Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice.

Recombination plays an integral role in the creation of novel genetic variation in sexually reproducing species. Despite this important role, the determinants and evolution of crossover hotspots have remained poorly understood in plants. Here, we present a comparative analysis of two rice () historical recombination maps from two subspecies ( and ) using 150 resequenced genomes. Fine-scale recombination rates and crossover hotspots were validated by comparison with a consensus genetic map and empirically derived crossovers, respectively. Strikingly, nearly 80% of crossover hotspots were unique to each subspecies, despite their relatively recent divergence and broad-scale correlated recombination rates. Crossover hotspots were enriched with and transposons and overlapped accessible chromatin regions. Increased nucleotide diversity and signatures of population differentiation augmented by and transposons were prevalent at subspecies-specific crossover hotspots. Motifs derived from lineage-specific and crossover hotspots were nearly identical in the two subspecies, implicating a core set of crossover motifs in rice. Finally, and transposons were associated with stabilized G/C bias within highly active hotspots, suggesting that hotspot activity can be fueled by de novo variation. These results provide evolutionary insight into historical crossover hotspots as potentially powerful drivers of sequence and subspecies evolution in plants.