Whole-genome resequencing reveals the genetic diversity, population structure and selection signatures in Chinese indigenous Kele pigs

A total of 66,204,339 autosomal single nucleotide polymorphisms (SNPs) were detected in the 120 pigs, and 21,738,497 SNPs were retained for further analysis after filtering. The results showed that KLPs had higher genetic diversity, along with the smallest FROH value compared to DUPs, LRPs, and YRPs. Moreover, KLPs displayed a relatively unique genetic structure with a higher LD decay, and the majority of individuals within the KLPs exhibited distant genetic distances and relationships. Totals of 688 selected regions were identified, including 723 published QTLs. Within the selected regions, 192 candidate genes were annotated, and seven genes were found to be functionally involved in coat color (<i>KIT</i>), immune response (<i>JAK2</i> and <i>SOCS1</i>), heart development (<i>NTRK3</i> and <i>SRF</i>), muscle growth and development (<i>VDR</i>), and fat deposition (<i>KDR</i>). These findings will provide valuable insights for the future conservation, breeding, and utilization of KLPs.