Figure 3.—

Haplotype data across the GS3 gene region. (A) The gene model for GS3 containing five exons and comprising ∼6.2 kb is shown horizontally along the top; the position of the C165A mutation is shown in red; and SNP positions with GS3 are connected by lines to the haplotype table below. Rows in the table correspond to gene haplotypes (GH), which are organized into groups on the basis of STRUCTURE analysis; columns indicate the distribution of polymorphisms at each SNP position; blue indicates the common Group 1 SNP allele; yellow indicates a variant SNP allele; and red highlights the presence of the A allele for long grain at the C165A SNP. The number and subpopulation identity of varieties carrying each haplotype are indicated in columns to the right. (B) Extended haplotype (EH) table corresponding to a 66.2-kb region flanking the GS3 gene; the position of the C165A mutation within the extended haplotype is indicated in red; colors are the same as described in A above; stippled yellow squares indicate the presence of a third allele; and SNP names and primers used to detect them (Table S1) are shown along the x-axis at the bottom.