A method for editing a plant genome includes coating a microparticle with at least one type of nucleic acid and/or at least one type of protein, introducing a deletion, insertion, or substitution into a target site in the genome of a plant by bombarding a shoot apex of the plant with the coated microparticle using a gene gun, growing the shoot apex bombarded with the coated microparticle to obtain a plant body, and selecting a genome-edited plant body from the plant body. The shoot apex of the plant is selected from the group consisting of a shoot apex of an embryo of a fully mature seed, a shoot apex of a young bud of a tuber, and a shoot apex of a terminal bud or a lateral bud.

Provided is a tobacco plant which is suitable for cultivation for harvesting leaf tobaccos. The present invention encompasses (i) a tobacco plant into which a mutation for suppressing the development of primary axillary buds is introduced, (ii) a method of obtaining the tobacco plant, (iii) a harvest from the tobacco plant, and (iv) a processed product of the harvest.

This invention relates to CRISPR-Cas nucleases codon optimized for expression in plants and nucleic acid constructs encoding base editors comprising a CRISPR-Cas nuclease and a deaminase domain, wherein the nucleic acid constructs are optimized for expression in a plant. The invention further relates to methods of modifying nucleic acids using the nucleic acid constructs.

Methods and compositions for plastid transformation and regeneration or development of transplastomic plants are provided. Embryo explants may be excised from seeds, and their meristematic tissue may be transformed directly without initiation of any callus phase before and/or after transformation. The present methods may be performed with fewer culturing steps relative to conventional methods, thereby enabling more rapid and efficient production of targeted transplastomic events in plants.

The present disclosure provides shatterproof (SHP) genes and plants and/or plant cells bearing one or more mutations in a shatterproof gene; as well as methods of making and using such plants. In some embodiments the plant or plant cell is resistant to preharvest dehiscence.

Compositions and methods are provided for the excision and replacement of an endogenous polynucleotide, such as a gene, using CRISPR-Cas systems. In some aspects, the gene is flanked by specific nucleotides that are targets of homology-directed repair, for the insertion of a replacement polynucleotide.

Compositions and methods are provided for agronomic trait modification of a target sequence in the genome of a plant or plant cell. The methods and compositions employ a guide RNA/Cas endonuclease system to provide an effective system for modifying or altering target sites within a genomic region of a plant, plant cell or seed to provide improvement in a desirable agronomic trait such as drought, yield, and stress tolerance. Breeding methods for selecting plants utilizing a two component RNA guide and Cas endonuclease system are also disclosed. Compositions and methods are also provided for editing a nucleotide sequence in the genome of a cell.

Methods are provided for genome editing. On example method includes editing a genome sequence of an organism with multiple edits simultaneously without precise knowledge of a phenotypic effect of each individual one of the multiple edits, wherein the multiple edits are selected based on a prediction of an aggregate phenotypic effect of the multiple edits on a phenotypic trait. The method also includes aggregating the multiple edits into multi-dimensional pools, whereby phenotypic effects of contrasting pools of edits are compared to ascertain which of the multiple edits are most likely to be causing large phenotypic effects while eliminating need to evaluate each edit separately. The organism may include one of: maize, soybean, wheat, sorghum, rice, cotton, rapeseed, sunflower, bean, tomato, squash, cucumber, melon, pepper, watermelon, eggplant, okra, pea, chickpea, lentil, peanut, onion, carrot, celery, beet, cauliflower, broccoli, cabbage, Brussels sprout, radish, black-eyed pea, potato, sweet-potato, sugar cane, cassava, and banana.

The present disclosure provides a viral-mediated genome-editing platform that facilitates multiplexing, obviates stable transformation, and is applicable across plant species. The RNA2 genome of the tobacco rattle virus (TRV) was engineered to carry and systemically deliver a guide RNA molecules into plants overexpressing Cas9 endonuclease. High genomic modification frequencies were observed in inoculated as well as systemic leaves including the plant growing points. This system facilitates multiplexing and can lead to germinal transmission of the genomic modifications in the progeny, thereby obviating the requirements of repeated transformations and tissue culture. The editing platform of the disclosure is useful in plant genome engineering and applicable across plant species amenable to viral infections for agricultural biotechnology applications.

Transgenic INIR12 maize plants comprising a vip3Aa19 or vip3Aa20 expression cassette linked to a secondary nopaline synthase terminator element which lack a selectable marker gene and/or which comprise modifications that provide for facile excision of the INIR12 transgenic locus from the maize plant genome are provided. Genomic DNA of INIR12 transgenic plants, detection of INIR12 plants and products thereof, methods of making INIR12 plants, and use of INIR12 plants to facilitate breeding are disclosed.