mop1 reshapes recombination landscapes in maize by modulating DNA methylation and chromatin states at MITEs

Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains poorly understood in many species. Here, we investigate the role of Mop1 (Mediator of paramutation1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. In both sexes, mop1 redistributes COs away from pericentromeric regions and toward chromosomal arms. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes, accompanied by elevated levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.