Fig. 4

Integration of ATAC-seq and RNA-seq data to understand how cis-regulatory DNA variants might underlie pig phenotypic differentiation. a Experimental design and sample collection for the RNA-seq and ATAC-seq analysis in Luchuan and Duroc pigs. b Enrichment of DNA variants under potential selection in DEG promoters. The enrichment of promoters of all protein-coding genes was set as a baseline group. * Represents a p-value < 0.05. c Enrichment of DNA variants under potential selection in ATAC-seq peaks with promoter regions excluded. * represents a p-value < 0.05. ** Represents a p-value < 0.01. d Number of DEG with highly differential promoter variants. e Number of DEG with distal diffCA having highly differential variants. f Luciferase reporter assays in C2C12 cells to evaluate the effect of highly differential DNA variants on enhancer activity. The genes on the x-axis labeled in blue are more highly expressed in the skeletal muscle of Luchuan while those in orange are more highly expressed in Duroc. ** represents a p-value < 0.01, * represents a p-value < 0.05