Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color

Simple Summary There are few reports on local pig breeds in Guizhou province. In this work, the population structure, genetic diversity, and selection characteristics of three foreign pig breeds and seven Guizhou local pig breeds were studied. Principal component analysis, adjacent tree analysis, and ADMIXTURE analysis showed that Chinese and Western pig breeds had different ancestral sources. Jianhe White Xiang pig (JHBX) had a distant genetic relationship with the other six local pig breeds in Guizhou province and had unique genetic characteristics. The genetic diversity of the JHBX population was low, and the genetic diversity of the remaining six Chinese native pig populations was generally at a moderate level. In addition, we also screened the candidate genes that affect the coat color phenotype of pigs in Guizhou province through selection signals. Our findings will advance our understanding of the genetic mechanisms underlying these germplasm characteristics.Abstract The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.