Characterization of non-crossover recombination spectrum by single-microspore sequencing in maize and rice

Meiotic DNA double-strand breaks (DSB) are crucial for chromosome recombination. The repair of DSB gives two outcomes: crossover (CO) and non-crossover (NCO). CO involves the bidirectional exchange between homologous chromosomes, whereas NCO refers to the unidirectional transfer of chromosome fragments. NCO can be categorized into NCO with gene conversion and NCO without gene conversion. Due to technological constraints, previous studies have focused more on CO than on NCO. In this study, we isolated single microspores from meiotic tetrads of maize (Zea mays) and rice (Oryza sativa) and conducted deep single-microspore genome sequencing to characterize NCO gene conversion (NCO-GC). Under highly stringent conditions, 101 CO and 902 NCO-GC tracts were identified in four maize tetrads, while 173 CO and 279 NCO-GC tracts were identified in six rice tetrads. In both maize and rice, NCO-GC was more prone to occur in the upstream and downstream of genes, as well as the introns. It also had a significant distribution in transposon regions. A common A-rich motif was enriched in the NCO-GC tracts of maize and rice. GC-biased gene conversion (gBGC) likely contributed to the bimodality of the GC content at the third codon position (GC3), and we discovered a significant proportional relationship between the number of DSBs and the GC content. These findings provide evidence that NCO-GC exhibits a distinct pattern compared with CO and may play an important role in gene and genome evolution.