Integrating genome-wide association analysis and selection signatures to identify the key genes affecting the primary economic traits of pigs

The meat quality of Bama Xiang pigs is superior, while Landrace pigs exhibit faster growth rates. Currently, research on the crossbreeding improvement of Bama Xiang pigs remains relatively limited. The primary goal of swine crossbreeding is to enhance the economic benefits for pig farms, with economic traits serving as key indicators for evaluating the economic performance of swine production. However, the genetic basis underlying the formation of economic traits in hybrid offspring remains unclear, which constrains further optimization of crossbreeding strategies. To elucidate the genomic basis of hybrids pigs F1 population, we integrated GWAS with selective scanning analysis, identifying 135 candidate SNP loci. A significant association signal was detected for adjusted backfat thickness at 100 kg on chromosome 12, which coincided with a selected region. Near the most significant locus, a closely linked gene (ALOX15) was identified, which plays a crucial role in fatty acid metabolism. Significant differences in phenotypic values were observed among different genotypes at the most significant locus, indicating that this locus represents a key mutation. The cDNA sequence of this gene comprised two haplotype modules, designated as dominant and the minor types. The main economic traits were enriched in pathways including growth hormone synthesis and secretion, and glucagon receptor activity. These research findings provide essential molecular markers for whole-genome selective breeding in pigs and offer a theoretical foundation for analyzing the molecular genetic mechanisms underlying economic traits in pigs. By assigning higher weights to candidate SNPs in genomic selection, the identified SNPs will contribute to the genetic improvement of major economic traits in pigs.