Association of SDR16C5, PLAG1, and ADCY4 Gene Polymorphisms with Body Size Traits in Bamei Pigs

Body size traits are pivotal indicators in pig breeding, directly influencing meat production performance and breeding efficiency. This study investigated the polymorphisms of SDR16C5, PLAG1, and ADCY4 genes in Qinghai Bamei pigs. Sixteen SNP loci were identified through Sanger sequencing, followed by population genetic parameter analysis and association studies. Results demonstrated that the SDR16C5 g.1570 G>C and ADCY4 g.519 T>C loci exhibited low polymorphism (PIC < 0.25), with the ADCY4 g.519 T>C locus showing significant deviation from Hardy–Weinberg equilibrium (p < 0.05). The remaining loci displayed moderate polymorphism (0.25 < PIC < 0.5) and conformed to Hardy–Weinberg equilibrium (p > 0.05). Association analysis revealed that PLAG1 gene loci g.44162 G>C and g.44471 A>G significantly affected multiple phenotypes. SDR16C5 gene g.1647 A>G locus showed that individuals with the GG genotype had significantly higher body weight than other genotypes (p < 0.05). The ADCY4 g.306 C>G and g.418 C>T loci were significantly associated with body length, height, and chest circumference (p < 0.05). Haplotype analysis identified superior body size performance in individuals carrying the SDR16C5-PLAG1 combined haplotypes (CACAG and GA/GG) and the ADCY4 CCTCCC haplotype. These findings validate the polymorphisms of SDR16C5, PLAG1, and ADCY4 genes as potential molecular markers for Bamei pig breeding, providing a theoretical foundation for functional gene exploration and innovative utilization of germplasm resources.