The present disclosure relates to methods of screening for gain of function mutations in non-coding regions of target genes. The target genes may be NPQ genes, including photosystem II subunit S (PsbS), zeaxanthin epoxidase (ZEP), and violaxanthin de-epoxidase (VDE). The present disclosure further relates to methods of improving commercial crop plants or crop seeds by introducing gain of function mutations in non-coding regions of target genes, and to improved commercial crop plants or crop seeds produced by the methods.

The disclosure relates to gene edited wheat plants, seeds, and compositions, as well as improvements to wheat plant breeding and methods for creating modifications in wheat plant genomes.

The disclosure provides a method of expressing an agronomically beneficial trait in a plant plastid comprising expressing an exogenous nucleic acid in the plant to produce non-photosynthetic mutant plants, and using callus grown from the mutant plants as recipients for introduction of a construct having a functional copy of the mutated gene and a gene conferring an agronomically beneficial trait. Embodiments provide for mutations in chloroplast-encoded genes, as well as mutations in nuclear-encoded genes targeted to the chloroplast that are required for photosynthesis. The disclosure also provides plants and plant parts produced from such methods, as well as kits for performing the methods as described.

Certain embodiments provide a polypeptide comprising a chloroplast-targeting amino acid sequence linked to an amino acid sequence that is capable of electrostatically binding to a nucleic acid molecule, as well as conjugates comprising such polypeptides and methods of use thereof.

Vascular sheath tissue-specific expression of phytochrome B or variants thereof in C3 plants increases photosynthesis rate and/or introduces a carbon refixation mechanism. The heritable genetic material of a C.sub.3 plant cell is altered such that one copy of phytochrome B, or active variant or functional fragment thereof is expressed specifically in vascular sheath cells. Whole plants are regenerated from these genetically altered plant cells. Alternatively, a Crispr modification of a native phytochrome locus in a plant cell is used to insert a vascular sheath-specific regulatory element, e.g. promoter or enhancer element, so that phytochrome B is expressed in vascular sheath cells of a regenerated whole plant. Genetically altered whole plants have increased yield-related traits, e.g. increased seed yield, resulting from the enhancement of photosynthesis and/or introduction of a carbon refixation mechanism.

Provided are methods of increasing nitrogen use efficiency, fertilizer use efficiency, yield, growth rate, vigor, biomass, oil content and/or abiotic stress tolerance of a plant by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: 2560, 2557, 184, 238, 188, 154-156, 158-161, 163-183, 185-187, 189-197, 200-237, 239-264, 266-269, 1351, 1365-1425, 1429-1457, 1459, 1461-1730, 1735, 1739-2397, 2533-2541, 2544-2556, 2558, 2559, 2561-2562 or 2563. Also provided are isolated polynucleotides and polypeptides which can be used to increase nitrogen use efficiency, fertilizer use efficiency, yield, growth rate, vigor, biomass, oil content and/or abiotic stress tolerance of a plant of a plant.

Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NO: 474-643, 645-679, 681-755, 757-760, 4806-6390, 6395-6396, 6401-6895, 6897-7249, 7251-7685, 7687-7693, 7695-7700, 7702-7708, 7710-7796, 7798-7816, 7818, 7820-7837, 7839-7840, 7842-7861, 7863-8134, 8136-8163 or 8164, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-170, 172-267, 269-424, 426-473, 761-2486, 2489-2494, 2496-4803 or 4804, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, harvest index, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

Provided are isolated polypeptides which are at least 80% homologous to SEQ ID NO: 474-643, 645-679, 681-755, 757-760, 4806-6390, 6395-6396, 6401-6895, 6897-7249, 7251-7685, 7687-7693, 7695-7700, 7702-7708, 7710-7796, 7798-7816, 7818, 7820-7837, 7839-7840, 7842-7861, 7863-8134, 8136-8163 or 8164, isolated polynucleotides which are at least 80% identical to SEQ ID NOs: 1-170, 172-267, 269-424, 426-473, 761-2486, 2489-2494, 2496-4803 or 4804, nucleic acid constructs comprising same, transgenic cells expressing same, transgenic plants expressing same and method of using same for increasing yield, harvest index, abiotic stress tolerance, growth rate, biomass, vigor, oil content, photosynthetic capacity, seed yield, fiber yield, fiber quality, fiber length, and/or nitrogen use efficiency of a plant.

The present invention relates to transgenic plants, or parts thereof, with modified traits, as well as methods of selecting and using these plants or parts. In particular, the present invention relates to a transgenic plant, or part thereof, comprising a first exogenous polynucleotide which encodes a transcription factor polypeptide that increases the expression of one or more glycolytic and/or fatty acid biosynthetic genes in the plant or part thereof, and a second exogenous polynucleotide which encodes a polypeptide involved in the biosynthesis of one or more non-polar lipids. Furthermore, in addition to an increased triacylglycerol (TAG) content relative to a corresponding wild-type plant or part thereof, the plant or part thereof have a modified phenotype selected from; an increased soluble protein content, an increased nitrogen content, a decreased carbon:nitrogen ratio, increased photosynthetic gene expression, increased photosynthetic capacity, decreased total dietary fibre (TDF) content, increased carbon content and an increased energy content.

Provided are heterologous nucleic acid constructs, vectors and methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.