Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape

Meiotic recombination is essential for generating genetic diversity, driving plant evolution, and enabling crop improvement, yet its uneven distribution across genomes constrains breeding efforts. Here, we investigated the multi-omic landmarks that shape the recombination landscape in Brassica napus by integrating epigenomic, genomic and transcriptomic data with recombination maps derived from large multi-parental rapeseed populations. Predictive machine-learning accurately predicted recombination rates and hotspot location using only feature information. Recombination was generally suppressed in centromeres and other repeat-rich, methylated regions and enriched in gene-dense, transcriptionally active domains. Proxies for chromatin configuration—such as DNA methylation, transposable elements or genes— consistently achieved the highest predictive power with the random forest algorithm. We discovered distinct recombination landscape patterns between subgenomes, with crossovers clustering near subtelomeres in the A subgenome and more evenly spread across the C subgenome. Models trained on A-subgenome data outperformed those based on the C subgenome, although combining both subgenomes improved overall accuracy.