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Targeted transgene integration via homologous recombination occurs at a very low frequency in plant cells compared to random integration, even when the incoming DNA comprises large stretches of sequence homologous to host DNA. As such, gene targeting in plants via homologous recombination has not been practical. Most recently, substantial increases in the frequency of homologous recombination have been observed following the induction of DNA double stranded breaks in host cells and apparent stimulation of cellular repair mechanisms. Restriction enzymes whose recognition sites are rare in the plant genome have been shown to stimulate homologous recombination following the formation and repair of DNA double stranded breaks in the host DNA. Strategies to achieve targeted DNA double stranded breaks have been developed by fusing zinc finger DNA binding proteins with sequence-independent nuclease domains derived from Type II restriction endonucleases [ABSTRACT FROM AUTHOR]