Distinct and Cooperative Roles of DNA Methylation and Meiotic Chromosome Architecture in Crossover Control

During meiosis, homologous chromosomes exchange segments in a process termed crossover recombination. Crossovers are non-randomly distributed along chromosomes, and in many eukaryotes, including plants, meiotic chromosome architecture and chromatin states control recombination landscapes. Whether these two components genetically interact has remained underexplored. To address this question, we combined Arabidopsis thaliana, hereinafter, Arabidopsis, mutations that disrupt meiotic chromosome architecture by depleting the meiotic chromosome axis (asy1/+) or synaptonemal complex (zyp1) with mutations in the DNA methyltransferases MET1 and CMT3 (met1/+ and cmt3), which lead to a loss of cytosine DNA methylation, the hallmark of heterochromatin, in the CG and CHG contexts, respectively. We quantified crossovers in telomere- and centromere-proximal chromosome intervals using fluorescent seed-based reporters and found that DNA methylation and meiotic chromosome architecture proteins can have distinct or cooperative roles in crossover control depending on the chromosome interval and DNA methylation context. We demonstrate that axis and synaptonemal complex act together with CG DNA methylation to control crossovers, while CHG DNA hypomethylation cannot fully restore a loss of centromere-proximal recombination caused by the depletion of ASY1 or ZYP1. Remarkably, increasing ASY1 dosage promotes crossovers within the pericentromere, representing a new non-epigenetic route to upregulate pericentromeric recombination. Author summaryMeiotic crossovers reshuffle genetic variation and are essential for evolution and crop breeding. However, crossovers occur unevenly along chromosomes, limiting genetic exchange in pericentromeric regions. Here, we investigate the genetic interactions between cytosine DNA methylation and meiotic chromosome architecture and show that, although heterochromatin depletion can permit pericentromeric crossovers, the structural integrity of the meiotic chromosome axis and the synaptonemal complex are essential to drive recombination. Remarkably, modulating the dosage of a chromosome axis protein provides a non-epigenetic strategy to increase pericentromeric crossovers, revealing new opportunities to reshape recombination landscapes in model and crop plants.