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During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the  Arabidopsis thaliana RAC1  and  RPP13  disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The  fancm ,  recq4a recq4b ,  figl1  and  msh2  mutants, or lines with increased  HEI10  dosage, are known to show increased crossovers throughout the genome. Surprisingly,  RAC1  crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within  RAC1 , in wild type,  fancm ,  recq4a recq4b  and  fancm recq4a recq4b  backgrounds. The  RAC1  recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the  RAC1  5′-end were relatively suppressed in  recq4a recq4b  backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.

Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes