BackgroundYellow seed breeding is an effective method to improve the oil content in rapeseed. Yellow seed coat color formation is influenced by various factors, and no clear mechanisms are known. In this study, Bulked segregant RNA-Seq (BSR-Seq) of BC9 population of Wuqi mustard (yellow seed) and Wugong mustard (brown seed) was used to identity the candidate genes controlling the yellow seed color in Brassica juncea L.ResultsYellow seed coat color gene was mapped to chromosome A09, and

more »

... ially expressed genes (DEGs) between brown and yellow bulks enriched in the flavonoid pathway. A significant correlation between the expression of BjF3H and BjTT5 and the content of the seed coat color related indexes was identified. Two intron polymorphism (IP) markers linked to the target gene were developed around BjF3H. Therefore, BjF3H was considered as the candidate gene. The BjF3H coding sequences (CDS) of Wuqi mustard and Wugong mustard are 1071-1077bp, encoding protein of 356-358 amino acids. One amino acid change (254, F/V) was identified in the conserved domain. This mutation site was detected in four Brassica rapa (B. rapa) and six Brassica juncea (B. juncea) lines, but not in Brassica napus (B. napus).ConclusionsThe results indicated BjF3H is a candidate gene that related to yellow seed coat color formation in Brassica juncea and provided a comprehensive understanding of the yellow seed coat color mechanism.