Abstract: Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, low-copy, and potentially active long terminal repeat (LTR) retrotransposons occurred in one or more of three rice lines studied that were introgressed by wild rice (Zizania latifolia Griseb.). For nine retrotransposons in which both the reverse-transcriptase (RT) region and the LTR region were available, largely concordant rearrangements occurred at both regions in five elements and at the RT region only in the remaining four elements. A marked proportion of the genomic changes was shared by two or all three introgression lines that were derived from a single F1 plant. This indicates that most of the genomic changes occurred at early developmental stages of the F1 somatic cells, which then gave rise to germline cells, and, hence, ensured inheritance of the changes to later generations. Possible causes and potential implications of the introgression-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant genome evolution and breeding.

Key words: genomic rearrangements, introgressive hybridization, long terminal repeat (LTR) retrotransposon, rice, Zizania.