Recombination is widely recognized for its role in generating genetic diversity and has a major impact on the efficiency of plant breeding. Although substantial progress has been made in deciphering the molecular mechanisms of meiotic recombination, how genetic and epigenetic factors shape this complex process, and how recombination, in turn, influences evolutionary trajectories, remains poorly understood. We investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with crossover numbers significantly reduced in male meiosis but unchanged in females, despite local shifts in crossover distribution. New crossovers occur in miniature inverted-repeat transposable elements (MITEs) near genes associated with open chromatin states. In parallel, we examine meiotic recombination in male and female meiosis using the parental lines of the maize nested association mapping (NAM) population. Our analyses reveal that meiotic recombination differs substantially in different maize genetic backgrounds, with tropical lines exhibiting higher female recombination frequencies and temperate lines showing higher male recombination frequencies. Finally, we explore the genomic and epigenomic features that distinguish maize and Brassica rapa subgenomes. Using eXplainable Artificial Intelligence (XAI) approaches, we identify recombination rate as the most influential and highly interconnected feature, despite nonsignificant mean differences between subgenomes. Our results highlight recombination and chromatin environment as major determinants of subgenome divergence in polyploid genomes. Together, our findings underscore the pivotal roles of DNA methylation, histone modifications, and transposable elements in regulating meiotic recombination and reveal how recombination contributes to biased genome fractionation and the evolution of duplicated genes.