Abstract
Oilseed rape (Brassica napus L.) is one of the world's most important oil crops. Seed oil content (SOC) and oleic acid content (C18:1) are major determinants of rapeseed oil quality. Identifying genomic loci and candidate genes associated with these traits is therefore important for improving the efficiency of molecular breeding. In this study, a recombinant inbred line (RIL) population comprising 188 B. napus lines was evaluated across three growing seasons, and SOC and C18:1 were measured. A genome-wide association study (GWAS) was performed using a mixed linear model (MLM) and more than 12,000 high-quality single-nucleotide polymorphisms (SNPs). Six and eight quantitative trait loci (QTLs) associated with SOC and C18:1, respectively, were detected. Based on the functional annotations and sequence variation of genes within these QTL intervals, five previously reported candidate genes were prioritized: BnaC01.LPAT5, BnaA06.ABCA2, BnaA07.PIN1, BnaC08.GEM, and BnaA03.MYB102. In addition, a consistently detected SNP cluster associated with multiple seed lipid-related datasets was detected on chromosome A09. By integrating genomic position, functional annotation, parental sequence variation, qRT-PCR expression data, and haplotype-phenotype associations, six genes within the A09 QTL region were newly prioritized as potential candidates associated with seed lipid accumulation. These genes exhibited significant differences in transcript abundance between the developing seeds of the two parental cultivars, GH06 and ZY821, at 20 days after flowering (DAF). Although these convergent lines of evidence support the prioritization of the six genes, their causal effects remain to be established through further functional validation. Overall, the QTLs and potentially favorable haplotypes identified in this study provide useful genetic resources for improving rapeseed oil quality, while the prioritized candidate genes provide targets for future functional studies and molecular breeding in B. napus.Supplementary information
The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01712-2.