Pan-genome analysis and abiotic stress expression of the SWEET gene family in Brassica napus

The SWEET (Sugars Will Eventually be Exported Transporters) gene family plays crucial roles in sugar transport, plant development, and abiotic stress responses. However, its pan-genomic characteristics and practical breeding potential in Brassica napus remain unclear. In this study, we systematically identified 96 BnSWEET genes across eight rapeseed genomes, revealing extensive presence/absence variations (PAVs) and clear classification into four subfamilies (Groups I–IV). Evolutionary analyses highlighted diverse selection pressures, with specific members (e.g., BnSWEET37 ) exhibiting strong signatures of positive selection (Ka/Ks > 1.0), while others were conserved under purifying selection. Haplotype analysis revealed that elite alleles of BnSWEET5 are significantly associated with seed oil content, silique length, and germination vigor. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified BnSWEET47 as a core regulatory hub coordinating sugar partitioning and secondary metabolism. Transcriptomic profiling and RT-qPCR validation confirmed that BnSWEET genes, particularly those representing specific structural and evolutionary variants (e.g., the PAV-specific BnSWEET26 ), exhibit highly heterogeneous and tissue-specific temporal expression patterns under multiple abiotic stresses. Overall, this study elucidates the evolutionary and functional divergence of the BnSWEET family and proposes a practical breeding pathway—utilizing the identified elite haplotypes and key PAV variants for precision germplasm screening—to optimize source-sink balance and enhance abiotic stress resilience in B. napus .