Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus

Understanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation (SV) and its role in intraspecific and ecogeographical diversification of Brassica napus, a recently evolved, globally important allopolyploid crop.

We perform whole-genome long-read DNA-sequencing and construct reference-guided genome assemblies for 94 accessions, including winter-type, spring-type, and East Asian oilseed, along with kale forms and swedes/rutabagas. We investigate pangenomic patterns of SVs and determine pangenome-wide distributions and frequencies of inversions, gene presence-absence variants, and collective SVs including insertions and deletions. Results reveal pangenome-wide patterns for insertions, deletions, inversions, and large chromosomal deletions/duplications, reflecting evolutionary diversification across morphotypes and ecotypes. Collective SVs are unevenly distributed and biased toward subgenome A, with asymmetrical selection pattern favoring subgenome C. Selection signatures for inversions exhibit no subgenome asymmetry; however, increased selection signal strength and frequency are detected in paracentric chromosome regions, highlighting evolutionary significance. Analysis of the candidate loci under selection identifies regions for collective SVs 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 distinguish 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.

These findings underscore functional and evolutionary significance of pangenomic SV formation during Brassica napus diversification. Information on SV patterns with putative functional relevance provides breeding insights, particularly for developing molecular markers to optimize performance of Brassica napus and other Brassica crops.