Figure 4
Gene structures of LOC_Os10g35920 and LOC_Os11g48090, the phenotypic variation explained by their haplotypes, and penetrance in the 3,000 rice genomes. (A) LOC_Os10g35920 was implicated by a single intronic SNP (GSc10.1) that had a significant association to cooked grain shape (GSc). The T allele of this SNP had the most influence in the GSc variation that when combined with the G alleles of the two promoter region SNPs has the potential to result in bolder grains. Mapping haplotype TGG in the 3,000 rice genomes showed that the haplotype was present only in japonica accessions, particularly tropical japonica. (B) The gene structure of LOC_Os11g48090 showed the position of the significantly associated SNPs positioned at the 3′-UTR of the gene. Plotting the variation of GWi with respect to the haplotypes formed by the significant SNPs showed that the accessions that were homozygous to the T and C alleles of these SNPs showed a tendency to be bolder both in raw and cooked grains. Mapping the haplotypes in the 3,000 rice genomes showed that all haplotypes have pervasive representations in all subspecies as well as those classified as admixtures.
