Allelic variation in BrF3’H is associated with flavonoid composition and leaf pigmentation in Chinese cabbage

Chinese cabbage ( Brassica rapa subsp. pekinensis ) displays a wide array of leaf colors determined by differential accumulation of anthocyanins, which enhance nutritional value and visual appeal. Although anthocyanin biosynthesis is well characterized, the molecular mechanisms underlying red and purple leaf coloration remain poorly understood. This study investigated the role of flavonoid 3’-hydroxylase (BrF3’H), a key enzyme mediating the B-ring hydroxylation, in modulating flavonoid composition and leaf color traits. Comparative metabolite profiling between purple (P) and red (R) lines revealed distinct flavonoid patterns. The P and R lines predominantly accumulated cyanidin- and pelargonidin-derived anthocyanins, respectively. Both lines contained kaempferol derivatives as the major flavonols, whereas the P line showed a higher relative proportion of quercetin-derived compounds than the R line. Correspondingly, BrF3’H transcript levels were significantly higher in the P line than in the R line. Sequence analysis identified a transposon insertion in the second exon of BrF3’H in the R line, predicted to encode a truncated protein lacking conserved C-terminal regions. Protein-protein interaction analysis revealed that BrF3’H from the P line interacted with upstream flavonoid biosynthetic enzymes, whereas these interactions were abolished for BrF3’H protein from the R line. Furthermore, this allelic variation was tightly linked to leaf color across additional lines, enabling the development of a molecular marker for phenotypic discrimination. Collectively, these findings indicate that BrF3’H allelic variation underlies differences in flavonoid composition and red and purple leaf pigmentation Chinese cabbage.