Genome-wide Association Analysis and Candidate Genes Identification for Pericarp Color in rice (Oryza sativa L.)

The unpolished whole rice grains having the pericarp intact are packed with nutrients and antioxidants. The colored pericarp provides health benefits against lifestyle diseases. The diversity in the pericarp color which can be red, brown or black in various shades is a reflection of differential antioxidants profile. However, a natural mutation in the Rc gene (coding for red pericarp) resulted in the production of rc allele (coding for white pericarp) which was subsequently selected during domestication. The objective of this study is to identify novel candidate genes for pericarp color using genome-wide association analysis. Three types of scoring systems were used for this work namely, the 1 to 8, 0 & 1 and 1 & 9 scoring systems. For the 1 to 8 and 0 & 1 scoring systems, 278 accessions of the 3K rice panel were visually sorted into eight pericarp groups (1 to 8 scoring system) having seeds with green, white, off-white, light red, red, dark red, brown, and black pericarp, respectively and later into two groups (0 & 1 scoring system) having seeds with colored and white pericarp, respectively. For the 1 & 9 scoring system, 254 accessions of the 278 accessions were sorted into two groups having seeds with white and red shaded pericarp colors, respectively. The genome wide association analysis revealed that a SNP in chromosome 7 corresponding to Rc gene along with a SNP in chromosome 1, which is novel, are significantly associated with the pericarp color with cumulative phenotypic variance of similar to 80% for the novel (1 to 8) pericarp scoring system. Meanwhile, a SNP in chromosome 7 which is also significantly associated with pericarp color with phenotypic variance 20.63% was identified using GWAS with the 1 & 9 scoring system. Haplotype analysis of the three significant SNPs (chr01_17821895; chr07_26810556; Rc gene) revealed significant differences for the Chi-square statistics (p value < 0.05*). Two candidate genes identified in this study, one gene coding for MAPKK6 and the other gene OPAQUE3, are also significantly associated with the pericarp color in rice. This study utilized three distinct pericarp scoring systems and identified novel genomic regions associated with pericarp color. These findings will assist in colored rice breeding efforts.