Appraisal of genetic variability and detection of sequence polymorphism in the Rc and Rd loci among the pigmented and non-pigmented genotypes of rice

Diverse, traditional landraces of indica rice with varying pigmentations are grown at the foothills of Eastern Himalayas. Interaction between two rice genes Rc and Rd is the major determining factor for diverse pigmentations. Rd regulates the synthesis of anthocyanidin, whereas Rc encodes a transcription factor for the expression of proanthocyanidins in rice. This study involved 24 genotypes of rice with varying pigmentation, collected from the Himalayan region and Eastern India for appraisal of genetic variability, character association, diversity regarding yield and grain-quality traits, and detection of sequence variation concerning Rc and Rd loci. Results revealed substantial genetic variability with significant genotype × year interaction for most of the traits. The tested genotypes were grouped into nine clusters based on Euclidean distance. Analyses of coding DNA and amino acid sequences revealed non-functional Rc gene with 14-bp deletion without or with a single nucleotide addition in the sixth exon, which led to premature stop codon formation or frameshift mutation in most of the black and white rice on the contrary to red rice genotypes. Furthermore, only a single white rice genotype was detected with a premature stop codon formation in the analyzed region of Rd . That mutation might be the probable cause for obstruction in anthocyanin and proanthocyanidin biosynthesis. Further studies are needed to identify the point mutations and premature stop codon (if any) in the Rd locus of various indica rice genotypes from these regions to unveil the evolutionary relevance of the Rd allele for aberrated dihydroflavonol-4-reductase protein formation.