Population Genomics Reveals Genetic Structure, Genomic Inbreeding, and Shared Homozygosity Hotspots in the Peruvian Paso Horse

The Peruvian Paso horse (PPH) is an iconic gaited breed recognized for its distinctive smooth gait, historical importance, and cultural value. However, genome-wide information on its genetic diversity, population structure, demographic history, and genomic inbreeding remains limited. This study characterized genomic diversity, population structure, linkage disequilibrium (LD), effective population size, and runs of homozygosity (ROH) in southern PPH using high-density SNP markers. A total of 141 individuals were genotyped with the Illumina Equine SNP70 BeadChip, and 49,610 autosomal SNPs passed quality control. Bayesian clustering identified three genetic clusters, with substantial admixture and weak differentiation indicating considerable connectivity among breeding lineages. Principal coordinates analysis supported these patterns and showed partial overlap among clusters. Genetic diversity was moderate, with observed heterozygosity ranging from 0.322 to 0.363 and negative inbreeding coefficients. Demographic analyses revealed contrasting patterns, with Cluster 2 showing the highest LD and lowest effective population size, whereas Cluster 1 exhibited the lowest LD and largest effective population size. ROH analyses revealed differences in genomic inbreeding, with Cluster 3 showing the highest FROH and greatest abundance of long homozygous segments. Several ROH hotspots were identified, including a chromosome 7 hotspot shared across clusters. Functional annotation highlighted genes associated with epigenetic regulation, tissue remodeling, skeletal development, and neuronal processes. Overall, southern PPH retains moderate genomic diversity despite population structure and localized autozygosity. These findings provide novel insights into the breed's genomic architecture and breeding history and support future conservation and sustainable breeding strategies.