A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica

Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C , OrC1 , from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica . Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica . Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI , OsF3H , OsANS , OsINS and OsANR and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1 , provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice. Author summary Accumulation of anthocyanin is a selection trait in rice domestication, whereas the mechanisms regulating the anthocyanin biosynthetic pathway in rice remain unresolved. Here, a novel allele of chromogen gene C from wild rice ( Oryza rufipongon ) was identified as a determinant regulator of anthocyanin biosynthesis. A key question is to what extent the involvement of the C1 gene can explain coloration variability of cultivated rice, where anthocyanin accumulation has been eliminated by artificial selection. Our results reveal the functional chromogen gene C from wild rice causes different coloration phenotypes, regulates various anthocyanin biosynthetic genes and produces different metabolites in indica and japonica . Artificial selection and domestication of the C1 gene in rice only occurs within the coding region of the two subspecies independently.