Figure 3: GWAS for gene expression.
From: RNA sequencing reveals the complex regulatory network in the maize kernel
The associations of the SNPs and the expression levels of each gene across 368 maize inbred lines are performed using linear mixed model. (a) The start position of the mapped genes in the maize genome is plotted against the position of the associated SNPs with the Bonferroni threshold (P<3.11 × 10−12). (b) The density of the distances between the lead SNP of each eQTL and its associated genes. If the lead SNP is in the upstream of the target gene, the distance from the SNP to the transcription start site was counted. If the lead SNP is in the downstream of the target gene, the distance from the SNP to the transcription end site was counted. Lead SNPs located in the annotated gene regions were excluded to avoid overweighting from enriched SNPs. (c) The distribution of the effects of local and distant eQTLs. Red line represents local association. (d) The distribution of the lead SNPs in local eQTLs.
