Identification of Candidate MYB Regulators of Seed Coat Color and Oil Content in Brassica napus

Yellow-seeded Brassica napus varieties are highly desirable for breeding due to their superior oil content and seed quality. Proanthocyanidins (PAs) are the major flavonoids determining seed coat color, which is closely associated with oil accumulation. MYB transcription factors, especially R2R3-MYBs, act as important regulators of flavonoid biosynthesis and multiple developmental processes and may be associated with variation in PA accumulation and oil content. In this study, we performed a genome-wide identification and characterization of PA biosynthesis-related genes and MYB transcription factors in B. napus, and a total of 102 PA biosynthesis-related genes (BnaPABGs) and 416 high-confidence R2R3-MYBs (BnaMYBs) were identified and characterized. Transcriptome profiling of yellow- and black-seeded accessions at distinct developmental stages uncovered divergent expression patterns of both PA-related genes and MYBs. Weighted gene co-expression network analysis (WGCNA) identified a central module that co-enriched the majority of PA biosynthesis-related genes along with numerous lipid metabolism-related genes, suggesting a potential co-expression relationship between flavonoid metabolism and oil accumulation during seed maturation. By integrating co-expression networks with previously reported quantitative trait loci (QTLs) for seed coat color and oil content, we identified candidate BnaMYBs potentially associated with seed coat pigmentation and oil accumulation. Among these candidates, BnaA08.MYB61, BnaC06.MYB63, and BnaC03.MYB56 were prioritized as candidate genes based on their expression patterns and co-expression relationships, while haplotype analyses provided additional support for BnaC03.MYB56 and BnaA08.MYB61. Haplotype analyses further revealed supported associations between natural variation at BnaC03.MYB56 and BnaA08.MYB61 loci and seed oil content, whereas BnaC06.MYB63 showed limited haplotype diversity. Collectively, our findings provide new insights into the potential relationship of flavonoid and lipid metabolism in B. napus seeds and provide candidate genetic resources for further functional investigation of seed coat pigmentation and oil accumulation in B. napus.