Furthermore, a plant, plant part, seed, or fruit comprising one or more plant cells produced by the method are disclosed herein as an aspect of the disclosure. In yet another aspect, disclosed herein is a plant, plant part, seed, or fruit comprising one or more plant cells comprising a targeted genomic modification to one or more alleles of an endogenous gene in the plant cell, wherein the genomic modification follows cleavage by a site specific nuclease, and wherein the genomic modification produces a mutation in the endogenous gene such that the endogenous gene produces a product that results in an herbicide tolerant plant cell. In another aspect, provided herein is a seed from a plant comprising the plant cell that is obtained as described herein. In certain embodiments, altering expression of one or more AHAS genes in a plant cell, the method comprising, expressing one or more DNA-binding domain containing proteins (e.g., zinc finger proteins) in the cell such that expression of AHAS is altered.

In other embodiments, the methods comprise using a pair of zinc finger nucleases to enhance gene expression, for example via targeted insertion of an exogenous sequence (e.g., donor sequence, GOI, or transgene) or expression enhancing element. In yet another aspect, disclosed herein is a plant cell comprising a targeted genomic modification to one or more alleles of an endogenous gene in the plant cell, wherein the genomic modification follows cleavage by a site specific nuclease, and wherein the genomic modification produces a mutation in the endogenous gene such that the endogenous gene produces a product that results in an herbicide tolerant plant cell. In an additional embodiment, a selection agent comprising an imidazolinone, or a sulfonylurea selection agent is used to select the plant cells. Polyploid plant cells contain multiple genomic allelic targets. In yet another aspect, described herein is a method of integrating one or more exogenous sequences into the genome of a plant cell, the method comprising: expressing one or more site specific nucleases in the plant cell, wherein the one or more nucleases target and cleave chromosomal DNA of one or more endogenous loci; integrating one or more exogenous sequences into the one or more endogenous loci within the genome of the plant cell, wherein the one or more endogenous loci are modified such that the endogenous gene is mutated to expresses a product that results in a selectable phenotype in the plant cell; and, selecting plant cells that express the selectable phenotype, wherein plant cells are selected which incorporate the one or free private sex cam more exogenous sequences.

In a still further aspect, a plant cell obtained according to any of the methods described herein is also provided. In another aspect, provided herein is fruit obtained from a plant comprising plant cell obtained as described herein. The DNA-binding domains and fusion proteins comprising these DNA-binding domains bind to and/or cleave two or more endogenous genes in a polyploid genome (e.g., an AHAS gene) within the coding region of the gene or in a non-coding sequence within or adjacent to the gene, such as, for example, a leader sequence, trailer sequence or intron, or promoter sequence, or within a non-transcribed region, either upstream or downstream of the coding region, for example the 3′ untranslated region. In yet another aspect, described herein is a method for introducing one or more exogenous sequences into the genome of a plant cell, the method comprising the steps of: (a) contacting the cell with the one or more exogenous sequences (e.g., sex with stephanie donor vector, transgene or GOI, or combinations thereof); and (b) expressing one or more nucleases (e.g., ZFNs, TALENs, meganucleases and/or CRISPR/Cas systems) as described herein in the cell, leah gotti sex wherein the one or more nucleases cleave chromosomal DNA; such that cleavage of chromosomal DNA in step (b) stimulates incorporation of the exogenous sequence into the genome by homologous recombination.

In another aspect, provided herein is a plant comprising a plant cell as described herein. In yet another embodiment, the zinc finger DNA-binding domain encodes a protein that binds to a target site selected from the group consisting of SEQ ID NOs:35-56 and 263-278. In a further embodiment, the plant is selected from the group consisting of wheat, soy, maize, potato, alfalfa, rice, barley, sunflower, tomato, Arabidopsis, cotton, Brassica species, and timothy grass. In another aspect, provided herein is a method for simultaneously altering multiple alleles across the multiple genomes of a polyploid plant cell, the method comprising, expressing one or more DNA-binding domain proteins (e.g., zinc finger proteins such as zinc finger nucleases) in the cell such that multiple alleles of the polyploid plant are altered. In a subsequent embodiment, the site specific nuclease is selected from the group consisting of a zinc finger nuclease, a TAL effector domain nuclease, a homing endonuclease, and a Crispr/Cas single guide RNA nuclease.