Plant genome modification using guide RNA/Cas endonuclease systems and methods of use

A method for modifying a target site in the genome of a plant cell, the method comprising:

• transforming at least one plant cell with a guide polynucleotide, a polynucleotide sequence encoding a Cas endonuclease, and an expression cassette encoding at least one developmental gene polypeptide, wherein the at least one developmental gene polypeptide comprises a Babyboom (BBM), an Ovule Development Protein 2 (ODP2), and/or a Wuschel (WUS) polypeptide, wherein the guide polynucleotide and the Cas endonuclease form a guide polynucleotide-Cas endonuclease complex that introduces a double-strand break at the target site in the plant cell, and wherein the at least one developmental gene polypeptide increases the frequency of modification of the target site by the guide polynucleotide-Cas endonuclease complex in the plant cell relative to a control plant cell comprising a guide polynucleotide-Cas endonuclease complex and not comprising an expression cassette encoding a developmental gene polypeptide;
• and
• regenerating a plantlet or a plant from the plant cell, the plantlet or plant comprising a modified target site, wherein the plantlet or the plant does not contain the Cas endonuclease or the expression cassette encoding the at least one developmental gene polypeptide.