SNP data set of the Peruvian Paso Horse from southern Peru

The dataset consisted of genome-wide SNP genotypes from 141 Peruvian Paso horses (Equus caballus) representing the southern population of the Peruvian Paso horse breed. Individuals were genotyped using the Illumina Equine SNP70 BeadChip. Genotype data were subjected to standard quality-control procedures, including filtering for SNP and individual call rates, minor allele frequency, and removal of non-autosomal markers. After quality control, 49,610 autosomal SNPs were retained and exported in Variant Call Format (VCF) for downstream population genomic analyses. The resulting VCF file contains genotype information used to investigate genetic diversity, population structure, linkage disequilibrium, effective population size, runs of homozygosity, genomic inbreeding, and shared homozygosity hotspots in the southern Peruvian Paso horse population.