Identification of candidate genes regulating seed oil and protein content in Brassica napus via integrated genome-wide association and transcriptome analysis.

Seed oil and protein content (SOP) are economically important traits in Brassica napus. Simultaneously improving these traits to cultivate high-oil and high-protein varieties is vital for maximizing production efficiency per unit area. This study investigated the total SOP in Brassica napus to identify regulatory genes, facilitating molecular breeding and enhancing the crop's commercial value. High-throughput genome resequencing yielded 385,692 high-quality single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) > 0.05. A genome-wide association study (GWAS) identified nine SNPs significantly associated with SOP: five on chromosomes C01 (1) and C03 (4), and four on chromosome A10. Individual SNPs explained 5.32%-7.02% of the phenotypic variance. GWAS screening revealed 428 candidate genes within the confidence intervals of significant SNPs. Comparative transcriptome analysis of seeds from lines with extremely high- and low- SOP across developmental stages in two environments (Guiyang and Xingyi) identified 117 common differentially expressed genes (DEGs). Integrating GWAS and transcriptomic data narrowed the candidates down to two key genes regulating SOP. By integrating transcriptome analysis and GWAS, we identified two priority candidate genes within significant SNP intervals that regulate SOP. This work establishes a foundation for breeding high-SOP Brassica napus varieties via molecular marker-assisted selection.