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

Abstract 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. Competing Interest Statement The authors have declared no competing interest. Footnotes (rod.snowdon{at}agrar.uni-giessen.de) - Abbreviations - ALE - accumulated local effects - AT dinucleotide - adenine–thymine dinucleotide - AUROC - area under the receiver operating characteristic curve - bp - base pair - cM/Mbp - centimorgan per megabase pair - CO - crossover - CpG - cytosine–phosphate–guanine (CG) - DNA/DTA - hAT transposons - DNA/DTC - CACTA transposons - DNA/DTH - Helitron transposons - DNA/DTM - Mutator transposons - DNA/DTT - Mariner/Tc1 transposons - DT - decision tree - FDR - false discovery rate - G (in CpG and CHG) - guanine - GB - gradient boosting - GC content - guanine–cytosine content - H (in CHH and CHG) - any nucleotide except guanine - Kbp - kilobase pair - LR - linear/logistic regression - LTR - long terminal repeat - Mbp - megabase pair - P - P-value - ρ - correlation coefficient - RdDM - RNA-dependent DNA methylation - RF - random forest - RIL - recombinant inbred line - R² - coefficient of determination - ROC - receiver operating characteristic - SD - standard deviation - siRNA - small interfering RNA - SNP - single nucleotide polymorphism - TE - transposable element - TPM - transcripts per million