Abstract: Compositions and methods are provided for genome 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 the genome of a plant, plant cell or seed. Also provided are compositions and methods employing a guide polynucleotide/Cas endonuclease system for genome modification of a nucleotide sequence in the genome of a cell or organism, for gene editing, and/or for inserting or deleting a polynucleotide of interest into or from the genome of a cell or organism. Once a genomic target site is identified, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest. Breeding methods and methods for selecting plants utilizing a two component RNA guide and Cas endonuclease system are also disclosed.

Abstract: Compositions and methods are provided for genome modification of a target sequence in the genome of a cell, using a novel Cas endonuclease. The methods and compositions employ a guide polynucleotide/endonuclease system to provide an effective system for modifying or altering target sequences within the genome of a cell or organism. Also provided are novel effectors and endonuclease systems and elements comprising such systems, such as guide polynucleotide/endonuclease systems comprising an endonuclease. Compositions and methods are also provided for guide polynucleotide/endonuclease systems comprising at least one endonuclease, optionally covalently or non-covalently linked to, or assembled with, at least one additional protein subunit, and for compositions and methods for direct delivery of endonucleases as ribonucleotide proteins.

Abstract: Methods and compositions are provided for the improvement of double-strand-break-inducing agent activity in eukaryotic cells, through the usage of one or more morphogenic factors or developmental genes. The morphogenic factor may be provided to the same cell or to a different cell than that comprising or receiving the double-strand-break-inducing agent. The morphogenic factor may be provided to a cell as a polynucleotide composition on a recombinant vector, and may be placed on the vector outside of a T-DNA border. The morphogenic factor may be provided via an upregulation of an endogenous gene. The morphogenic factor, or the double-strand-break-inducing agent, may further comprise a cell penetrating peptide. The morphogenic factor may be co-introduced with a vector comprising RepA.

Abstract: Compositions and methods are provided for large scale manipulation of genomic regions and chromosomal engineering of plant genomes that include paracentric inversions, rearrangement of pericentromeric chromosomal segments, chromosomal translocations and inversions thereof. These advanced breeding techniques provide enhanced genetic diversity within existing breeding population and increase genetic gain. Wild or outcrosses between two different crop species that can be crossed are also within scope of the disclosure. Site-specific genome manipulation tools such as CRISPR-Cas systems enable targeted chromosomal engineering of crop plants, including stable, inheritable, large-scale centromeric inversions.

Abstract: Compositions and methods are provided for novel Cas9 orthologs, including, but not limiting to, novel guide polynucleotide/Cas9 endonucleases complexes, single or dual guide RNAs, guide RNA elements, and Cas9 endonucleases. The present disclosure also describes methods for creating a double strand break in a target polynucleotide, methods for genome modification of a target sequence under various in vivo and in vitro conditions, in the genome of a cell, for gene editing, and for inserting a polynucleotide of interest into the genome of a cell. Also provided are nucleic acid constructs and cells having a modified target site or altered polynucleotide of interest produced by the methods described herein.

Abstract: Novel engineered non-natural deaminases are provided. Methods and compositions are provided for modifying the genome of a cell, including a plant cell. Genome modification through guided CRISPR polypeptides and multiple deaminases are provided. Engineered non-natural novel deaminases, including adenosine deaminases are provided. These novel deaminases have improved activity in cells including plant cells.

Abstract: Compositions and methods are provided for genome modification of a target sequence in the genome of a cell, using a novel Cas endonuclease. The methods and compositions employ a guide polynucleotide/endonuclease system to provide an effective system for modifying or altering target sequences within the genome of a cell or organism. Also provided are novel effectors and endonuclease systems and elements comprising such systems, such as guide polynucleotide/endonuclease systems comprising an endonuclease. Compositions and methods are also provided for guide polynucleotide/endonuclease systems comprising at least one endonuclease, optionally covalently or non-covalently linked to, or assembled with, at least one additional protein subunit, and for compositions and methods for direct delivery of endonucleases as ribonucleotide proteins.

Abstract: Compositions and methods are provided for high-efficiency large scale manipulation of genomic regions and chromosomal engineering of plant genomes. Enhancement of chromosomal modification includes the provision of one or more linker oligonucleotides complementary to the distinct chromosomal ends following double strand breaks, increasing the temperature effect and/or recurrent cutting by an endonuclease to facilitate higher chromosomal modification including large segment translocations and recombination. Site-specific directed DNA breaks under one or more of the experimental conditions (including CRISPR-Cas systems) disclosed enhance targeted recombination frequencies, crossover efficiency and movement of large chromosomal segments in crop plant cells.

Abstract: The invention provides DNA compositions that relate to transgenic insect resistant maize plants. Also provided are assays for detecting the presence of the maize DP-004114-3 event based on the DNA sequence of the recombinant construct inserted into the maize genome and the DNA sequences flanking the insertion site. Kits and conditions useful in conducting the assays are provided.

Abstract: Novel engineered non-natural deaminases are provided. Methods and compositions are provided for modifying the genome of a cell, including a plant cell. Genome modification through guided CRISPR polypeptides and multiple deaminases are provided. Engineered non-natural novel deaminases, including adenosine deaminases are provided. These novel deaminases have improved activity in cells including plant cells.

Abstract: Compositions and methods are provided for novel Cas9 orthologs, including, but not limiting to, novel guide polynucleotide/Cas9 endonucleases complexes, single or dual guide RNAs, guide RNA elements, and Cas9 endonucleases. The present disclosure also describes methods for creating a double strand break in a target polynucleotide, methods for genome modification of a target sequence under various in vivo and in vitro conditions, in the genome of a cell, for gene editing, and for inserting a polynucleotide of interest into the genome of a cell. Also provided are nucleic acid constructs and cells having a modified target site or altered polynucleotide of interest produced by the methods described herein.

Abstract: Methods and compositions are provided for the identification, detection, characterization, and/or utilization of double strand breaks in a target polynucleotide; the identification, detection, characterization, and/or utilization of cutting sites for double-strand-break-inducing agents; and the identification, detection, characterization, and/or utilization of double-strand-break-inducing agents.

Abstract: Methods for the identification of variant recognition sites for rare cutting engineered double strand break inducing agents and compositions thereof are provided. Further provided are nucleic acid constructs, yeast, plants, plant cells, explants, seeds and grain having the of variant recognition sites. Various methods of identifying variant recognition sites with increased substrate activity for a rare cutting engineered double strand break inducing agents are provided.

Abstract: Methods and compositions are provided for the transient expression and activity of site-specific DNA modifying agent, morphogenic factors or developmental genes, either alone or in combination for eukaryotic cells. The morphogenic factor and DNA modifying agent may be provided to the same cell or to a different cell than that which was originally transformed. The morphogenic factor, or the double-strand-break-inducing agent, may further comprise a cell penetrating peptide. Exogenously provided DNA modifying agents and/or morphogenic factors need not be segregated away in future generations due to transient activities in the desired cell.

Abstract: Compositions and methods are provided for genome modification of a target sequence in the genome of a cell, using novel engineered Cas endonucleases. The methods and compositions employ a guide polynucleotide/endonuclease system to provide an effective system for modifying or altering target sequences within the genome of a cell or organism. Also provided are novel effectors and endonuclease systems and elements comprising such systems, such as guide polynucleotide/endonuclease systems comprising an endonuclease. Compositions and methods are also provided for guide polynucleotide/endonuclease systems comprising at least one endonuclease, optionally covalently or non-covalently linked to, or assembled with, at least one additional protein subunit, and for compositions and methods for direct delivery of endonucleases as ribonucleotide proteins.

Abstract: The present disclosure involves the production of Waxy maize. Compositions and methods are provided for knocking out expression of the Waxy (Wx1) gene in maize by making double strand breaks at one or more target sites in an endogenous WX1 encoding sequence. Some methods employ one or more guide polynucleotides and a Cas endonuclease, wherein Cas endonuclease is guided by the one or more guide polynucleotides to recognize and introduce double strand breaks at specific target sites in and around the Wx1 gene. Also provided are compositions and methods for the production of Waxy maize plant cells, plant explants, seeds and grain.

Abstract: Compositions and methods are provided for genome modification of a target sequence in the genome of a cell, using a novel Cas endonuclease. The methods and compositions employ a guide polynucleotide/endonuclease system to provide an effective system for modifying or altering target sequences within the genome of a cell or organism. Also provided are novel effectors and endonuclease systems and elements comprising such systems, such as guide polynucleotide/endonuclease systems comprising an endonuclease. Compositions and methods are also provided for guide polynucleotide/endonuclease systems comprising at least one endonuclease, optionally covalently or non-covalently linked to, or assembled with, at least one additional protein subunit, and for compositions and methods for direct delivery of endonucleases as ribonucleotide proteins.

Abstract: Compositions and methods are provided for genome 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 the genome of a plant, plant cell or seed. Also provided are compositions and methods employing a guide polynucleotide/Cas endonuclease system for genome modification of a nucleotide sequence in the genome of a cell or organism, for gene editing, and/or for inserting or deleting a polynucleotide of interest into or from the genome of a cell or organism. Once a genomic target site is identified, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest. Breeding methods and methods for selecting plants utilizing a two component RNA guide and Cas endonuclease system are also disclosed.

Abstract: Compositions and methods are provided for genome 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 the genome of a plant, plant cell or seed. Also provided are compositions and methods employing a guide polynucleotide/Cas endonuclease system for genome modification of a nucleotide sequence in the genome of a cell or organism, for gene editing, and/or for inserting or deleting a polynucleotide of interest into or from the genome of a cell or organism. Once a genomic target site is identified, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest. Breeding methods and methods for selecting plants utilizing a two component RNA guide and Cas endonuclease system are also disclosed.

Abstract: Methods and compositions are provided for the use of anti-CRISPR (ACR) proteins in plants, including modulation of Cas endonuclease activity, improvement of frequency of homologous recombination, control of Cas endonuclease activity during various cell cycles, spatial and/or temporal regulation of Cas endonuclease activity in plants, usage in gene activation or repression, as well as reduction of off-target polynucleotide cleavage.