MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism

Acknowledgements: We thank Raphael Mercier (Max Planck Institute for Plant Breeding Research, Cologne) for sharing fancm zip4, recq4a recq4b mutants in Col and Ler backgrounds. We thank Michal R. Gdula (Adam Mickiewicz University, Poznan) for the critical reading of the manuscript. The computations were performed at the Poznan Supercomputing and Networking Center (grant 312). This work was supported by the National Science Center, Poland (NCN) grants 2016/22/E/NZ2/00455 and 2020/39/I/NZ2/02464 to P.A.Z., 2021/41/N/NZ2/01226 to J.D., the Foundation for Polish Science grant (POIR.04.04.00-00-5C0F/17-00) to P.A.Z.Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism