Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus

BackgroundUnderstanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation and its role in intraspecific and ecogeographical diversification of Brassica napus, a recently evolved, globally important allopolyploid crop. ResultsWe performed whole-genome long-read DNA-sequencing and constructed reference-guided genome assemblies for 94 diverse, homozygous accessions, including winter-type, spring-type, and East Asian oilseed, along with kale forms and swedes/rutabagas. We investigated pangenomic patterns of genomic structural variants (SV) and determined pangenome-wide distributions and frequencies of inversions, gene presence-absence variants, and collective SV including insertions and deletions. Results revealed pangenome-wide patterns for insertions, deletions, inversions, and large chromosomal deletions/duplications, reflecting evolutionary diversification across morphotypes and ecotypes. Collective SV were unevenly distributed and biased toward subgenome A, with asymmetrical selection pattern favoring subgenome C. Selection signatures for inversions exhibited no subgenome asymmetry; however, selection signal strength and frequency increased in paracentric chromosome regions, highlighting their evolutionary significance. Selective sweep analysis identified regions for collective SV and inversions, harboring genes for organ formation, cell division and expansion in swede, and stress responses in East Asian oilseed rape. Large chromosomal duplications and deletions distinguished swede from oilseed rape, particularly in subgenome C, including copy-number variation in flowering-time genes BnFLC.C09 and BnATX2.C08, and cell wall development gene BnCEL2.C08. ConclusionsThese findings underscore functional and evolutionary significance of pangenomic SV formation during B. napus diversification. Information on SV patterns with putative functional relevance, provides breeding insights, particularly for developing molecular markers to optimize performance of B. napus and other Brassica crops.