Selective sweep analysis reveals candidate genes related to immunity in Licha black pig

In modern pig breeding, the cost used for epidemic prevention and disease cause huge economic burden to enterprises. Generally, disease resistance is closely related to immune function, some serum immune indicators and blood routine indicators can reflect the body's immune capacity, including immunoglobulins (Ig), interferons (IFN), and interleukins (IL). However, the knowledge of immune regulation in pig is relatively scant. The Licha black pig, a distinguished local breed in China, is known for its tolerance to roughage and robust resistance to adverse conditions. In this study, the immune indicators such as IgA, IgG, IgM, IFNγ, IL4, and IL12 were measured and served as the categorized criteria to divide Licha black pigs into different groups. Through selective sweep analysis of genomic data from distinct groups, several immune-related genes in Licha black pig were identified, including LYVE1, CFAP54, SYMD4, and SEC63. Further, it revealed that there are the significant differences in the genotype frequencies of these candidate genes at non-synonymous mutation sites between groups, as well as immune indicators across different genotypes of candidate genes. This study provides new insights into the genetic loci associated with immune traits in Licha black pig.