−24 Triticum aestivum transcriptional activator. 113 G568 BH994972 1.00E−64 Brassica oleracea oeh20b03.b1 B. oleracea002 Brassica olerac 113 G568 AF288616 2.00E−42 Populus balsamifera subsp. trichocarpa x Populus deltoides 113 G568 BU834855 1.00E−25 Populus tremula x T066E09 Populus apica Populus tremuloides 113 G568 BU819252 5.00E−23 Populus tremula UA41BPE07 Populus tremula cambium cDNA libr 113 G568 AC123571 7.00E−17 Medicago truncatula clone mth 1-14n3, WORKING DRAFT SEQUENCE 113 G568 AV914686 8.00E−14 Hordeum vulgare subsp. AV914686 K. Sato vulgare unpublished 113 G568 AF001454 8.00E−14 Helianthus annuus Dc3 promoter-binding factor-2 (DPBF-2) mR 113 G568 BE657320 1.00E−13 Glycine max GM700001A20B6 Gm- r1070 Glycine max cDNA clone G 113 G568 CA765468 2.00E−13 Oryza sativa (indica AF53-Rpf_07_J23_T7_086 cultivar-group) 113 G568 AL819191 2.00E−13 Triticum aestivum AL819191 n: 129 Triticum aestivum cDNA clo 113 G568 gi13435335 4.20E−47 Populus x generosa basic leucine zipper transcription fac 113 G568 gi22324425 6.30E−23 Oryza saliva (japonica bZIP transcription cultivar-group) 113 G568 gi2228773 3.30E−17 Helianthus annuus Dc3 promoter-binding factor-2. 113 G568 gi21693583 8.70E−15 Triticum aestivum ABA response element binding factor. 113 G568 gi5821255 4.90E−13 Oryza sativa TRAB1. 113 G568 gi13775111 4.20E−12 Phaseolus vulgaris bZIP transcription factor 6. 113 G568 gi7406677 3.30E−11 Vitis vinifera putative ripening-related bZIP protein. 113 G568 gi14571808 2.90E−10 Nicotiana tabacum phi-2. 113 G568 gi6018699 3.10E−10 Lycopersicon THY5 protein. esculentum 113 G568 gi1352613 3.20E−10 Zea mays OCS-ELEMENT BINDING FACTOR 1 (OCSBF-1). 115 G584 PVU18348 1.00E−166 Phaseolus vulgaris phaseolin G-box binding protein PG1 (PG1 115 G584 BH696428 5.00E−94 Brassica oleracea BOMCR67TF BO_2_3_KB Brassica oleracea gen 115 G584 AF011557 7.00E−80 Lycopersicon jasmonic acid 3 (LEJA3) esculentum mRNA, parti 115 G584 BI434651 9.00E−75 Solanum tuberosum EST537412 P. infestans- challenged leaf So 115 G584 AF061107 2.00E−70 Zea mays transcription factor MYC7E mRNA, partial cds. 115 G584 BG453241 3.00E−70 Medicago truncatula NF090G06LF1F1049 Developing leaf Medica 115 G584 AAAA01004195 2.00E−68 Oryza sativa (indica ( ) scaffold004195 cultivar-group) 115 G584 AC060755 6.00E−68 Oryza sativa chromosome 10 clone OSJNBa0003O19, *** SEQUENC 115 G584 BG446831 7.00E−67 Gossypium arboreum GA_Eb0039H18f Gossypium arboreum 7-10 d 115 G584 BI968400 2.00E−62 Glycine max GM830005A12E12 Gm- r1083 Glycine max cDNA clone 115 G584 gi1142619 3.90E−155 Phaseolus vulgaris phaseolin G-box binding protein PG1. 115 G584 gi12643064 1.00E−131 Oryza sativa putative MYC transcription factor. 115 G584 gi4321762 4.30E−130 Zea mays transcription factor MYC7E. 115 G584 gi6175252 2.30E−62 Lycopersicon jasmonic acid 3. esculentum 115 G584 gi19571087 2.70E−47 Oryza sativa (japonica contains EST AU031 cultivar-group) 115 G584 gi10998404 1.40E−37 Petunia x hybrida anthocyanin 1. 115 G584 gi4519201 9.30E−30 Perilla frutescens MYC-GP. 115 G584 gi166428 8.00E−28 Antirrhinum majus DEL. 115 G584 gi13346182 3.00E−27 Gossypium hirsutum GHDEL65. 115 G584 gi3650292 5.10E−18 Gerbera hybrida GMYC1 protein. 117 G585 AF336280 1.00E−165 Gossypium hirsutum GHDEL65 (ghdel65) mRNA, complete cds. 117 G585 AMADEL 1.00E−147 Antirrhinum majus DEL (delila) mRNA, complete cds. 117 G585 AB024050 1.00E−142 Perilla frutescens mRNA for MYC-RP, complete cds. 117 G585 AF020545 1.00E−135 Petunia x hybrida bHLH transcription factor JAF13 (jaf13) m 117 G585 GHY7709 1.00E−107 Gerbera hybrida mRNA for bHLH transcription factor. 117 G585 AX540498 1.00E−104 Lotus uliginosus Sequence 2 from Patent WO0210412. 117 G585 ZMA251719 9.00E−81 Zea mays mRNA for transcription factor (hopi gene). 117 G585 AF503363 3.00E−67 Lotus japonicus myc-like regulatory protein (TAN1) mRNA, pa 117 G585 BI308638 7.00E−67 Medicago truncatula EST530048 GPOD Medicago truncatula cDNA 117 G585 BU875274 1.00E−57 Populus balsamifera V004CE04 Populus flo subsp. trichocarpa 117 G585 gi13346182 6.30E−156 Gossypium hirsutum GHDEL65. 117 G585 gi166428 5.70E−139 Antirrhinum majus DEL. 117 G585 gi4519199 2.60E−127 Perilla frutescens MYC-RP. 117 G585 gi3127045 5.40E−127 Petunia x hybrida bHLH transcription factor JAF13. 117 G585 gi3650292 1.30E−93 Gerbera hybrida GMYC1 protein. 117 G585 gi8052457 2.00E−87 Zea mays transcription factor. 117 G585 gi1086540 2.20E−86 Oryza sativa Ra. 117 G585 gi20467247 2.40E−83 Lotus uliginosus myc-like regulatory protein. 117 G585 gi20467249 5.90E−66 Lotus japonicus myc-like regulatory protein. 117 G585 gi21429235 1.70E−50 Onobrychis viciifolia basic helix-loop-helix regulatory p 119 G590 AW782148 1.00E−49 Glycine max sm02b05.y1 Gm-c1027 Glycine max cDNA clone GENO 119 G590 AW649972 5.00E−45 Lycopersicon EST328426 tomato esculentum germinating seedli 119 G590 BZ045178 2.00E−37 Brassica oleracea 1kf53d05.g1 B. oleracea002 Brassica olerac 119 G590 BM408345 3.00E−31 Solanum tuberosum EST582672 potato roots Solanum tuberosum 119 G590 BM065639 4.00E−31 Capsicum annuum KS07005G09 KS07 Capsicum annuum cDNA, mRNA 119 G590 BI308330 1.00E−30 Medicago truncatula EST529740 GPOD Medicago truncatula cDNA 119 G590 BQ134415 5.00E−28 Zea mays 1091016H12.y2 1091 - Immature ear with common ESTs 119 G590 BU866069 1.00E−25 Populus tremula x S062C11 Populus imbib Populus tremuloides 119 G590 AU290290 1.00E−24 Zinnia elegans AU290290 zinnia cultured mesophyll cell equa 119 G590 BU574318 1.00E−24 Prunus dulcis PA_Ea0007A10f Almond developing seed Prunus 119 G590 gi15451582 7.80E−32 Oryza sativa Putative SPATULA. 119 G590 gi23495742 8.20E−28 Oryza sativa (japonica putative phytochro cultivar-group) 119 G590 gi5923912 5.40E−10 Tulipa gesneriana bHLH transcription factor GBOF-1. 119 G590 gi527657 1.40E−09 Pennisetum glaucum myc-like regulatory R gene product. 119 G590 gi6166283 2.30E−09 Pinus taeda helix-loop-helix protein 1A. 119 G590 gi527665 4.80E−09 Sorghum bicolor myc-like regulatory R gene product. 119 G590 gi527661 1.00E−08 Phyllostachys acuta myc-like regulatory R gene product. 119 G590 gi1086534 1.70E−08 Oryza officinalis transcriptional activator Ra homolog. 119 G590 gi1086526 2.80E−08 Oryza australiensis transcriptional activator Ra homolog. 119 G590 gi1086538 4.60E−08 Oryza rufipogon transcriptional activator Rb homolog. 121 G594 BE807866 4.00E−38 Glycine max ss31c06.y1 Gm-c1061 Glycine max cDNA clone GENO 121 G594 BQ875608 5.00E−38 Lactuca sativa QGI8J14.yg.ab1 QG_ABCDI lettuce salinas Lact 121 G594 BU791131 1.00E−36 Populus balsamifera subsp. trichocarpa x Populus deltoides 121 G594 CA015610 9.00E−35 Hordeum vulgare subsp. HT14N12r HT Hordeum vulgare vulgare 121 G594 BF200249 2.00E−34 Triticum monococcum WHE2254_F11_L22ZE Triticum monococcum s 121 G594 BM497415 6.00E−34 Avicennia marina 901269 Avicennia marina leaf cDNA Library 121 G594 AW906522 4.00E−33 Solanum tuberosum EST342644 potato stolon, Cornell Universi 121 G594 AI731417 5.00E−33 Gossypium hirsutum BNLGHi9478 Six-day Cotton fiber Gossypiu 121 G594 BE455695 5.00E−33 Hordeum vulgare HVSMEg0019A10f Hordeum vulgare pre- anthesis 121 G594 BE360329 5.00E−33 Sorghum bicolor DG1_62_C04.g1_A002 Dark Grown 1 (DG 1) Sorgh 121 G594 gi20804997 2.20E−34 Oryza sativa (japonica DNA-binding protei cultivar-group) 121 G594 gi11862964 6.00E−34 Oryza sativa hypothetical protein. 121 G594 gi5923912 3.40E−31 Tulipa gesneriana bHLH transcription factor GBOF-1. 121 G594 gi6166283 4.30E−10 Pinus taeda helix-loop-helix protein 1A. 121 G594 gi13346182 3.80E−06 Gossypium hirsutum GHDEL65. 121 G594 gi527665 4.80E−06 Sorghum bicolor myc-like regulatory R gene product. 121 G594 gi527661 6.20E−06 Phyllostachys acuta myc-like regulatory R gene product. 121 G594 gi4206118 6.60E−06 Mesembryanthemum transporter homolog. crystallinum 121 G594 gi527657 1.30E−05 Pennisetum glaucum myc-like regulatory R gene product. 121 G594 gi1086526 0.0001 Oryza australiensis transcriptional activator Ra homolog. 123 G597 BE600816 5.00E−62 Sorghum bicolor PI1_90_E07.b1_A002 Pathogen induced 1 (PI1) 123 G597 AY106980 3.00E−60 Zea mays PCO106555 mRNA sequence. 123 G597 BQ765321 3.00E−58 Hordeum vulgare EBro03_SQ006_H21_R root, 3 week, waterlogge 123 G597 CA501339 2.00E−57 Triticum aestivum WHE4032_D07_H14ZT Wheat meiotic anther cD 123 G597 BQ841090 1.00E−56 Aegilops speltoides WHE4206_H10_O20ZS Aegilops speltoides p 123 G597 BG465540 8.00E−56 Sorghum propinquum RHIZ2_45_G09.b1_A003 Rhizome2 (RHIZ2) So 123 G597 AW928863 7.00E−53 Lycopersicon E5T337651 tomato flower esculentum buds 8 mm t 123 G597 BQ856774 4.00E−51 Lactuca sativa QGB5L17.yg.ab1 QG_ABCDI lettuce salinas Lact 123 G597 BU926769 5.00E−51 Glycine max sas91d09.y1 Gm-c1036 Glycine max cDNA clone SOY 123 G597 BJ473026 1.00E−50 Hordeum vulgare subsp. BJ473026 K. Sato vulgare unpublished 123 G597 gi12643044 1.60E−65 Oryza sativa putative AT-Hook DNA- binding protein. 123 G597 gi2213536 3.20E−49 Pisum sativum DNA-binding protein PD1. 123 G597 gi4165183 2.90E−41 Antirrhinum majus SAP1 protein. 123 G597 gi24418033 4.20E−15 Oryza sativa (japonica Hypothetical prote cultivar-group) 123 G597 gi13992574 0.00058 Triticum timopheevii glutenin HMW subunit 1Ax. 123 G597 gi100787 0.0011 Triticum aestivum glutenin high molecular weight chain 1A 123 G597 gi7188720 0.0032 Aegilops ventricosa x-type high molecular weight glutenin 123 G597 gi456124 0.066 Nicotiana tabacum DNA-binding protein. 123 G597 gi21218057 0.076 Chlamydomonas putative Pi-transporter reinhardtii homolog 123 G597 gi21779920 0.14 Aegilops tauschii HMW-glutenin. 125 G598 BH488116 9.00E−41 Brassica oleracea BOHPM37TF BOHP Brassica oleracea genomic 125 G598 BG455043 9.00E−38 Medicago truncatula NF112G09LF1F1069 Developing leaf Medica 125 G598 BQ856793 3.00E−35 Lactuca sativa QGB5M13.yg.ab1 QG_ABCDI lettuce salinas Lact 125 G598 AW932217 3.00E−33 Lycopersicon EST358060 tomato fruit esculentum mature green 125 G598 BQ511117 5.00E−31 Solanum tuberosum EST618532 Generation of a set of potato c 125 G598 AP003981 3.00E−30 Oryza sativa chromosome 7 clone OJ1019_E02, *** SEQUENCING 125 G598 AAAA01001857 3.00E−30 Oryza sativa (indica ( ) scaffold001857 cultivar-group) 125 G598 AC135958 7.00E−30 Oryza sativa (japonica ( ) chromosome 3 clo cultivar-group) 125 G598 BG319716 9.00E−23 Zea mays Zm03_06a07_A Zm03_AAFC_ECORC_cold stressed_maize_s 125 G598 BU025013 2.00E−20 Helianthus annuus QHF7D11.yg.ab1 QH_EFGHJ sunflower RHA280 125 G598 gi1881585 0.059 Solanum tuberosum remorin. 125 G598 gi15289949 0.11 Oryza sativa (japonica hypothetical prote cultivar-group) 125 G598 gi4883530 0.32 Lycopersicon remorin 2. esculentum 125 G598 gi13161367 0.96 Oryza sativa hypothetical protein. 125 G598 gi13775109 0.97 Phaseolus vulgaris bZIP transcription factor 3. 125 G598 gi8096269 0.98 Nicotiana tabacum KED. 125 G598 gi2598161 0.98 Pinus strobus NADPH: protochlorophyllide oxidoreductase po 125 G598 gi1183880 0.99 Brassica napus oleosin-like protein. 125 G598 gi22002966 1 Hordeum vulgare subsp. putative CENP-E like kinet vulgare 125 G598 gi4185307 1 Zea mays unknown. 127 G634 OSGT2 2.00E−47 Oryza sativa O. sativa gt-2 gene. 127 G634 BU049946 1.00E−46 Zea mays 1111017E09.y1 1111 - Unigene III from Maize Genome 127 G634 AF372499 6.00E−38 Glycine max GT-2 factor mRNA, partial cds. 127 G634 AB052729 4.00E−37 Pisum sativum mRNA for DNA-binding protein DF1, complete cd 127 G634 BU889446 4.00E−36 Populus tremula P021A05 Populus petioles cDNA library Popul 127 G634 BH436958 2.00E−35 Brassica oleracea BOHBE67TF BOHB Brassica oleracea genomic 127 G634 AI777252 3.00E−35 Lycopersicon EST258217 tomato esculentum resistant, Cornell 127 G634 AW686754 1.00E−33 Medicago truncatula NF042C08NR1F1000 Nodulated root Medicag 127 G634 AV410715 4.00E−33 Lotus japonicus AV410715 Lotus japonicus young plants (two- 127 G634 AI730933 8.00E−30 Gossypium hirsutum BNLGHi8208 Six-day Cotton fiber Gossypiu 127 G634 gi13786451 3.20E−78 Oryza sativa putative transcription factor. 127 G634 gi13646986 3.50E−66 Pisum sativum DNA-binding protein DF1. 127 G634 gi18182311 2.70E−38 Glycine max GT-2 factor. 127 G634 gi20161567 8.90E−11 Oryza sativa (japonica hypothetical prote cultivar-group) 127 G634 gi170271 4.70E−08 Nicotiana tabacum DNA-binding protein. 127 G634 gi18349 0.0027 Daucus carota glycine rich protein (AA 1 - 96). 127 G634 gi21388658 0.027 Physcomitrella patens glycine-rich RNA binding protein. 127 G634 gi21322752 0.052 Triticum aestivum cold shock protein-1. 127 G634 gi3126963 0.057 Elaeagnus umbellata acidic chitinase. 127 G634 gi1166450 0.087 Lycopersicon Tfm5. esculentum 129 G635 BH528345 1.00E−117 Brassica oleracea BOGNZ34TR BOGN Brassica oleracca genomic 129 G635 BQ916526 4.00E−71 Helianthus annuus QHB18C05.yg.ab1 QH_ABCDI sunflower RHA801 129 G635 AY110231 1.00E−68 Zea mays CL852_1 mRNA sequence. 129 G635 BI139375 3.00E−42 Populus balsamifera F130P49Y Populus flo subsp. trichocarpa 129 G635 BQ850859 3.00E−42 Lactuca sativa QGB13M04.yg.ab1 QG_ABCDI lettuce salinas Lac 129 G635 AC137603 6.00E−40 Medicago truncatula clone mth2-14b10, WORKING DRAFT SEQUENC 129 G635 BF269947 6.00E−37 Gossypium arboreum GA_Eb0006B11f Gossypium arboreum 7-10 d 129 G635 AW760602 5.00E−34 Glycine max s152e02.y1 Gm-c1027 Glycine max cDNA clone GENO 129 G635 BJ464004 1.00E−30 Hordeum vulgare subsp. BJ464004 K. Sato vulgare unpublished 129 G635 AAAA01000007 1.00E−30 Oryza sativa (indica ( ) scaffold000007 cultivar-group) 129 G635 gi21741458 3.30E−08 Oryza sativa OJ000223_09.14. 129 G635 gi170271 1.20E−07 Nicotiana tabacum DNA-binding protein. 129 G635 gi18182309 3.00E−06 Glycine max GT-2 factor. 129 G635 gi13646986 3.10E−05 Pisum sativum DNA-binding protein DF1. 129 G635 gi22128704 0.02 Oryza sativa (japonica hypothetical prote cultivar-group) 129 G635 gi7208779 0.04 Cicer arietinum hypothetical protein. 129 G635 gi1279563 0.056 Medicago sativa nuM1. 129 G635 gi15144506 0.066 Lycopersicon unknown. esculentum 129 G635 gi349585 0.36 Volvox carteri histone H1-I. 129 G635 gi2911292 0.49 Capsicum annuum prosystemin. 131 G636 AB052729 1.00E−134 Pisum sativum mRNA for DNA-binding protein DF1, complete cd 131 G636 OSGT2 1.00E−109 Oryza sativa O. sativa gt-2 gene. 131 G636 AF372498 1.00E−103 Glycine max GT-2 factor mRNA, partial cds. 131 G636 AAAA01017145 1.00E−101 Oryza sativa (indica ( ) scaffold017145 cultivar-group) 131 G636 BH521870 4.00E−89 Brassica oleracea BOGMP76TF BOGM Brassica oleracea genomic 131 G636 AP004868 2.00E−79 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 131 G636 BU894555 2.00E−69 Populus tremula x X011B09 Populus wood Populus tremuloides 131 G636 BG446849 2.00E−57 Gossypium arboreum GA_Eb0039I22f Gossypium arboreum 7-10 d 131 G636 AW032956 3.00E−52 Lycopersicon EST276515 tomato callus, esculentum TAMU Lycop 131 G636 AC135565 4.00E−49 Medicago truncatula clone mth2-19b12, WORKING DRAFT SEQUENC 131 G636 gi13646986 4.50E−111 Pisum sativum DNA-binding protein DF1. 131 G636 gi18182309 4.00E−99 Glycine max GT-2 factor. 131 G636 gi13786451 5.30E−98 Oryza sativa putative transcription factor. 131 G636 gi170271 4.30E−13 Nicotiana tabacum DNA-binding protein. 131 G636 gi20161567 4.00E−09 Oryza sativa (japonica hypothetical prote cultivar-group) 131 G636 gi10636140 0.00014 Aegilops speltoides gamma-gliadin. 131 G636 gi442524 0.00015 Hordeum vulgare C-hordein. 131 G636 gi15148391 0.00021 Triticum aestivum gamma-gliadin. 131 G636 gi225589 0.00021 Hordeum vulgare var. hordein C. distichum 131 G636 gi4584086 0.00061 Spermatozopsis similis p210 protein. 133 G638 BZ034676 3.00E−87 Brassica oleracea oef83a05.g1 B. oleracea002 Brassica olerac 133 G638 BQ866994 6.00E−55 Lactuca sativa QGC9I02.yg.ab1 QG_ABCDI lettuce salinas Lact 133 G638 BM110736 1.00E−54 Solanum tuberosum EST558272 potato roots Solanum tuberosum 133 G638 BF646615 9.00E−48 Medicago truncatula NF066C08EC1F1065 Elicited cell culture 133 G638 OSGT2 3.00E−36 Oryza sativa O.sativa gt-2 gene. 133 G638 AP004868 4.00E−33 Oryza sativa (japonica ( ) chromosome 2 clo cultivar-group) 133 G638 AB052729 2.00E−32 Pisum sativum mRNA for DNA-binding protein DF1, complete cd 133 G638 AI777252 4.00E−29 Lycopersicon EST258217 tomato esculentum resistant, Cornell 133 G638 BM500043 2.00E−28 Zea mays 952036C09.y1 952 - BMS tissue from Walbot Lab (red 133 G638 AF372499 5.00E−28 Glycine max GT-2 factor mRNA, partial cds. 133 G638 gi20249 2.00E−49 Oryza sativa gt-2. 133 G638 gi13646986 4.30E−45 Pisum sativum DNA-binding protein DF1. 133 G638 gi18182311 1.10E−30 Glycine max GT-2 factor. 133 G638 gi20161567 2.60E−07 Oryza sativa (japonica hypothetical prote cultivar-group) 133 G638 gi170271 3.40E−06 Nicotiana tabacum DNA-binding protein. 133 G638 gi21068672 3.60E−05 Cicer arietinum putative glicine-rich protein. 133 G638 gi20257673 4.60E−05 Zea mays glycine-rich RNA binding protein. 133 G638 gi21388660 0.00014 Physcomitrella patens glycine-rich RNA-binding protein. 133 G638 gi9755844 0.00033 Brassica napus putative glycine-rich protein. 133 G638 gi1166450 0.00037 Lycopersicon Tfm5. esculentum 135 G652 BH926980 5.00E−90 Brassica oleracea odi21g11.g1 B. oleracea002 Brassica olerac 135 G652 NSGRP2MR 1.00E−71 Nicotiana sylvestris N.sylvestris mRNA for glycine rich pro 135 G652 AI812203 7.00E−65 Zea mays 605086G09.y1 605 - Endosperm cDNA library from Sch 135 G652 BM408211 4.00E−64 Solanum tuberosum EST582538 potato roots Solanum tuberosum 135 G652 AP003879 6.00E−64 Oryza sativa chromosome 8 clone OJ1123_A02, *** SEQUENCING 135 G652 AP004591 6.00E−64 Oryza sativa (japonica ( ) chromosome 8 clo cultivar-group) 135 G652 AAAA01000576 7.00E−63 Oryza sativa (indica ( ) scaffold000576 cultivar-group) 135 G652 AB066265 1.00E−62 Triticum aestivum WCSP1 mRNA for cold shock protein-1, comp 135 G652 BQ840577 2.00E−62 Aegilops speltoides WHE4201_B07_C13ZS Aegilops speltoides p 135 G652 BE035242 1.00E−53 Mesembryanthemum MO03A01 MO crystallinum Mesembryanthemum c 135 G652 gi121631 9.30E−68 Nicotiana sylvestris GLYCINE-RICH CELL WALL STRUCTURAL PR 135 G652 gi21322752 1.70E−61 Triticum aestivum cold shock protein-1. 135 G652 gi121628 5.00E−26 Phaseolus vulgaris GLYCINE-RICH CELL WALL STRUCTURAL PROT 135 G652 gi395147 7.10E−25 Nicotiana tabacum glycine-rich protein. 135 G652 gi17821 1.40E−23 Brassica napus glycine-rich_protein_(aa1- 291). 135 G652 gi121627 1.80E−23 Petunia x hybrida GLYCINE-RICH CELL WALL STRUCTURAL PROTE 135 G652 gi225181 1.80E−23 Petunia sp. Gly rich structural protein. 135 G652 gi15528745 2.00E−22 Oryza sativa contains ESTs AU093876(E1018), AU0938 77(E1018 135 G652 gi21327989 2.00E−22 Oryza sativa (japonica contains ESTs AU09 cultivar-group) 135 G652 gi21388660 4.40E−22 Physcomitrella patens glycine-rich RNA-binding protein. 137 G663 AF146702 6.00E−54 Petunia x hybrida An2 protein (an2) mRNA, an2-V26 allele, c 137 G663 AF146703 3.00E−53 Petunia integrifolia An2 protein (an2) mRNA, an2-S9 allele, 137 G663 BQ990780 4.00E−51 Lactuca sativa QGF21B10.yg.ab1 QG_EFGHJ lettuce serriola La 137 G663 BE462282 3.00E−50 Lycopersicon EST324546 tomato flower esculentum buds 0-3 mm 137 G663 AB073013 6.00E−50 Vitis labrusca x Vitis VlmybA2 gene for myb- vinifera relate 137 G663 AF146709 2.00E−49 Petunia axillaris An2 truncated protein (an2) mRNA, an2-S7 137 G663 BH480961 3.00E−47 Brassica oleracea BOGZT54TF BOGZ Brassica oleracea genomic 137 G663 BF635572 6.00E−42 Medicago truncatula NF104H01DT1F1014 Drought Medicago trunc 137 G663 BQ105368 2.00E−41 Rosa hybrid cultivar fc0707.e Rose Petals (Fragrant Cloud) 137 G663 AF336278 2.00E−41 Gossypium hirsutum BNLGHi233 (bnlghi6233) mRNA, complete cd 137 G663 gi7673084 1.10E−53 Petunia x hybrida An2 protein. 137 G663 gi7673086 3.90E−53 Petunia integrifolia An2 protein. 137 G663 gi22266667 2.30E−50 Vitis labrusca x Vitis myb-related transcription vinifera 137 G663 gi7673096 1.30E−47 Petunia axillaris An2 truncated protein. 137 G663 gi13346178 2.30E−41 Gossypium hirsutum BNLGHi233. 137 G663 gi1101770 8.40E−41 Picea mariana MYB-like transcriptional factor MBF1. 137 G663 gi22535556 1.20E−39 Oryza sativa(japonica myb-related protei cultivar-group) 137 G663 gi2605623 1.20E−39 Oryza sativa OSMYB4. 137 G663 gi2343273 4.80E−39 Zea mays PL transcription factor. 137 G663 gi4138299 4.80E−39 Oryza sativa subsp. transcriptional activator. indica 139 G664 AF336286 2.00E−89 Gossypium hirsutum GHMYB9 (ghmyb9) mRNA, complete cds. 139 G664 LETHM27 7.00E−88 Lycopersicon L. esculentum mRNA for esculentum THM27 protein 139 G664 BG442984 9.00E−83 Gossypium arboreum GA_Ea0019B05f Gossypium arboreum 7-10 d 139 G664 BM112753 1.00E−80 Solanum tuberosum EST560289 potato roots Solanum tuberosum 139 G664 AY108280 5.00E−78 Zea mays PCO132931 mRNA sequence. 139 G664 BF716393 2.00E−76 Glycine max saa19f01.y1 Gm-c1058 Glycine max cDNA clone GEN 139 G664 BH537477 5.00E−76 Brassica oleracea BOGIR45TF BOG1 Brassica oleracea genomic 139 G664 HVMYB1 1.00E−75 Hordeum vulgare H. vulgare myb1 mRNA. 139 G664 AW775893 1.00E−74 Medicago truncatula EST334958 DSIL Medicago truncatula cDNA 139 G664 BQ855835 8.00E−73 Lactuca sativa QGB27N20.yg.ab1 QG_ABCDI lettuce salinas Lac 139 G664 gi13346194 3.50E−88 Gossypium hirsutum GHMYB9. 139 G664 gi1167484 8.00E−85 Lycopersicon transcription factor. esculentum 139 G664 gi82308 3.20E−74 Antirrhinum majus myb protein 308 - garden snapdragon. 139 G664 gi19072766 5.30E−73 Oryza sativa typical P-type R2R3 Myb protein. 139 G664 gi127579 3.80E−71 Hordeum vulgare MYB-RELATED PROTEIN HV1. 139 G664 gi227030 3.80E−71 Hordeum vulgare var. myb-related gene Hv1. distichum 139 G664 gi19386839 3.00E−69 Oryza sativa (japonica putative myb-relat cultivar-group) 139 G664 gi127582 8.10E−69 Zea mays MYB-RELATED PROTEIN ZM38. 139 G664 gi23476285 2.10E−61 Gossypioides kirkii myb-like transcription factor 1. 139 G664 gi23476281 9.10E−61 Gossypium raimondii myb-like transcription factor 1. 141 G674 BE021475 2.00E−47 Glycine max sm59a03.y1 Gm-c1028 Glycine max cDNA clone GENO 141 G674 AY104558 1.00E−43 Zea mays PCO116495 mRNA sequence. 141 G674 BE402501 3.00E−43 Triticum aestivum CSB008F03F990908 ITEC CSB Wheat Endosperm 141 G674 AW672062 2.00E−42 Sorghum bicolor LG1_354_G05.b1_A002 Light Grown 1 (LG1) Sor 141 G674 CA002506 2.00E−42 Hordeum vulgare subsp. HS07L12r HS Hordeum vulgare vulgare 141 G674 AW691296 3.00E−42 Medicago truncatula NF040A12ST1F1000 Developing stem Medica 141 G674 BM356984 2.00E−41 Triphysaria versicolor 12II-D5 Triphysaria versicolor root- 141 G674 BQ290999 2.00E−41 Pinus taeda NXRV054_D07_F NXRV (Nsf Xylem Root wood Vertica 141 G674 AW626100 3.00E−40 Lycopersicon EST320007 tomato radicle, esculentum 5 d post- 141 G674 BQ802392 6.00E−40 Triticum monococcum WHE2825_D09_G17ZS Triticum monococcum v 141 G674 gi13486737 5.20E−42 Oryza sativa putative transcription factor (myb). 141 G674 gi22093837 3.70E−41 Oryza sativa (japonica contains ESTs AU10 cultivar-group) 141 G674 gi19059 2.40E−37 Hordeum vulgare MybHv33. 141 G674 gi5139802 8.10E−37 Glycine max GmMYB29A1. 141 G674 gi1167486 1.30E−36 Lycopersicon transcription factor. esculentum 141 G674 gi82310 9.30E−36 Antirrhinum majus myb protein 330 - garden snapdragon. 141 G674 gi13346188 3.20E−35 Gossypium hirsutum GHMYB25. 141 G674 gi22266673 4.00E−35 Vitis labrusca x Vitis myb-related transcription vinifera 141 G674 gi6552389 1.40E−34 Nicotiana tabacum myb-related transcription factor LBM4. 141 G674 gi15082210 1.70E−34 Fragaria x ananassa transcription factor MYB1. 143 G676 AF502295 1.00E−109 Cucumis sativus werewolf (WER) mRNA, partial cds. 143 G676 BF275643 2.00E−56 Gossypium arboreum GA_Eb0024J14f Gossypium arboreum 7-10 d 143 G676 BZ078562 3.00E−47 Brassica oleracea lkz44b07.b1 B. oleracea002 Brassica olerac 143 G676 AF034130 3.00E−42 Gossypium hirsutum MYB-like DNA-binding domain protein (Cmy 143 G676 BU830456 4.00E−42 Populus tremula x T008E08 Populus apica Populus tremuloides 143 G676 AF401220 6.00E−42 Fragaria x ananassa transcription factor MYB1 (MYB1) mRNA, 143 G676 AI771837 2.00E−41 Lycopersicon EST252937 tomato ovary, esculentum TAMU Lycope 143 G676 BE124666 4.00E−41 Medicago truncatula EST393701 GVN Medicago truncatula cDNA 143 G676 BG881996 9.00E−41 Glycine max sae92f10.y1 Gm-c1065 Glycine max cDNA clone GEN 143 G676 AF474115 2.00E−40 Zea mays typical P-type R2R3 Myb protein (Myb1) gene, parti 143 G676 gi20514371 1.10E−103 Cucumis sativus werewolf. 143 G676 gi1101770 4.10E−43 Picea mariana MYB-like transcriptional factor MBF1. 143 G676 gi23476291 2.50E−42 Gossypium raimondii myb-like transcription factor 2. 143 G676 gi2921332 3.20E−42 Gossypium hirsutum MYB-like DNA-binding domain protein. 143 G676 gi23476293 6.60E−42 Gossypium herbaceum myb-like transcription factor 2. 143 G676 gi15082210 1.10E−41 Fragaria x ananassa transcription factor MYB1. 143 G676 gi23476297 1.40E−41 Gossypioides kirkii myb-like transcription factor 3. 143 G676 gi19072734 6.00E−41 Zea mays typical P-type R2R3 Myb protein. 143 G676 gi82308 1.20E−40 Antirrhinum majus myb protein 308 - garden snapdragon. 143 G676 gi1167484 3.30E−40 Lycopersicon transcription factor. esculentum 145 G680 PVU420902 1.00E−149 Phaseolus vulgaris mRNA for LHY protein. 145 G680 BH579338 8.00E−93 Brassica oleracea BOGDR44TF BOGD Brassica oleracea genomic 145 G680 AAAA01009649 3.00E−59 Oryza sativa (indica ( ) scaffold009649 cultivar-group) 145 G680 AP004460 2.00E−58 Oryza sativa (japonica ( ) chromosome 8 clo cultivar-group) 145 G680 BU868664 3.00E−56 Populus balsamifera M118F07 Populus flow subsp. trichocarpa 145 G680 BE331563 2.00E−54 Glycine max sp15d08.y1 Gm-c1042 Glycine max cDNA clone GENO 145 G680 BG524104 2.00E−49 Stevia rebaudiana 38-82 Stevia field grown leaf cDNA Stevia 145 G680 AW979367 2.00E−46 Lycopersicon EST310415 tomato root esculentum deficiency, C 145 G680 BM322287 3.00E−45 Sorghum bicolor PIC1_2_F02.b1_A002 Pathogen-infected compat 145 G680 AY103618 5.00E−45 Zea mays PCO118792 mRNA sequence. 145 G680 gi21213868 1.40E−144 Phaseolus vulgaris LHY protein. 145 G680 gi15528628 4.80E−24 Oryza sativa hypothetical protein˜similar to Oryza sativa 145 G680 gi18461206 1.10E−07 Oryza sativa (japonica contains ESTs AU10 cultivar-group) 145 G680 gi18874263 6.60E−07 Antirrhinum majus MYB-like transcription factor DIVARICAT 145 G680 gi12406993 1.70E−06 Hordeum vulgare MCB1 protein. 145 G680 gi12005328 3.20E−06 Hevea brasiliensis unknown. 145 G680 gi20067661 3.40E−06 Zea mays one repeat myb transcriptional factor. 145 G680 gi6688529 1.20E−05 Lycopersicon I-box binding factor. esculentum 145 G680 gi19911577 0.00036 Glycine max syringolide-induced protein 1-3-1A. 145 G680 gi7677132 0.012 Secale cereale c-myb-like transcription factor. 147 G682 BU831849 8.00E−25 Populus tremula x T026E01 Populus apica Populus tremuloides 147 G682 BU872107 8.00E−25 Populus balsamifera Q039C07 Populus flow subsp. trichocarpa 147 G682 BM437313 1.00E−20 Vitis vinifera VVA017F06_54121 An expressed sequence tag da 147 G682 BI699876 4.00E−19 Glycine max sag49b09.y1 Gm-c1081 Glycine max cDNA clone GEN 147 G682 BH961028 1.00E−16 Brassica oleracea odj30d06.g1 B. oleracea002 Brassica olerac 147 G682 AL750151 2.00E−14 Pinus pinaster AL750151 AS Pinus pinaster cDNA clone AS06C1 147 G682 BJ476463 1.00E−13 Hordeum vulgare subsp. BJ476463 K. Sato vulgare unpublished 147 G682 AJ485557 1.00E−13 Hordeum vulgare AJ485557 S00011 Hordeum vulgare cDNA clone 147 G682 CA762299 2.00E−13 Oryza sativa (indica BR060003B10F03.ab1 IRR cultivar-group) 147 G682 CA736777 2.00E−12 Triticum aestivum wpils.pk008.n12 wpils Triticum aestivum c 147 G682 gi23476287 8.30E−12 Gossypium hirsutum myb-like transcription factor 2. 147 G682 gi23476291 8.30E−12 Gossypium raimondii myb-like transcription factor 2. 147 G682 gi23476293 8.30E−12 Gossypium herbaceum myb-like transcription factor 2. 147 G682 gi23476295 8.30E−12 Gossypioides kirkii myb-like transcription factor 2. 147 G682 gi15042120 2.20E−11 Zea luxurians CI protein. 147 G682 gi19548449 2.20E−11 Zea mays P-type R2R3 Myb protein. 147 G682 gi9954118 2.80E−11 Solanum tuberosum tuber-specific and sucrose- responsive e 147 G682 gi15042108 4.60E−11 Zea mays subsp. CI protein. parviglumis 147 G682 gi15082210 1.50E−10 Fragaria x ananassa transcription factor MYB1. 147 G682 gi22266669 1.50E−10 Vitis labrusca x Vitis myb-related transcription vinifera 149 G715 BG591677 9.00E−91 Solanum tuberosum EST499519 P. infestans- challenged leaf So 149 G715 AW776719 2.00E−89 Medicago truncatula EST335784 DSIL Medicago truncatula cDNA 149 G715 BE208917 2.00E−87 Citrus x paradisi GF-FV-P3F5 Marsh grapefruit young flavedo 149 G715 BQ411597 1.00E−86 Gossypium arboreum GA_Ed0041B06f Gossypium arboreum 7-10 d 149 G715 BM065544 4.00E−86 Capsicum annuum KS07004F12 KS07 Capsicum annuum cDNA, mRNA 149 G715 BI701620 4.00E−83 Glycine max sai18a04.y1 Gm-c1053 Glycine max cDNA clone GEN 149 G715 BH725354 2.00E−79 Brassica oleracea BOHVO37TF BO_2_3_KB Brassica oleracea gen 149 G715 AW093662 6.00E−77 Lycopersicon EST286842 tomato mixed esculentum elicitor, BT 149 G715 AW399586 2.00E−67 Lycopersicon pennellii EST310086 L. pennellii trichome, Cor 149 G715 AC134235 8.00E−66 Oryza sativa (japonica ( ) chromosome 3 clo cultivar-group) 149 G715 gi5257260 2.00E−52 Oryza sativa Similar to sequence of BAC F7G19 from Arabid 149 G715 gi20804442 1.80E−20 Oryza sativa (japonica hypothetical prote cultivar-group) 149 G715 gi18481626 3.70E−08 Zea mays repressor protein. 149 G715 gi1778097 0.19 Pinus taeda expansin. 149 G715 gi2130105 0.44 Triticum aestivum histone H2A.4 - wheat. 149 G715 gi297871 0.47 Picea abies histone H2A. 149 G715 gi5106924 0.56 Medicago truncatula putative cell wall protein. 149 G715 gi1247386 0.6 Nicotiana alata PRP2. 149 G715 gi121981 0.8 Volvox carteri HISTONE H2A-III. 149 G715 gi1708102 0.8 Chlamydomonas HISTONE H2A. reinhardtii 151 G720 BH650015 1.00E−68 Brassica oleracea BOMOG70TF BO_2_3_KB Brassica oleracea gen 151 G720 BG450227 3.00E−55 Medicago truncatula NF015E11DT1F1087 Drought Medicago trunc 151 G720 BG642566 7.00E−50 Lycopersicon EST510760 tomato esculentum shoot/meristem Lyc 151 G720 BG887673 3.00E−45 Solanum tuberosum EST513524 cSTD Solanum tuberosum cDNA clo 151 G720 BU878634 5.00E−45 Populus balsamifera V049F07 Populus flow subsp. trichocarpa 151 G720 BQ594416 4.00E−42 Beta vulgaris E012444-024-024-N22-SP6 MPIZ-ADIS-024-develop 151 G720 AF318581 4.00E−41 Oryza sativa putative transcription factor OsGLK1 (Glk1) mR 151 G720 AF318579 1.00E−39 Zea mays putative transcription factor GOLDEN 2 mRNA, compl 151 G720 BU004944 5.00E−37 Lactuca sativa QGG6K14.yg.ab1 QG_EFGHJ lettuce serriola Lac 151 G720 AW618051 4.00E−34 Lycopersicon pennellii EST314101 L. pennellii trichome, Cor 151 G720 gi13940496 1.20E−38 Zea mays putative transcription factor ZmGLK1. 151 G720 gi24308616 2.20E−27 Oryza sativa (japonica Putative response cultivar-group) 151 G720 gi13940498 2.10E−26 Oryza sativa putative transcription factor OsGLK1. 151 G720 gi4519671 1.10E−08 Nicotiana tabacum transfactor. 151 G720 gi6942190 3.50E−08 Mesembryanthemum CDPK substrate protein 1; C crystallinum 151 G720 gi5916207 1.90E−06 Chlamydomonas regulatory protein of P- reinhardtii starvat 151 G720 gi10198182 0.016 Cladrastis kentukea ENOD2. 151 G720 gi100216 0.02 Lycopersicon extensin class II (clone uJ-2)- esculentum 151 G720 gi169878 0.032 Sesbania rostrata nodulin. 151 G720 gi1808688 0.041 Sporobolus stapfianus hypothetical protein. 153 G736 BH959523 2.00E−65 Brassica oleracea odh52c03.b1 B. oleracea002 Brassica olerac 153 G736 BU868493 2.00E−43 Populus balsamifera M116E08 Populus flow subsp. trichocarpa 153 G736 AW648389 4.00E−38 Lycopersicon EST326843 tomato esculentum germinating seedli 153 G736 CA810654 4.00E−37 Vitis vinifera CA22LIO1IVF-E1 CA22LI Vitis vinifera cDNA cl 153 G736 BE323614 4.00E−34 Medicago truncatula NF006A11PL1F1081 Phosphate starved leaf 153 G736 BE474759 3.00E−29 Glycine max sp68c07.y1 Gm-c1044 Glycine max cDNA clone GENO 153 G736 AP005167 7.00E−28 Oryza sativa (japonica ( ) chromosome 7 clo cultivar-group) 153 G736 AAAA01004298 7.00E−28 Oryza sativa (indica ( ) scaffold004298 cultivar-group) 153 G736 CA753311 2.00E−27 Oryza sativa 00210011068.D09_0106282 29W.scf IR62266 Oryza s 153 G736 BJ471540 3.00E−27 Hordeum vulgare subsp. BJ471540 K. Sato vulgare unpublished 153 G736 gi19071625 5.30E−30 Oryza sativa (japonica putative zinc fing cultivar-group) 153 G736 gi15451553 6.50E−30 Oryza sativa Putative H-protein promoter binding factor-2 153 G736 gi21538791 1.70E−27 Hordeum vulgare subsp. dof zinc finger protein. vulgare 153 G736 gi1669341 1.20E−26 Cucurbita maxima AOBP (ascorbate oxidase promoter-binding 153 G736 gi3929325 1.00E−22 Dendrobium grex putative DNA-binding prot Madame Thong-In 153 G736 gi3777436 1.30E−22 Hordeum vulgare DNA binding protein. 153 G736 gi2393775 1.20E−21 Zea mays prolamin box binding factor. 153 G736 gi1360078 2.40E−21 Nicotiana tabacum Zn finger protein. 153 G736 gi3790264 3.90E−21 Triticum aestivum PBF protein. 153 G736 gi7688355 6.40E−21 Solanum tuberosum Dof zinc finger protein. 155 G748 D45066 6.00E−91 Cucurbita maxima mRNA for AOBP (ascorbate oxidase promoter- 155 G748 BH530891 3.00E−69 Brassica oleracea BOHIF05TR BOHI Brassica oleracea genomic 155 G748 AP001383 3.00E−63 Oryza sativa genomic DNA, chromosome 1, clone: P0453A06. 155 G748 AAAA01004298 1.00E−62 Oryza sativa (indica ( ) scaffold004298 cultivar-group) 155 G748 AP005167 1.00E−62 Oryza sativa (japonica ( ) chromosome 7 clo cultivar-group) 155 G748 CA783807 2.00E−56 Glycine max sat57f01.y1 Gm-c1056 Glycine max cDNA clone SOY 155 G748 AC137986 1.00E−48 Medicago truncatula clone mth2-7g6, WORKTNG DRAFT SEQUENCE, 155 G748 AW029804 1.00E−46 Lycopers