Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association

Abstract

Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color attributes of whole grain or brown rice are usually undesirable and need to be improved. To decipher the genetic basis of color variation in the whole grain rice, we conducted a genome-wide association analysis of three parameters of grain colors (brightness, redness, and yellowness) in a panel of 682 rice accessions. Twenty-six loci were identified for the color parameters, implying that grain color is under polygenic control. Among them, some major-effect loci were co-localized with the previously identified genes such as Rc and Rd. To eliminate the possible mask of Rc on other loci influencing grain color, we performed the association analysis in a subset of the panel that excluded the pigmented (red and black) rice. Eighteen loci or SNPs were detected to be associated with grain color in the subpopulation, many of which were not reported before. Two significant peak SNP regions on chromosomes 1 and 9 were validated using near-isogenic lines. Based on differential expression analysis of annotated genes within the SNP regions and metabolic analysis of pooled extreme samples, we found at least three annotated genes as potential candidates involved in the flavonoid metabolic pathway related to pericarp color. These results provide insights into the genetic basis of rice grain color and facilitate genomic breeding to improve appearance and commercial quality of whole grain rice.

Genetic mapping and molecular mechanism behind color variation in the Asian vine snake

“…All data supporting the findings in this study are available within this article and its additional files. The reference genome raw sequencing data, whole-genome sequencing data, and RNA-seq data have been deposited at NCBI Sequence Read Archive under accession number PRJNA926696, PRJNA928843, and PRJNA929071, respectively [91][92][93]. The genome assembly has been deposited in NCBI GenBank under accession number JAQQSC000000000 as well as in Genome Warehouse, National Genomics Data Center (NGDC) under accession number PRJCA014549 [94,95].…”

Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize

“…Chatham and Juvik performed association mapping in purple corn populations, Major QTLs for anthocyanin type were identified: Pr1 , R1 and the plant color-associated MYB, Pl1 [ 4 ]. The GWAS of colour variation in rice, twenty-six loci were identified, and at least three candidates involved in the flavonoid metabolic pathway [ 41 ]. In durum wheat, The genetic mapping identified 4 QTLs disclosed the candidate genes Pp-A3 , Pp-B1 , R-A1 , R-B , bHLH ( Myc-1 ) and MYB ( Mpc1 , Myb10 ) [ 42 ].…”