Fig. 6

Nucleotide diversity at cis-eQTL within subpopulations for 3,053 rice accessions. Average nucleotide diversity (π) for 100 kb regions surrounding Indica-specific, Japonica-specific, and shared eQTL are pictured in panels A, B, and C, respectively. For each, subpopulation and class of eQTL (e.g.Indica-specific, Japonica-specific, and shared) π was calculated for each SNP within 100 kb of the most significant eQTL SNP. π for the eQTL windows were compared to a genome wide (GW) average in which regions with eQTL and site with low diversity (MAF <0.01 in 10 of 12 subpopulations) were excluded. Asterisks indicate significant differences between GW and eQTL regions determined using a two-sided Student’s t-test (* p< 0.05; ** p< 0.001). Subpopulations are named following [27] (aro: aromatic; ind1A: indica-1A; ind1B: indica-1B; ind2: indica-2; indx: indica-X; japx: japonica-X; subtrop: subtropical japonica; temp: temperate japonica; trop: tropical japonica)