Double-strand break (DSB) repair is essential for cell survival and for the maintenance of genome integrity. In this study, we utilized I-Sce I, an endonuclease from yeast with an 18-bp recognition site to introduce DSB in maize and rice cells. We then employed PCR to characterize the inaccurate repair events that removed the I-Sce I recognition site. Of 82 and 84 inaccurate repair events characterized in maize and rice, more than 72% inaccurate repairs were associated with deletions. Of the deletion repairs, small deletions (1-9 nucleotides) happened more frequently than large deletions. The sequences flanking these deletions and insertions have the hallmarks of illegitimate recombination. These results are compatible with models suggesting that inaccurate repair of DSBs is the major factor responsible for the rapid removal of unselected DNA from higher plant genomes. The sizes of inaccurate repairs are not necessarily associated with genome size variation in monocot species.
