Abstract: The present invention provides gene targets, constructs and methods for the genetic control of plant disease caused by multiple plant viruses. The present invention relates to achieving a plant protective effect through the identification of target coding sequences and the use of recombinant DNA technologies for post-transcriptionally repressing or inhibiting expression of the target coding sequences of plant-parasitic viruses. Protein-expression based approaches may also be utilized to augment phenotype resistance. Thus, transcription of a single transgenic event comprising one or more plant expression cassettes can allow for broad spectrum resistance of a plant to multiple plant viral strains and species among the geminiviruses, tospoviruses, and potexviruses.

Abstract: The invention provides polynucleotide and polypeptide sequences isolated from P. radiata and E. grandis that are involved in wood and cell wall biosynthesis. Methods for using the sequences, along with constructs and transgenic plants, are provided also.

Abstract: Double-stranded RNA (dsRNA) induces sequence-specific post-transcriptional gene silencing in many organisms by a process known as RNA interference (RNAi). Using a Drosophila in vitro system, we demonstrate that 19-23 nt short RNA fragments are the sequence-specific mediators of RNAi. The short interfering RNAs (siRNAs) are generated by an RNase III-like processing reaction from long dsRNA. Chemically synthesized siRNA duplexes with overhanging 3? ends mediate efficient target RNA cleavage in the lysate, and the cleavage site is located near the center of the region spanned by the guiding siRNA. Furthermore, we provide evidence that the direction of dsRNA processing determines whether sense or antisense target RNA can be cleaved by the produced siRNP complex.

Abstract: The invention provides constructs and methods of screening for constructs useful in conferring resistance in plants to pests by gene silencing. The invention also provides pest-resistant plants transformed with the present constructs. One screening method of the invention comprises the steps of: selecting at least one pest target nucleotide sequence, producing a plurality of dsRNA test agents that target the pest target nucleotide sequence, testing and scoring the plurality of dsRNA test agents for toxicity to the pest, and producing a silencing construct based on a superior-scoring test agent.

Abstract: The present invention relates to isolated nucleic acid molecules and their corresponding encoded polypeptides able confer the trait of modulated plant size, vegetative growth, organ number, plant architecture, sterility or seedling lethality in plants. The present invention further relates to the use of these nucleic acid molecules and polypeptides in making transgenic plants, plant cells, plant materials or seeds of a plant having such modulated growth or phenotype characteristics that are altered with respect to wild type plants grown under similar conditions.

Abstract: The present invention relates to p450 enzymes and nucleic acid sequences encoding p450 enzymes in Nicotiana, and methods of using those enzymes and nucleic acid sequences to alter plant phenotypes.

Abstract: The present invention discloses transgenic plants having an altered level of NAP protein compared to that of a non-transgenic plant, where the transgenic plants display an altered leaf senescence phenotype relative to a non-transgenic plant, as well as mutant plants comprising an inactivated NAP gene, where mutant plants display a delayed leaf senescence phenotype compared to that of a non-mutant plant. The present invention also discloses methods for delaying leaf senescence in a plant, as well as methods of making a mutant plant having a decreased level of NAP protein compared to that of a non-mutant plant, where the mutant plant displays a delayed leaf senescence phenotype relative to a non-mutant plant. Methods for causing precocious leaf senescence or promoting leaf senescence in a plant are also disclosed. Also disclosed are methods of identifying a candidate plant suitable for breeding that displays a delayed leaf senescence and/or enhanced yield phenotype.

Abstract: Isolated nucleic acid fragments comprising precursor miRNA, and artificial miRNAs and their use in down-regulating gene expression are described.

Abstract: A method for producing a rose characterized by artificially suppressing the rose endogenous metabolic pathway and expressing the pansy gene coding for flavonoid 3?,5?-hydroxylase.

Abstract: This invention provides a non-natural transgenic plant cell expressing at least one invertebrate miRNA in planta for suppression of a target gene of an invertebrate pest or of a symbiont associated with the invertebrate pest, recombinant DNA constructs for expression of at least one invertebrate miRNA in planta and methods of use thereof, a non-natural transgenic plant containing the non-natural transgenic plant cell of this invention, a non-natural transgenic plant grown from the non-natural transgenic plant cell of this invention, and non-natural transgenic seed produced by the non-natural transgenic plants, as well as commodity products produced from a non-natural transgenic plant cell, plant, or seed of this invention.

Abstract: The gene encoding N-methylputrescine oxidase (MPO) and constructs comprising such DNA are provided, including methods of regulating MPO expression independently or with other alkaloid biosynthesis genes to modulate alkaloid production in plants and host cells. MPO genes or fragments thereof are useful for reducing pyrrolidine or tropane alkaloid production in plants, for increasing pyrrolidine or tropane alkaloid production in plants, and for producing an MPO enzyme in host cells.

Abstract: An isolated polypeptide containing an amino acid sequence at least 70% identical to a Tubby-like protein (SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11), and an isolated nucleic acid encoding the polypeptide. Disclosed is an isolated nucleic acid that, under stringent conditions, hybridizes to a probe containing one of SEQ ID NOs:1-11; or its complementary sequence. Also disclosed are (1) a transformed cell or a transgenic plant containing such a nucleic acid and (2) a transformed cell or a transgenic plant having a reduced level(s) of one or more of the Tubby-like proteins. Also within the scope of the invention are methods for making the transformed cells or transgenic plants.

Abstract: This invention discloses recombinant DNA constructs that transcribe to RNA having improved resistance to a plant RNase III enzyme, and methods for their use in making transgenic plant cells, plants, seeds, and products derived therefrom. Also provided are compositions and methods for imparting to a plant resistance to a pest or pathogen of the plant.

Abstract: Compositions and methods for modulating expression of gene products are provided. Compositions comprise suppression cassettes that comprise a convergent promoter pair operably linked to a silencing element that, upon expression, is capable of decreasing the expression of one or more target polynucleotides of interest. Compositions of the invention also include transformed plants, plant cells, plant tissues, and plant seeds. Methods of transformation and regeneration of plants comprising the novel constructs are provided. The methods find use in regulating gene expression, particularly genes associated with agronomic traits of interest. Further provided are promoter sequences, cells, plants, and vectors comprising these promoter sequences and methods of their use.

Abstract: This invention discloses recombinant DNA constructs encoding phased small RNAs useful in regulating expression of one or more genes of interest. Also disclosed by this invention are transgenic plant cells, plants, and seeds containing a recombinant DNA construct of this invention.

Abstract: Methods are provided for increasing the resistance of plants to hypoxic or anoxic conditions. Such methods may be applied to increase the penetrance of plant roots in the growth medium or into soil. The methods according to the invention may include providing plants with a stress tolerance gene. Similar effects can be obtained by applying chemical compounds, including neonicotinoid compounds, to the plants.

Abstract: Soybean ubiquitin promoters is from the soybean SUBI-3 polyubiquitin gene and processes for expressing nucleic acids of interest in transgenic plants under the control of the soybean ubiquitin promoter pare described. Higher expression levels of the nucleic acids are achieved when the promoter is included.

Abstract: The present invention provides molecular constructs and methods for use thereof, including constructs including heterologous miRNA recognition sites, constructs for gene suppression including a gene suppression element embedded within an intron flanked on one or on both sides by non-protein-coding sequence, constructs containing engineered miRNA or miRNA precursors, and constructs for suppression of production of mature microRNA in a cell. Also provided are transgenic plant cells, plants, and seeds containing such constructs, and methods for their use. The invention further provides transgenic plant cells, plants, and seeds containing recombinant DNA for the ligand-controlled expression of a target sequence, which may be endogenous or exogenous. Also disclosed are novel miRNAs and miRNA precursors from crop plants including maize and soy.

Abstract: Various embodiments are directed to transgenic plants, including transgenic tobacco plants and derivative seeds, genetically modified to impede the transport of Cadmium (Cd) from the root system to aerial portions of transgenic plants by reducing the expression levels of HMA-related transporters. Various embodiments are directed to transgenic tobacco plants genetically modified to stably express a RNAi construct encoding RNAi polynucleotides that enable the degradation of endogenous NtHMA RNA variants. Reduced expression of NtHMA transporters in transgenic plants results in substantially reduced content of Cadmium (Cd) in the leaf lamina. Various consumable products that are substantially free or substantially reduced in Cd content can be produced by incorporating leaves derived from transgenic tobacco plants modified to reduce the expression of NtHMA transporters.

Abstract: Embodiments of the present invention relate generally to new bioenergy crops and methods of creating new bioenergy crops. For example, genes encoding microRNAs (miRNAs) are used to create transgenic crops. In some embodiments, over-expression of miRNA is used to produce transgenic perennials, such as trees, with altered lignin content or composition. In some embodiments, the transgenic perennials are Populus spp. In some embodiments, the miRNA is a member of the miR156 family. In some embodiments, the gene is Zea mays Cg1.

Abstract: Methods and compositions are provided which employ a silencing element that, when ingested by a pest, are capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant. Target polynucleotides for specific protein classes and target polynucleotides set forth in SEQ ID NOS:1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or active variants or fragments thereof are provided, wherein a decrease in expression of one or more sequences in the target pest controls the pest. Further provided are silencing elements which when ingested by the pest decrease the level of the target polypeptide and thereby control the pest. Plants, plant part, bacteria and host cells comprising the silencing elements or an active variant or fragment thereof are also provided.

Abstract: The invention relates to a method of generating or increasing a pathogen resistance in plants by reducing the expression of at least one Armadillo repeat polypeptide or a functional equivalent thereof. The invention relates to novel nucleic acid sequences coding for a Hordeum vulgare Armadillo repeat (HvARM) polynucleotide and describes homologous sequences (ARM1) thereof, and to their use in methods for obtaining a pathogen resistance in plants e, and to nucleic acid constructs, expression cassettes and vectors which comprise these sequences and which are suitable for mediating a fungal resistance in plants. The invention furthermore relates to transgenic organisms, in particular plants, which are transformed with these expression cassettes or vectors, and to cultures, parts or transgenic propagation material derived therefrom.

Abstract: The present invention is directed to compositions and methods for altering the levels of seed proteins in cereal grain. The invention is directed to the alteration of seed protein levels in plant grain, resulting in grain with increased digestibility/nutrient availability, improved amino acid composition/nutritional value, increased response to feed processing, improved silage quality, and increased efficiency of wet milling.

Abstract: A eukaryotic input circuit: computationally designed receptors, synthetic eukaryotic signal transduction pathways, and a synthetic signal sensitive promoter that allow highly specific transcriptional induction in response to an externally provided ligand is disclosed. The input circuit is able to specifically bind a targeted substance and transmit a signal to the nucleus where transcription of a gene is activated. An output circuit serves as a simple readout system of the substance detected by the input circuit. The readout circuit exemplified here is a degreening circuit which causes plants to turn white. Activation of the degreening circuit can be detected by eye, or remotely with a variety of machines (hand-held, aircraft or satellite based) and is also resettable. When linked the input circuit if operably linked to the output circuit, produces a functional plant detector.

Abstract: Methods of, and compositions for, assembling one or more transcription units in a genome without a linked selectable marker or other unwanted transcription unit are provided. Also provided methods of, and compositions for, assembling one or more transcription units in a genome with a reduced frequency of vector backbone.

Abstract: The invention provides methods for modifying lignin content and composition in plants and achieving associated benefits therefrom involving altered expression of newly discovered MYB4 transcription factors. Nucleic acid constructs for modifying MYB4 transcription factor expression are described. By over-expressing the identified MYB4 transcription factors, for example, an accompanying decrease in lignin content may be achieved. Plants are provided by the invention comprising such modifications, as are methods for their preparation and use.

Abstract: This invention provides methods for producing a non-natural hybrid seed. Also disclosed are specific miRNAs and miRNA recognition sites useful for conferring inducible sterility on a crop plant, and recombinant DNA construct including such exogenous miRNA recognition sites.

Abstract: The present invention relates to methods for increasing digestibility and/or crude protein of a plant by modifying lignin biosynthesis of the plant. The methods involve the manipulation of the expression level of genes in the lignin biosynthesis pathway by directly reducing the expression of genes using miRNA or using regulation of transcription factors. Expression cassettes for achieving such gene expression manipulation and transgenic plant cells and plants comprising the constructs and cassettes are also provided. Transcription regulating nucleotide sequences for use in the expression cassettes have also been developed as well as methods of using these sequences and cassettes.

Abstract: A DNA polynucleotide is described herein having a modified sequence of a target gene, wherein any one type of nucleotide in the target gene sequence has been chemically modified to another type of nucleotide; and a complementary sequence of the unmodified target gene; wherein either one of the modified sequence or the complementary sequence is in a reverse orientation to the other sequence; and wherein the RNA sequence transcribed from the DNA polynucleotide forms a duplex between the modified sequence and the complementary sequence so that a long double stranded RNA (IdsRNA) duplex forms between the modified and complementary sequences with base pair mismatches where the nucleotides have been modified, the IdsRNA duplex being capable of inhibiting expression of the target gene. RNA polynucleotides and IdsRNA duplexes transcribed by the DNA polynucleotide are also described, as is a method for producing the IdsRNA duplexes. These IdsRNA duplexes can be used in gene silencing.

Abstract: The present disclosure concerns methods and compositions relating to UXS polypeptides and/or nucleic acids encoding UXS polypeptides. In certain claims, the methods and compositions are of use to improve digestibility and/or ease of grain processing. Such improvements relate to a modulation in arabinoxylan and/or hemicellulose content in transgenic plants. Such plants can, for example, comprise one or more nucleic acid sequences that inhibit expression of one or more UDP-Xylose Synthase (UXS) genes.

Abstract: The invention provides an enzyme having a lignan-hydroxylating activity, particularly an enzyme capable of catalyzing the reaction of transferring a hydroxyl group to a lignan, an enzyme capable of catalyzing the hydroxylation of piperitol to 9-hydroxylpiperitol or pinoresinol to 9-hydroxylpinoresinol. The invention provides a polypeptide having a lignan-hydroxylating activity; a polynucleotide encoding the same; a vector or transformant comprising the polynucleotide; a method for producing a polypeptide having a lignan-hydroxylating activity which comprises using the transformant; and so on. The transformant wherein the polynucleotide is expressibly introduced is useful for the hydroxylation of a lignan or for the production of a product using the same in the food sector and a variety of industry sectors.

Abstract: The present invention is directed to compositions and methods for altering the levels of seed proteins in cereal grain. The invention is directed to the alteration of seed protein levels in plant grain, resulting in grain with increased digestibility/nutrient availability, improved amino acid composition/nutritional value, increased response to feed processing, improved silage quality, and increased efficiency of wet milling.

Abstract: The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: Polynucleotides encoding polypeptides that comprise the biosynthetic pathway for phenylpropanoids and flavonoids in the coffee plant are disclosed. Also disclosed are methods for using these polynucleotides and polypeptides for the manipulation of flavor, aroma, and other features of coffee beans, as well as the manipulation resistance to pathogen, herbivore, and insect attack in the coffee plant.

Abstract: Isolated nucleic acid fragments comprising precursor miRNA, and artificial miRNAs and their use in down-regulating gene expression are described.

Abstract: The present invention relates to a method for identifying and isolating native plant nucleic acid sequences that may function as T-DNAs or T-DNA border-like sequences, effecting the transfer of one polynucleotide into another polynucleotide. The present invention also provides a modified tuber, such as a genetically modified mature tuber, that comprises at least one trait that is not exhibited by a non-modified tuber of the same species.

Abstract: The present invention provides compositions and methods for modulating flowering time in plants. Maize RAP2.7 nucleotide sequences are disclosed which upon overexpression cause later flowering and when inhibited cause earlier flowering. Also disclosed is a DNA sequence which acts as a regulator/enhancer of RAP2.7, termed VGT1. This sequence does not code for any known protein, but acts as either a RNAi element or a regulatory DNA or RNA element that either directly regulates expression of flowering genes such as Rap2.7 or specifically targets expression of other genes which control flowering genes such as Rap2.7. This element this can be used as a sequence—based marker to identify inbred and hybrids which have altered maturity. Methods for expressing these nucleotide sequences in a plant for modifying maturity and flowering in plants are provided as well as expression constructs, vectors, transformed cells and plants.

Abstract: Polynucleotides encoding polypeptides that comprise the biosynthetic pathway for carotenoids and apocarotenoids in the coffee plant are disclosed. Also disclosed are a promoter sequence from a coffee carotenoid gene, and methods for using these polynucleotides, polypeptides, and promoter sequences for gene regulation and the manipulation of flavor, aroma, and other features of coffee beans, as well as the manipulation of photosynthesis in the coffee plant.

Abstract: The present invention relates to a new plant breeding process. The process improves the agronomic performance of crop plants by using genetic material that is also used in classical breeding. Instead of sexually recombining entire genomes at random, as is done in classical breeding, specific genetic elements are rearranged in vitro and inserted back into individual plant cells. Plants obtained through this new plant breeding process do not contain foreign nucleic acid but only contain nucleic acid from the plant species selected for transformation or plants that are sexually compatible with the selected plant species. Plants developed through this new plant breeding process are provided. In particular, potato plants displaying improved tuber storage and health characteristics are provided.

Abstract: A method for efficiently producing homozygous organisms from a heterozygous non-human starting organism, comprising providing of a heterozygous starting organism; allowing the starting organism to produce haploid cells; creating homozygous organisms from the haploid cells thus obtained; and selecting the organisms having the desired set of chromosomes, wherein during production of the haploid cells no recombination occurs in order to obtain a limited number of genetically different haploid cells. Recombination can also be prevented or suppressed.

Abstract: Naturally occurring and synthetic novel stress-related miRNAs are provided which can be used to modify the stress tolerance of plants.

Abstract: Regulatory regions suitable for directing the expression of a heterologous polynucleotide under light conditions in which the red/far red ratio is less than 1 are described, as well as nucleic acid constructs that include these regulatory regions. Also disclosed are transgenic plants that contain such constructs and methods of producing such transgenic plants.

Abstract: The present invention provides molecular constructs and methods for use thereof, including constructs including heterologous miRNA recognition sites, constructs for gene suppression including a gene suppression element embedded within an intron flanked on one or on both sides by non-protein-coding sequence, constructs containing engineered miRNA or miRNA precursors, and constructs for suppression of production of mature microRNA in a cell. Also provided are transgenic plant cells, plants, and seeds containing such constructs, and methods for their use. The invention further provides transgenic plant cells, plants, and seeds containing recombinant DNA for the ligand-controlled expression of a target sequence, which may be endogenous or exogenous. Also disclosed are novel miRNAs and miRNA precursors from crop plants including maize and soy.

Abstract: The present invention relates to a method for producing syringyl lignin in gymnosperms. The production of syringyl lignin in gymnosperms is accomplished by genetically transforming a gymnosperm genome, which does not normally contain genes which code for enzymes necessary for production of syringyl lignin, with DNA which codes for enzymes found in angiosperms associated with production of syringyl lignin. The expression of the inserted DNA is mediated using host promoter regions in the gymnosperm.

Abstract: Methods and compositions for transforming plants to express polynucleotides capable of gene silencing gene expression in pathogens of beneficial insets such as IAPV, Nosema species and Varroa mites, and methods for using the transgenic plants for reducing infection and susceptibility of bees to Colony Collapse Disorder are provided.

Abstract: The invention provides methods and compositions useful in target sequence suppression and target sequence validation. The invention provides polynucleotide constructs useful for gene silencing, as well as cells, plants and seeds comprising the polynucleotides. The invention also provides a method for using microRNA to silence a target sequence.

Abstract: The present invention relates to a new plant breeding process. The process improves the agronomic performance of crop plants by using genetic material that is also used in classical breeding. Instead of sexually recombining entire genomes at random, as is done in classical breeding, specific genetic elements are rearranged in vitro and inserted back into individual plant cells. Plants obtained through this new plant breeding process do not contain foreign nucleic acid but only contain nucleic acid from the plant species selected for transformation or plants that are sexually compatible with the selected plant species. Plants developed through this new plant breeding process are provided. In particular, potato plants displaying improved tuber storage and health characteristics are provided.

Abstract: The present invention relates to p450 enzymes and nucleic acid sequences encoding p450 enzymes in Nicotiana, and methods of using those enzymes and nucleic acid sequences to alter plant phenotypes.

Abstract: Rice having reduced levels of starch branching enzymes produce grain having a high relative amylose content in the endosperm. The rice grain of this invention can be of a non-shrunken phenotype despite a lesion in the amylopectin synthesis pathway and may be transgenic or nontransgenic.

Abstract: The present invention provides compositions and methods for modulating flowering time in plants. Maize RAP2.7 nucleotide sequences are disclosed which upon overexpression cause later flowering and when inhibited cause earlier flowering. Also disclosed is a DNA sequence which acts as a regulator/enhancer of RAP2.7, termed VGT1. This sequence does not code for any known protein, but acts as either a RNAi element or a regulatory DNA or RNA element that either directly regulates expression of flowering genes such as Rap2.7 or specifically targets expression of other genes which control flowering genes such as Rap2.7. This element this can be used as a sequence-based marker to identify inbred and hybrids which have altered maturity. Methods for expressing these nucleotide sequences in a plant for modifying maturity and flowering in plants are provided as well as expression constructs, vectors, transformed cells and plants.