Compositions and methods are provided for modifying a nucleotide sequence in the genome of a plant cell, without the use of a selectable marker. The methods and compositions employ a guide polynucleotide/Cas endonuclease system to make a double strand break in a target site located in a nucleotide sequence and plant cells are obtained without the use of a selectable marker, and to provide an effective system for modifying target sites within the genome of a plant, plant cell or seed. Compositions and methods are also provided for producing a plant cell, callus tissue or plant having a modified nucleotide sequence in its genome, without the use of a selectable marker.
