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 DNA recombination and genome evolution. In this study we show that presence of sequence divergence (polymorphism) between homologous chromosomes increases the local recombination rate in Arabidopsis thaliana. This effect is observed genome-wide, turning cold regions of the genome hot. This relocation of COs towards polymorphic regions occurs at the expense of non-polymorphic ones, which become colder. This global overhaul of the CO landscape is dependent on the mismatch repair (MMR) machinery. This 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.