Disclosed is a method for deleting a region of DNA in a plant, the method comprising: providing a first viable plant containing genomic DNA, comprising, in the 5&rsquo； to 3&rsquo； direction: a first recognition sequence, a region of DNA to be deleted from the plant, and a second recognition sequence； providing a second viable plant containing genomic DNA, comprising a DNA encoding either: a zinc finger nuclease (ZFN) engineered to cleave the genomic DNA at the first and second recognition sequences where the recognition sequences are identical, or a first DNA encoding a ZFN engineered to cleave the genomic DNA at the first recognition sequence and a second DNA encoding a ZFN engineered to cleave the genomic DNA at the second recognition sequence； crossing the first and second viable plants such that F1 seed is produced on either the first or the second viable plant； growing a resultant F1 plant, wherein the region of DNA is absent from the genomic DNA.
