Genetic Association Analysis of Skin Traits and the TAF11 Gene in Shenxian Pigs

This study aimed to characterize the site-specific variation in skin traits of Shenxian pigs and to identify key genetic loci regulating skin thickness. A total of 50 Shenxian pigs were selected, and skin samples were collected from nine different anatomical sites. Total skin thickness was precisely measured, and collagen content was determined for each site. Based on literature review and database screening, TAF11 was identified as a candidate gene. Genotyping of the g.35543837 locus was performed using Sanger sequencing and KASP, followed by association analysis between different genotypes and skin thickness traits. The results showed significant site-specific variations in skin thickness (1.26–7.20 mm) and collagen content (7.01–24.54 g/100 g) in Shenxian pigs. Association analysis revealed that the TAF11 g.35543837 C > G variant was significantly associated with increased skin thickness, with the effect being particularly evident in gilt. Individuals with the CG genotype exhibited greater skin thickness at multiple anatomical sites compared with those carrying the CC genotype. This study preliminarily identified a potential locus associated with skin thickness in Shenxian pigs within the TAF11 gene. The sex-dependent effect observed at this locus provides a new clue for understanding the genetic basis of this complex trait and offers valuable information for the genetic improvement of skin-related traits in Shenxian pigs.