Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants

To gain further understanding of the mechanisms involved in Agrobacterium-mediated genetic transformation and T-DNA integration, we analysed 156 T-DNA/rice, 69 T-DNA/T-DNA and 11 T-DNA/vector backbone (VB) junctions, which included 171 left borders (LB) and 134 right borders (RB). Conserved cleavage was observed in 6% of the LB and 43% of the RB. Terminal microhomology (1–10 bp) was identified in 58% of T-DNA/rice, 43% of T-DNA/T-DNA and 82% of T-DNA/VB junctions, and this occurred particularly at the LB junctions. Approximately 32% of both T-DNA/rice and T-DNA/T-DNA junctions harboured 1–344 bp of filler DNA that was derived mainly from the T-DNA region adjacent to the breakpoint and/or from the rice genome flanking the T-DNA integration site. Structure of the filler DNA was more complicated at the T-DNA/T-DNA junction than at the T-DNA/rice junction, indicating the presence of T-DNA recombination or rearrangement prior to or during T-DNA integration. When two T-DNAs were integrated in the inverted repeat configuration, significant truncation was always observed in one of the two T-DNAs whereas with direct repeat configuration, a large truncation was less frequent. Most integration events analysed in this study could be addressed by previously proposed models; however, the characteristics of the T-DNA repeats and the complicated filler DNA between two T-DNA copies imply that multiple mechanisms are involved in the formation of T-DNA repeats as well as in T-DNA integration in plants.