Fig. 6: Conservation of gene expression, cis-eQTL and complex trait genetics between pigs and humans.

a, Enrichment (Fisher’s exact test) of pig eGenes with human eGenes across 17 matching tissues. Red triangles: matching tissues. b, Pearson’s correlation of eQTL effect size in orthologous genes (n = 15,944) between pigs and humans. c, Expression levels, TAU values and tissue-sharing levels for four groups of orthologous genes across 17 tissues in pigs. Neither, 3,993 non-eGenes in both species; human-specific, 8,174 eGenes; pig-specific, 3,882 eGenes; shared, 10,574 eGenes in both species. Two-sided Wilcoxon rank-sum test, ***P < 0.001. Diamond, median; error bar, upper/lower quartiles. d, LOEUF in the four groups of orthologous genes in ten evenly spaced expression level bins. One-sided Wilcoxon rank-sum test, NS P > 0.05, *P < 0.05, **P < 0.01 and ***P < 0.001. The diamond and error bar are the same as in c. e, Significance (−log₁₀(P)) of Pearson’s r of orthologous gene effect size between pig (n = 268) and human (n = 136) traits derived from TWAS. Each bar represents a pig–human trait pair in the same tissue (n = 11) and the within-domain blocks of color correspond to different human traits. The number of tested genes for each of the pairs is shown in Supplementary Table 30. The text in the middle of the circle represents the significant examples of pig–human trait pairs in different thresholds. For each example, it includes human trait (top), pig trait (bottom) and TWAS tissue (left). P_{cutoff 1}: FDR < 10% across all tested combinations. P_{cutoff 2}: Bonferroni-corrected P < 5% within each trait–tissue pair of humans. f, Differences in the number of significant genes (FDR < 5%) from cross-species (pig and human) meta-TWAS, compared to those from human TWAS. Supplementary Tables 18 and 29 present a detailed description of pig traits and human traits, respectively. g, FDR of discovered genes in human TWAS (RawTWAS) and cross-species meta-TWAS in the brain for BFT (pig) and weight (human). h, Pearson’s r between TWAS significances (color bar) of genes in pig BFT and their heritability enrichments (mean ± s.e.) in human weight. The orthologous genes were divided into ten evenly spaced bins by sorting the P values of TWAS in the brain of pig BFT. Shading: standard error of the fitting line.