Candidate Gene Identification and Genomic Prediction for Key Reproductive Traits in Yorkshire, Landrace, and Duroc Pigs

The study analyzed ten reproductive traits in three major commercial breeds—Yorkshire, Landrace, and Duroc—raised under uniform management. Genetic parameters were estimated using a repeatability animal model in ASReml, genome-wide association studies (GWAS) were performed with 46,358 post-QC SNPs using GCTA, and genomic prediction was evaluated with GBLUP. Heritability estimates were low to moderate, with gestation length (GL) highest (0.33–0.41). GWAS identified significant loci across breeds: in Yorkshire, 37 genome-wide significant SNPs across 17 SSCs for seven traits; in Landrace, 16 SNPs for TNB and one for NBW; and in Duroc, 31 SNPs across 12 SSCs (predominantly for TNB). Among these SNPs, CNC10042060, CNC10160995, and CNCB10003799 were consistently associated with TNB in both Yorkshire and Duroc pigs. Additionally, five SNPs, CNC10012965, CNC10042060, CNC10120451, CNCB10003799, and CNCB10007759, showed significant associations with NBW in Yorkshire and Landrace pigs. Candidate genes mapped within ±1 Mb of significant SNPs were enriched for biologically plausible pathways. Genomic prediction accuracies ranged from low to high depending on trait and breed, such as reaching 0.68 for GL in 39 Yorkshire and 0.59 in Landrace. These results delineate shared and breed-specific genetic architectures, provide actionable markers and candidate genes, and can accelerate genetic gains in commercial breeding programs.