The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids

In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover formation is poorly understood. To analyze this in Arabidopsis, we developed the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show here that structural variants do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyzed hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots showed reduced activity in msh2. In lines where only the hotspot-containing interval was heterozygous, crossover numbers increased above those in the inbred (homozygous). We conclude that local polymorphism shapes crossover distribution by stimulating hotspot activity and thus contributes to plant genome evolution.