Identification of novel genes involved in anthocyanin and proanthocyanidin pigments accumulation in rice tissues using genome-wide association study (GWAS)

As natural mutants, some rice varieties have brown pericarp and/or purple stem and leaves. The brown and purple colors caused by the accumulation of proanthocyanidin and anthocyanin pigments, respectively, belong to flavonoids. The anthocyanin and proanthocyanidin pigments are biosynthesized by the phenylpropanoid pathway and are modulated by several structural and regulatory gene families. In this study chromosome loci involved in the accumulation of anthocyanidin pigments in purple stems and leaves and the accumulation of proanthocyanidin pigments in brown pericarp were identified using 44K SNP array in 282 rice varieties based on association mapping method. Based on genes annotation database of rice and significant SNP signals obtained from association mapping analysis, 30 chromosome positions including Chalcone isomerase, Chalcone synthase, Leucoanthocyanidin reductase, bHLH, MYB, WDR, and B-Box coding genes were identified as candidate influencer genes in proanthocyanidin pigmentation in the rice grain pericarp. According the mentioned method, 39 genes were introduced as likely involved genes in purple stem appearance including, bHLH, MYB, WDR, B-Box, F3H, ChI, Glucosyltransferase and also 23 genes were detected for leaf pigmentation, including bHLH, Myb, WD40, B-Box and Glucosyltransferase coding genes. Considering to this fact that progenitor and domesticating process for all the rice cultivars are not the same, and many structural and regulatory genes are introduced for controlling anthocyanin pigment accumulation, it seems that in different cultivars, one or some of these introduced genes can be influencer gene for the accumulation of this pigment.