Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.

Abstract

Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits^® Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.