THE STRUCTURES OF INTEGRATION SITES IN TRANSGENIC RICE

Extensive genomic sequencing and sequence motif analysis have been con ducted over the integration sites of two transgenic rice plants, #478 and #559, carrying the luciferase gene and/or hygromycin phosphotransf erase gene. The transgenes reside in a region with inverted structure and a large duplication of rice genome over 2 kb. Integration was foun d at the AT-rich region and/or at the repetitive sequence region, incl uding a SAR-like structure, retrotransposon and telomere repeats. The presence of a patch of sequence homology between plasmid and target DN A, and a small region of duplication involving the target DNA around t he recombination site, implicated illegitimate recombination in the pr ocess of gene integration. Massive rearrangement of genomic DNA includ ing deletion or translocation was also observed at the integration sit e and the flanking region of the transgene. The recognition sites of D NA topoisomerases I or II were observed in the rearranged sequences. S ince only three junctions of transgenic rice were implicated in the il legitimate recombination and extensive rearrangement of the rice genom e, rice protoplasts may be active in this process.