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Seed coat colour is an important nutritional quality trait. Variations in anthocyanins and flavonoids induce the diversity of seed coat colour in adzuki bean ( Vigna angularis  L.). Red seed coat and black seed coat are important adzuki bean cultivars. Insights into the differences of flavonoid metabolic pathways between black and red adzuki bean are significant. In this study, we explored that the difference in seed coat colour between the red (Jingnong6) and the black (AG118) is caused by the accumulation of anthocyanins. The RNA-sequencing (RNA-Seq) and real-time reverse transcription (qRT)-PCR results showed that the  Vigna angularis  L. seed coat color ( VaSDC1 ) gene, an R2R3-MYB transcription factor, should be the key gene to regulate the black and red seed coat colours. In three different colouring staes of seed development,  VaSDC1  was specifically expressed in the black seed coat (AG118) landrace, which activates the structural genes of flavonoid metabolic pathways. As a result, this caused a substantial accumulation of anthocyanins and created a dark blue-black colour. In the red (Jingnong6) seed coat variety, low expression levels of  VaSDC1  resulted in a lower accumulation of anthocyanins than in AG118. In addition,  VaSDC1  was genetically mapped in the interval between simple-sequence repeat (SSR) markers  Sca326-12 ,  Sca326-4 , and  BAgs007  on chromosome 3 using an F 4  segregating population derived from the cross between Jingnong6 and AG118. These results will facilitate the improvement of nutritional quality breeding in adzuki beans.

VaSDC1 Is Involved in Modulation of Flavonoid Metabolic Pathways in Black and Red Seed Coats in Adzuki Bean (Vigna angularis L.)