This invention relates to compositions and methods for modifying CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLV3/ESR-RELATED) (CLE) genes in plants to increase increased kernel row number, optionally without substantially decreasing the length of the ears. The invention further relates to plants having increased kernel row number, optionally without substantially decreasing the length of the ears, produced using the methods and compositions of the invention.

The disclosure provides methods of making gene-edited plants that are resistant to downy mildew, such as plants with reduced expression of homoserine kinase (HSK), 2-oxoglutarate-Fe(II) oxygenase (2OGO), or both. The disclosure further provides methods of making gene-edited modified plants that are cold tolerant, such as plants with reduced expression of MYB14. In some examples, CRISPR/Cas methods are used, wherein the plants include a mutated HSK, 2OGO, and/or MYB14 gene resulting in reduced expression and/or gene activity. Plants generated using the methods are provided. Such plants can include other desirable traits. HSK, 2OGO, and/or MYB14 nucleic acid and protein molecules are provided, as are gRNAs specific for HSK, 2OGO, or MYB14 and vectors containing such.

Provided are compositions comprising polynucleotides and polypeptides for the improvement of agronomic traits in plants, in particular maize plants. Also provided are recombinant DNA constructs, plants, plant cells, seed, grain comprising the polynucleotides and/or polypeptides. Additionally, various methods of employing the polynucleotides and genetic modifications in plants, such as methods for increasing yield of a plant are also provided herein.

Provided herein are compositions and methods for modifying a predetermined nucleic acid sequence. A programmable nucleoprotein molecular complex containing a polypeptide moiety and a specificity conferring nucleic acid (SCNA) which assembles in-vivo, in a target cell, and is capable of interacting with the predetermined target nucleic acid sequence is provided. The programmable nucleoprotein molecular complex is capable of specifically modifying and/or editing a target site within the target nucleic acid sequence and/or modifying the function of the target nucleic acid sequence.

Provided herein are systems, methods, and compositions for the modification of target DNA sequences. More particularly, systems, methods, and compositions for cleaving a target DNA in eukaryotic cells with a guide RNA capable of hybridizing with a target sequence and an RNA-guided DNA nuclease are provided. Also provided are vectors and vector systems which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods for identifying and validating novel CRISPR systems.

The invention discloses a method for improving rice yield and a protein used thereof. The invention provides a method for cultivating the target rice, comprising the following steps of inhibiting the activity of RAY1 protein in original rice to obtain target rice; compared with the original rice, the target rice shows higher yield and/or larger grain size and/or stronger resistance to rice blast and/or higher plant height and/or longer stem internode length; the RAY1 protein is a protein composed of an amino acid sequence shown as SEQ ID No. 1 in a sequence list. The invention uses CRISPR/Cas9 technology to realize site-directed editing rice RAY1 gene, through knocking out rice RAY1 gene by frameshift mutation, the protein RAY1 is inactivated, and a new generation of rice germplasm with significantly improved yield is obtained.

Methods and systems for delivering biological materials such as nucleic acids and/or proteins to the interior of a plant cell are provided. Such methods and systems include those where biological material is non-covalently complexed with a magnetic particle and accelerated multiple times toward a plant cell.

The disclosure relates to methods of producing genome edited plant cells, genome edited plant calli, and genome edited plants with genome edits at multiple genomic sites. The disclosure also relates to systems and kits for producing genome edited plant cells with genome edits at multiple genomic sites. Disclosed methods include those where a guide RNA (gRNA) directed to a first genomic DNA site, a donor DNA template polynucleotide, and a polynucleotide comprising a DNA molecule encoding a second gRNA directed to a second genomic DNA site are introduced into a plant cell and genome edited cell having an insertion of the donor DNA template polynucleotide or fragment thereof in the first genomic DNA site and a DNA modification at the second genomic DNA site is selected.

The disclosure relates to methods of producing genome edited plant cells, genome edited plant calli, as well as genome edited plants. The methods comprise first introducing into a plant cell the polypeptide element(s) of a genome-editing system and, subsequently, introducing the polynucleotide element(s) of the genome-editing system into a plant cell that is already expressing the polypeptide element(s).

Provided herein include methods and compositions for making targeted changes to a DNA sequence. In various aspects and embodiments, methods and compositions for modifying a DNA sequence in a cell (such as a plant, bacterial, yeast, fungal, algal, or mammalian cell) are provided. In some aspects and embodiments the modification of DNA involves combining gene repair oligonucleotides with approaches that enhance the availability of components of the target cell gene repair mechanisms, such as a DNA cutter.