Structural analysis of transgene rearrangements and effects on expression in transgenic maize plants generated by particle bombardment

We cotransformed maize embryogenic callus with two plasmids. one carrying t he linked markers bar and gusA, and the other carrying the Bacillus thuring iensis cry1Ab gene. Molecular analysis of regenerated transgenic plants rev ealed a diverse range of transgene structures, including intact, truncated and internally-rearranged copies, and copies interspersed with genomic DNA. We found rearrangements associated with both functional and nonfunctional transgenes. We also found that rearrangements could affect the selected mar ker gene bar as well as the nonselected transgenes. Rearrangements often ca used loss of transgene expression, but some rearranged transgenes were expr essed normally. Conversely, while intact transgenes were often expressed, w e also detected some nonexpressed copies, probably reflecting epigenetic si lencing mechanisms. All the transgenic lines we studied contained multiple transgenes, generally comprising a mixed array of intact and rearranged cop ies. Rearrangement is rarely given serious consideration as a factor contri buting to transgene silencing and variable transgene expression, but our da ta show that undetected rearrangements may have a major effect on transgene expression. This has significant implications, especially in studies attem pting to correlate transgene copy number and expression levels.