Compositions and methods are provided for the targeted integration of a polynucleotide sequence of interest into the genome of a plant or plant cell. The methods and compositions employ recognition sites for endonucleases and endonucleases in combination with site-specific recombination sites/recombinases to provide an effective system for establishing target sites within the genome of a plant, plant cell or seed. Once such target sites are established, a variety of methods can be employed to further modify the target sites such that they contain a variety of polynucleotides of interest.