The role of methylation and structural variants in shaping the recombination landscape of barley.

Meiotic recombination is not only a key mechanism for sexual adaptation in eukaryotes but crucial for the accumulation of beneficial alleles in breeding populations. The effective manipulation of recombination requires, however, a better understanding of the mechanisms regulating the rate and distribution of recombination events in genomes. Here, we identified the genomic features that best explain the recombination variation among a diverse set of segregating populations of barley at a resolution of 1 Mbp and investigated how methylation and structural variants (SVs) determine crossover (CO) hotspots and coldspots at a high resolution of 10 kb. Hotspots were found to be in proximity to genes, and the genetic effects not assigned to methylation were found to be the most important factor explaining differences in recombination rates among populations, along with the methylation and the parental sequence divergence. Interestingly, coldspots were associated with the inheritance of a highly methylated genomic fragment from one parent only, but hotspots were identified at genomic segments where both parents were equally low methylated. The parental sequence divergence was shown to have a sigmoidal correlation with recombination, indicating an upper limit of mismatch among homologous chromosomes for CO formation. SVs were shown to be correlated with CO suppression, and their type and size were not found to influence that effect. The joint act of methylation and SVs was associated with the location of coldspots in barley, and the weight of their relative effect depends on the genomic region. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in proximity to genes and being modulated by local levels of methylation and SV load.