The quality traits of rapeseed are critical genetic characteristics that determine seed value and its applications. Heterosis manifests not only in yield traits but also in quality traits. In this study, multiple interspecific and intraspecific hybrid crosses were generated to evaluate their heterosis effects. Our results demonstrated that the heterosis of oil content, oleic acid, linoleic acid, and linolenic acid was higher in the winter × spring crosses than in the winter × winter crosses, whereas the opposite was true for erucic acid and glucosinolate. Furthermore, we identified a substantial numerous SNP markers through targeted sequencing and mapped the heterosis-related loci for the corresponding traits in the F1 population. A lot of 233, 46, 247, 192, 203, and 64 QTLs were identified as being associated with the seed traits of erucic acid, glucosinolates, oleic acid, linoleic acid, linolenic acid, oil content and their heterosis. These were consolidated into 425 consensus QTLs (cq-QTLs). By integrating RNA-seq data, we identified 10 pathways involved in lipid and pyruvate metabolism, among which 28 candidate genes were annotated. These conclusions showed that these cq-QTLs can serve as hotspots for mining regulatory genes related to the heterosis of rapeseed quality traits, laying a foundation for research on the heterosis of rapeseed quality traits.
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