Extended Data Fig. 7: Breed sharing and interaction cis-eQTL (bieQTL).
From: A compendium of genetic regulatory effects across pig tissues
a, Sample size of muscle RNA-Seq data across eight breed groups. b,c, Expression levels of NMNAT1 (b) and COMMD10 (c) at three genotypes of cis-eQTL in muscle across eight breed groups. d, The cis-eQTL discovered in each breed group (rows) that can be replicated (π1) across all other breed groups (columns). e, The heatmap of tissues regarding the pairwise Spearman’s correlation (ρ) of cis-eQTL effect sizes. Tissues are grouped by hierarchical clustering (bottom). Violin plot (left) represents Spearman’s correlation between the target group and the rest. f, Pearson’s correlation (r) of effect size between cis-eQTL from the multi-breed meta-analysis (y-axis) and those from the combined muscle population (x-axis). The P value was obtained from Pearson’s r test. g, Overlap of cis-eQTL detected from the combined muscle population (Combined) and those detected in single-breed (Single) cis-eQTL mapping (shared in at least two breeds). h,i, Examples of bieQTL in muscle. Each dot in (h, CA14) and (i, ATE1) represents an individual and is colored by three genotypes. Gene expression levels and ancestry enrichment scores are inverse normal transformed. The two-sided P value is calculated by the linear regression bieQTL model. The lines are fitted by a linear regression model using the geom_smooth function from ggplot2 (v3.3.2) in R (v4.0.2).
