Abstract: Disclosed herein are compositions and methods for effecting alterations at a defined location in the genome of a plant cell or plant protoplast. Further disclosed are methods using an RNA-guided nuclease to alter a target nucleotide sequence in a cell or protoplast of a plant; embodiments of such methods include treatments with chemical or physical reagents or treatment of the cell or protoplast with a specific thermal regime, such as a heat treatment.

Abstract: A genetically engineered land plant that expresses a plant CCP1-like mitochondrial transporter protein is provided. The genetically engineered land plant comprises a modified gene for the plant CCP1-like mitochondrial transporter protein. The plant CCP1-like mitochondrial transporter protein is an ortholog of CCP1 of Chlamydomonas reinhardtii of SEQ ID NO: 1 derived from a source land plant. The plant CCP1-like mitochondrial transporter protein is localized to mitochondria of the genetically engineered land plant based on a mitochondrial targeting signal intrinsic to the plant CCP1-like mitochondrial transporter protein. The modified gene comprises (i) a promoter and (ii) a nucleic acid sequence encoding the plant CCP1-like mitochondrial transporter protein. The promoter is non-cognate with respect to the nucleic acid sequence.

Abstract: Plant cell cultures as well as related methods, systems, and compositions for increasing the frequency and efficiency of plant genome editing are provided. Various plant cell growth conditions and/or treatments where such increases in gene editing frequencies are obtained are disclosed.

Abstract: A genetically engineered plant that expresses a 6-phosphogluconate dehydratase (EDD) and/or a 2-keto-3-deoxy-6-phosphogluconate aldolase (EDA) is provided. The plant comprises at least one of a first or second modified gene. The first modified gene comprises a first promoter and a nucleic acid sequence encoding the EDD. The first promoter is non-cognate with respect to the nucleic acid sequence encoding the EDD. The first modified gene is configured so transcription of the nucleic acid sequence encoding the EDD is initiated from the first promoter and results in expression of the EDD. The second modified gene comprises a second promoter and a nucleic acid sequence encoding the EDA. The second promoter is non-cognate with respect to the nucleic acid sequence encoding the EDA. The second modified gene is configured so transcription of the nucleic acid sequence encoding the EDA is initiated from the second promoter and results in expression of the EDA.

Abstract: A modified plant is provided. The modified plant includes a polynucleotide including a promoter operably linked to a coding sequence. The coding sequence encodes a transcription factor that has at least 30% sequence identity to one or more of SEQ ID NOs: 27, 204, 10, 19, 1-9, 11-18, 20-26, 28-203, 205, 237, or 242-310. The promoter is non-cognate with respect to the coding sequence. Also provided is a method for producing a modified plant having increased seed yield and/or oil content in comparison to a reference plant by transformation. Also provided is a method for producing a modified plant having increased seed yield and/or oil content in comparison to a reference plant by editing.

Abstract: A transgenic land plant that expresses a polyhydroxy alkanoate synthase seed specifically, with cytosolic localization is disclosed. The plant includes a nucleic acid encoding the polyhydroxy alkanoate synthase and a seed-specific promoter operably linked to the nucleic acid. The seed-specific promoter drives expression of the polyhydroxy alkanoate synthase in cytosol of cells of seeds of the plant. The polyhydroxy alkanoate synthase includes a catalytic domain. The polyhydroxy alkanoate synthase does not include any sequence positioned to mediate translocation of the catalytic domain across any membrane of the cells, thereby resulting in the polyhydroxy alkanoate synthase being expressed seed specifically, with cytosolic localization.

Abstract: Plant cell cultures as well as related methods, systems, and compositions for increasing the frequency and efficiency of plant genome editing are provided. Various plant cell growth conditions and/or treatments where such increases in gene editing frequencies are obtained are disclosed.

Abstract: A genetically engineered land plant that expresses a protein that has homology to a plant invertase inhibitor and/or a pectin methylesterase inhibitor and that increases seed yield with increased expression (“an ISY protein”) is disclosed. The plant comprises a modified gene for the ISY protein. The ISY protein comprises one or more of an ISY protein of Camelina sativa comprising SEQ ID NO: 2 or a fragment, Camelina sativa homolog, or ortholog thereof. The modified gene comprises a promoter and a nucleic acid sequence encoding the ISY protein. The promoter is non-cognate with respect to the nucleic acid sequence encoding the ISY protein. The modified gene is configured such that transcription of the nucleic acid sequence is initiated from the promoter and results in expression of the ISY protein. A genetically engineered land plant that expresses an RNA that increases seed yield with increased expression also is disclosed.

Abstract: Plant cell cultures as well as related methods, systems, and compositions for increasing the frequency and efficiency of plant genome editing are provided. Various plant cell growth conditions and/or treatments where such increases in gene editing frequencies are obtained are disclosed.

Abstract: Genetically engineered plants that express a quinone-utilizing malate dehydrogenase (MQO) are provided. The plant comprises a modified gene for the quinone-utilizing malate dehydrogenase. The modified gene comprises (i) a promoter and (ii) a nucleic acid sequence encoding the quinone-utilizing malate dehydrogenase. The promoter is non-cognate with respect to the nucleic acid sequence encoding the quinone-utilizing malate dehydrogenase. The modified gene is configured such that transcription of the nucleic acid sequence is initiated from the promoter and results in expression of the quinone-utilizing malate dehydrogenase. The plants can express the quinone-utilizing malate dehydrogenase in mitochondria of cells of the plants. Conversion of malate to oxaloacetate in the mitochondria can be increased, resulting in increased crop performance and/or seed, fruit or tuber yield. Methods and compositions for making the plants also are provided.

Abstract: A genetically engineered land plant that expresses a plant CCP1-like mitochondrial transporter protein is provided. The genetically engineered land plant comprises a modified gene for the plant CCP1-like mitochondrial transporter protein. The plant CCP1-like mitochondrial transporter protein is an ortholog of CCP1 of Chlamydomonas reinhardtii of SEQ ID NO: 1 derived from a source land plant. The plant CCP1-like mitochondrial transporter protein is localized to mitochondria of the genetically engineered land plant based on a mitochondrial targeting signal intrinsic to the plant CCP1-like mitochondrial transporter protein. The modified gene comprises (i) a promoter and (ii) a nucleic acid sequence encoding the plant CCP1-like mitochondrial transporter protein. The promoter is non-cognate with respect to the nucleic acid sequence.

Abstract: A genetically engineered land plant that expresses an LCID/E protein is provided. The plant comprises a modified gene for the LCID/E protein. The LCID/E protein comprises (i) LCD of Chlamydomonas reinhardtii of SEQ ID NO: 4, (ii) LCIE of Chlamydomonas reinhardtii of SEQ ID NO: 5, or (iii) an algal or plant ortholog of LCID/E. The LCID/E protein is localized to chloroplasts of the plant based on a plastidial targeting signal. The modified gene for the LCID/E protein comprises (i) a promoter and (ii) a nucleic acid sequence encoding the LCID/E protein. The promoter is non-cognate with respect to the nucleic acid sequence encoding the LCID/E protein. The modified gene for the LCID/E protein is configured such that transcription of the nucleic acid sequence is initiated from the promoter and results in expression of the LCID/E protein. Optionally, the plant also expresses a CCP1 mitochondrial transporter protein and/or pyruvate carboxylase.

Abstract: A land plant is disclosed. The land plant has increased expression of a mitochondrial transporter protein such that the flux of metabolites through the mitochondrial membrane is increased and the land plant has higher performance and/or yield as compared to a reference land plant not having the increased expression of the mitochondrial transporter protein. Another land plant also is disclosed. The land plant has increased expression of a plastidial dicarboxylate transporter protein such that the flux of metabolites through the plastidial membrane is increased and the land plant has higher performance and/or yield as compared to a reference land plant not having the increased expression of the plastidial dicarboxylate transporter protein.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently produce alkanes, and in particular the use of such organisms for the commercial production of alkanes and related molecules. Other materials, methods, and compositions are also described.

Abstract: The present disclosure identifies pathways and mechanisms to confer production of carbon-based products of interest such as ethanol, ethylene, chemicals, polymers, n-alkanes, isoprenoids, pharmaceutical products or intermediates thereof in photoautotrophic organisms such that these organisms efficiently convert carbon dioxide and light into carbon-based products of interest, and in particular the use of such organisms for the commercial production of ethanol, ethylene, chemicals, polymers, n-alkanes, isoprenoids, pharmaceutical products or intermediates thereof.

Abstract: The present disclosure identifies pathways and mechanisms to confer photoautotrophic properties to a heterotrophic organism. The resultant engineered cell or organism will uniquely enable efficient conversion of carbon dioxide and light into biomass and carbon-based products of interest.

Abstract: The present disclosure identifies pathways and mechanisms to confer production of carbon-based products of interest such as ethanol, ethylene, chemicals, polymers, n-alkanes, isoprenoids, pharmaceutical products or intermediates thereof in photoautotrophic organisms such that these organisms efficiently convert carbon dioxide and light into carbon-based products of interest, and in particular the use of such organisms for the commercial production of ethanol, ethylene, chemicals, polymers, n-alkanes, isoprenoids, pharmaceutical products or intermediates thereof.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently produce alkanes, and in particular the use of such organisms for the commercial production of alkanes and related molecules. Other materials, methods, and compositions are also described.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently produce alkanes, and in particular the use of such organisms for the commercial production of alkanes and related molecules. Other materials, methods, and compositions are also described.

Abstract: The present disclosure identifies methods and compositions for modifying photoautotrophic organisms as hosts, such that the organisms efficiently produce alkanes, and in particular the use of such organisms for the commercial production of alkanes and related molecules. Other materials, methods, and compositions are also described.