Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana.

Meiotic recombination, via the formation of crossovers (COs), re-assorts parental alleles and dictate which traits are inherited together, or not. The recombination rate is not homogeneous across the genome, and uncovering the causes of these fluctuations can inform our understanding of recombination and genome evolution. In this study we show that presence of sequence divergence (polymorphism) between homologous chromosomes can dictate where crossovers are formed in Arabidopsis thaliana. Indeed, presence of polymorphism increases the local recombination rate, turning cold regions of the genome hot. This relocation occurs at the expense of non-polymorphic regions, which become colder. This global overhaul of the CO landscape is dependent on the mismatch repair (MMR) machinery. Our data suggests that MMR has a pro-CO role, driving COs to regions of the genome where it could detect sequence differences between homologous chromosomes. Our study demonstrates that polymorphism can be a major recombination driver in A. thaliana.