Integrated Whole-Genome Resequencing and Transcriptomic Analyses to Reveal Breed-Specific Selection Signatures of Cardiac-Related Genes in Wuzhishan Pigs

The WZS minipig, native to the Hainan province of China, is characterized by excellent meat palatability. In addition, this breed represents a promising animal model for human disease research, especially for cardiac diseases. Whole-genome resequencing is a powerful approach for guiding breeding decisions. By identifying mutations and conserved regions linked to environmental adaptability and physiological fitness, this method supports both the genetic improvement in pig breeds and their application as animal models for human disease research. However, the genomic locations of high and low nucleotide diversity regions harboring cardiac-related genes in the WZS genome remain unclear. In this study, cardiac-related genes were selected based on whole-genome resequencing data previously released by our research team, including 147 samples from five breeds (PRJCA054653), and detected RNA expression patterns of heart tissues across five growing periods. Between-breed analysis indicated that WZS pigs exhibited the highest nucleotide diversity among the five breeds and underwent a recently diverged lineage. A non-redundant 236-gene set was identified from the union of three gene subsets, of which the functional genes enriched in KEGG (67) and GO terms (192) were primarily implicated in cardiac muscle structure and energy metabolism, supplemented by additional genes selected based on high expression levels (52) and DEGs (44). Specifically, the DEGs of ACTC1, TNNC1, TNNT2, COX4I1, and MYH7 were highly expressed in the heart and enriched in the cardiac contraction pathway. The findings provide candidate genes for breeding and support the future use of WZS pigs as an improved animal model for human cardiac research.