Fig. 2
From: A role for heritable transcriptomic variation in maize adaptation to temperate environments
Expression and splicing quantitative trait loci (QTLs) and their relations. a Relationship between expression heritability (H2) and cumulative percentage of expression variation explained (PVE) for all eQTLs identified for a given gene. b Proportion of expression heritability (H2) explained by eQTLs. c Rapid linkage disequilibrium (LD) decay in the maize genome allows a highly resolved location for cis-sQTLs relative to their targets. 5ŚS : 5 prime splicing site; 3ŚS : 3 prime splicing site. d cis-expression QTLs (cis-eQTLs) are enriched at transcription start and stop sites, while cis-splicing QTLs (cis-sQTLs) tend to reside in gene bodies. TSS, transcription start site; TES, transcription end site. e LD r2 distribution of the cis-eQTLs and cis-sQTLs identified for the same genes. f Co-localization of highly linked (r2 > 0.6) cis-eQTLs and cis-sQTLs relative to their target genes. g COMPACT PLANT2 (ct2) is co-regulated by cis-regulatory elements affecting both gene expression levels (eQTL) and splicing variation (sQTL). LD r2 is color coded and the lead SNP of eQTL (SNP name: 1-16367395, located at chr1:16,742,202) is highlighted as a purple diamond in the right panel. h Box plots of gene-level expression (FPKM) and splicing variation of the target intron (PSI) in ct2 in maize lines carrying different alleles of the lead SNP representing eQTL (chr1:16,742,202 T/C) (top panel) and the lead SNP representing the sQTL (chr1:16,742,200 C/T) (bottom panel). i Cysteine synthase 2 (cys2) is associated with both a cis-eQTL and a cis-sQTL. LD r2 is color coded and the lead SNP of eQTL (SNP name: 1-177050943, located at chr1:179,018,890) is highlighted as a purple diamond in the right panel. The two lead SNPs of eQTL and sQTL are not highly linked, indicating that the two regulatory elements may function independently. j Box plots of gene level expression (FPKM) and splicing-variation of the target intron (PSI) in cys2 in maize lines carrying different alleles of the lead SNP representing eQTL (chr1:179,018,890 C/T) (top panel) and the lead SNP representing the sQTL (chr1:179,011,485 G/T) (bottom panel)