Fig. 6: The genome-wide impact of breeding selection on gene expression regulation.
a Number of DEGs for each pair of sub-populations. b Sharing of DEGs between sub-populations. c UMAP plot of the dimensionality reduction analysis of the DEG expression matrix. d Heatmap of the 8 modes of DEGs. The numbers on the left represent the count of DEGs. The dashed box in the middle highlights representative cloned genes of known function among the DEGs, and the right side shows functional enrichment for each module (M3–M8) (two-sided Fisher’s exact test, Benjamini–Hochberg for multiple comparisons, p-adjust < 0.05. The bubble size corresponds to the number of genes annotated to a given term, and the color scale represents fold enrichment). e FST values of genic regions for DEGs and non-DEGs: for MCCs vs. LRs, DEGs (n = 3564) and non-DEGs (n = 49,972); for USMCs vs. LRs, DEGs (n = 3222) and non-DEGs (n = 50,309); and for USMCs vs. MCCs, DEGs (n = 1721) and non-DEGs (n = 51,413). Two-sided Wilcoxon rank-sum test, p < 2.2 × 10–16 for all comparisons (DEGs vs. non-DEGs). Dots within the boxes indicate the FST values. f FST values of eQTLs for DEGs and non-DEGs. For MCCs vs. LRs, DEGs (n = 4715) and non-DEGs (n = 35,893); for USMCs vs. LRs, DEGs (n = 4162) and non-DEGs (n = 36,288); and for USMCs vs. MCCs, DEGs (n = 3304) and non-DEGs (n = 36,715). Two-sided Wilcoxon rank-sum test, p < 2.2 × 10–16 for all comparisons (DEGs vs. non-DEGs). Dots within the boxes indicate the FST values. g Relationships between the FST values of DEGs and the degree of differential expression. The data are presented as the mean values ± SEM. h Relationships between the FST values of eQTLs for DEGs and non-DEGs and the strength of eQTL signals. The data are presented as the mean values ± SEM. i XP-CLR scores of DEGs and non-DEGs: for MCCs vs. LRs, DEGs (n = 1788) and non-DEGs (n = 17,974); for USMCs vs. LRs, DEGs (n = 1596) and non-DEGs (n = 19,813). Two-sided Wilcoxon rank-sum test: p = 1.35 × 10–6 for MCCs vs. LRs and p = 2.89 × 10–4 for USMCs vs. LRs (DEGs vs. non-DEGs). Dots within the boxes indicate XP-CLR scores. j XP-CLR scores of eQTLs for DEGs and non-DEGs: for MCCs vs. LRs, DEGs (n = 4196) and non-DEGs (n = 31,363); for USMC vs. LR, DEGs (n = 3641) and non-DEGs (n = 31,887). Two-sided Wilcoxon rank-sum test: p = 5.02 × 10–8 for MCC vs. LR and 7.54 × 10–4 for USMC vs. LR (DEGs vs. non-DEGs). Dots within the boxes indicate XP-CLR scores. k Relationships between the XP-CLR scores of DEGs and the degree of differential expression. The data are presented as the mean values ± SEM. l Relationships between the XP-CLR scores of eQTLs for DEGs and non-DEGs. The data are presented as the mean values ± SEM. All boxes depict the median and interquartile range (IQR). The whiskers extend to the most extreme data points within 1.5 × IQR from the quartiles, and points outside this range are shown as outliers. Source data are provided as a Source Data file.
