Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds

SIMPLE SUMMARY: In this study, we identify the promoters, typical enhancers (TEs), and super-enhancers (SEs) in the livers of Chinese local and Western commercial pig breeds. Western breeds included fewer SEs in number, while more QTLs of growth-related economic traits were associated with these SEs. Comparison among different porcine tissues and liver tissues from pigs, humans, and mice suggested a high tissue specificity of SE. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding. ABSTRACT: The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.