Localization of heterosis loci for yield traits and identification of candidate genes in Brassica napus

Utilizing hybrid vigor is a pivotal strategy for breeding high-yield and high-quality rapeseed (Brassica napus) cultivars. However, the underlying molecular mechanisms remain poorly understand. In this study, we systematically evaluated heterosis using multiple interspecific and intraspecific hybrid crosses. Our findings revealed that yield-related traits exhibited stronger heterosis in the winter × spring crosses than in the winter × winter crosses. Through targeted sequencing, we obtained numerous SNP markers and performed QTL analysis for heterosis of related traits in the F₁ population. A total of 361 consensus QTLs (cq-QTLs) and 34 consensus QTLs specifically for seed weight (cqSW-QTLs) were identified. By integrating RNA-seq data from crosses with contrasting seed weight heterosis and leveraging functional annotations, we screened nine candidate genes implicated in regulation of seed weight and its heterosis. These genes encode the following proteins: oil body-associated protein 2A, translocator protein homolog, serine/threonine-protein kinase Aurora-3, GDSL esterase/lipase At1g54790, F-box/LRR-repeat protein At5g63520, phospholipase A2-alpha, sugar transport protein 4, cytochrome P450 76C4, and bZIP transcription factor 44. Our results lay a theoretical foundation for identifying heterosis-related loci, mining candidate genes, and clarifying the molecular mechanisms underlying heterosis in rapeseed.