Genomic Diversity, Inbreeding, and Selection Signatures in Duroc, Landrace, and Yorkshire Pigs from a Long-Term Closed Breeding System

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 100K SNP panel (n = 37,041 SNPs shared among breeds). 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 analyses revealed different patterns of autozygosity, with DD exhibiting more long ROHs indicative of recent inbreeding, while YY harbored a higher number of short ROHs, 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. Generation Proxy Selection Mapping (GPSM) identified genomic regions under ongoing selection by associating SNP genotypes with proxy for generation number. In total, 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 characteristics. Notably, no genes were shared across breeds within ROH islands, suggesting breed-specific historical selection signatures. However, GPSM revealed 35 genes shared between DD and YY, and one QTL (longissimus muscle depth) shared across all three breeds, indicating partially convergent selection targets. Despite differences in the genomic regions associated with overlapping traits, functional annotations of GPSM significant loci and ROH islands suggest potential functional convergence or pleiotropic effects.