Figure 3.

Mapping of the GWAS peak on chromosome 6 associated with debranched starch structure showing (A) the linkage disequilibrium plot of the 38 SNPs most significantly associated with PAM and PAP measured using the SEC method. A scaled section of the chromosome underlying this region is shown where the positions of the genes are labeled with red boxes sized according to their annotation in the Nipponbare reference genome (release 7). The positions of the 38 SNPs are also indicated where the names of the 11 tag SNPs are highlighted in red. The log₁₀-scaled association P values of these 38 SNPs are shown in the bar plot where bars reflect their relative effect sizes. Also shown are (B) the eight haplotypes formed from the 11 tag SNPs where specific phenotypic ranges for both PAM and PAP are explained by specific haplotypes. The distribution of these eight haplotypes (C) is then checked with data from The 3000 Rice Genomes Project (2014) in which it was shown that haplotypes representing higher PAM values appear prominently among the indica and aus subspecies, while the haplotypes representing lower PAM values appear prominently among the japonica, predominantly in temperate japonica, and haplotypes belonging to intermediate PAM are represented in aromatics subspecies.