Extended Data Figure 7: Genome-wide association mapping of the genetic architecture of transcripts that covary significantly with fitness in the Indica population under drought conditions.
From: The strength and pattern of natural selection on gene expression in rice
Three out of eight transcripts are partially controlled by trans-eQTLs (illustrated for expression of the glycine-rich family protein-coding gene Os11g0209000 under drought conditions). Supplementary Table 27 provides results for other transcripts and for expression principal components or eigengenes as suites of transcripts. a, PCA of 179,634 SNP markers from the Indica population that were selected for analysis; the three principal components, plus a fourth, were included as cofactors in the multi-locus linear mixed model. b, Distribution of expected versus observed P values for associations between SNP markers and Os11g0209000 expression in a Q–Q plot. n = 131 genotypes; multi-locus linear mixed model, two-sided, Bonferroni-adjusted P < 0.05 for 179,634 SNP markers. c, The Manhattan plot indicates two significant trans-eQTL peaks for expression of Os11g0209000 (gene location indicated with vertical red bar). Only the top approximately 5% of SNPs (10,000 SNPs) are shown.
