Meiotic recombination generates new genetic combinations and ensures proper chromosome segregation, yet its regulation remains unclear in many species. Here, we show that Mediator of paramutation1 (Mop1), a regulator of DNA methylation, affects the recombination landscape in maize. High-resolution crossover mapping reveals that loss of MOP1 reduces crossover numbers during male meiosis, while the total number in female meiosis remains largely unchanged despite local shifts in crossover distribution. We find that new crossovers occur on miniature inverted-repeat transposable elements (MITEs), particularly in regions with greater genetic diversity. Analysis of DNA methylation and histone modifications, together with gene expression, shows that loss of MOP1 reduces methylation at MITEs near genes enriched with histone marks linked to open and active chromatin, and downregulates a gene required for chromosome organization. Together, these findings suggest that both chromosome structure and transposon methylation contribute to recombination control, providing insights into epigenetic control of genetic variation.
© 2025. The Author(s).