Integration of Selection Signatures and Protein Interactions Reveals NR6A1, PAPPA2, and PIK3C2B as the Promising Candidate Genes Underlying the Characteristics of Licha Black Pig

SIMPLE SUMMARY: Licha black pig is a Chinese breed known for their large body length and appropriate fat deposition. Body length is an important production trait, while fat deposition is known to affect meat quality. However, their genetic characteristics of Licha black pigs have not been well studied. We analyzed the genomic information of 891 individuals of LI pigs, commercial pigs, and other Chinese indigenous pigs, identifying breed characteristics using runs of homozygosity, haplotype, and F(ST) selection signatures, which further annotated using protein-protein interaction networks and RNA expression data from FarmGTEx. Our study offers valuable insights into the mechanisms that impact pig body length and fat deposition, which can be applied in breeding to improve meat quality and commercial profitability. ABSTRACT: Licha black (LI) pig has the specific characteristics of larger body length and appropriate fat deposition among Chinese indigenous pigs. Body length is one of the external traits that affect production performance, and fat deposition influences meat quality. However, the genetic characteristics of LI pigs have not yet been systematically uncovered. Here, the genomic information from 891 individuals of LI pigs, commercial pigs, and other Chinese indigenous pigs was used to analyze the breed characteristics of the LI pig with runs of homozygosity, haplotype, and F(ST) selection signatures. The results showed the growth traits-related genes (i.e., NR6A1 and PAPPA2) and the fatness traits-related gene (i.e., PIK3C2B) were the promising candidate genes that closely related to the characteristics of LI pigs. In addition, the protein–protein interaction network revealed the potential interactions between the promising candidate genes and the FASN gene. The RNA expression data from FarmGTEx indicated that the RNA expression levels of NR6A1, PAPPA2, PIK3C2B, and FASN were highly correlated in the ileum. This study provides valuable molecular insights into the mechanisms that affect pig body length and fat deposition, which can be used in the further breeding process to improve meat quality and commercial profitability.