Analysis of the Genetic Diversity and Genetic Structure of Jiangshan Black Pigs Using Single Nucleotide Polymorphism (SNP) Chips

Simple Summary This study investigated the genetic attributes of the Jiangshan black pig conservation population, with a specific focus on genetic diversity, family structure, and levels of inbreeding. The results provide significant insights for the management and conservation of a pig population with limited numbers. The study proposes the use of genomic data by breeders to improve breeding practices, especially by taking into account familial relationships. Suggestions include maintaining an equitable distribution of male and female pigs within each family and choosing individuals with a kinship coefficient lower than 0.1 for breeding purposes.Abstract The Jiangshan black pig is an indigenous pig breed in China, renowned for its superior meat quality and adaptability to roughage. However, the population of Jiangshan black pigs has dwindled due to the introduction of cosmopolitan pig breeds and the outbreak of African swine fever, putting them at risk of extinction. To offer insights into the conservation and breeding of Jiangshan black pigs, this study involved 118 Jiangshan black pigs as the research subjects and employed the Zhongxin-1 Porcine Breeding Array PLUS chip to detect whole-genome SNPs. Additionally, various software tools were utilized to accurately analyze the genetic diversity, phylogenetic relationship, inbreeding coefficient, and pedigree structure of the Jiangshan black pig conservation population. The findings indicated that the effective population size (Ne) of the Jiangshan black pig was 4.9, with an average inbreeding coefficient of 0.253 within the population. A genetic relationship analysis identified that the 16 male pigs were clustered into four families, and the 100 female pigs were also assigned to these familial groups. Furthermore, two female pigs were classified as "other" due to their distant genetic relatedness to all the males. These results contribute to a better understanding of the current status of the conservation of the Jiangshan black pig population and offer a theoretical foundation for the development of conservation strategies.