Equine

Peruvian Equine Genomics: Application of Third-Generation Sequencing (TGS) and High-Density SNP Genotyping in the Peruvian Paso Horse

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Abstract

The Peruvian Paso Horse (PPH) is an emblematic Peruvian genetic resource valued for its unique four-beat gait and cultural significance, yet limited genomic information has constrained evidence-based breeding and conservation. This study aimed to generate foundational genomic resources for the PPH and to characterize genetic diversity, population structure, and genomic inbreeding using complementary sequencing and genotyping approaches. We produced an integrative genomic characterization combining PacBio HiFi long reads, Illumina short reads, Hi-C scaffolding, and high-density SNP genotyping. Whole-genome sequencing and k-mer modeling estimated a haploid genome size of ~2.39 Gb and low heterozygosity, consistent with the high contiguity achieved in the HiFi-Hi-C nuclear assembly, and the mitochondrial genome (16,617 bp) was fully resolved and structurally consistent with other Equidae. Mitochondrial phylogenetic analysis based on one PPH complete mitogenome and 680 publicly available equine mitogenomes (total n = 681) placed the PPH within a European-breed clade including Westphalian, Maremmano, Holsteiner, and Shagya-Arab, as well as sequences labeled as unspecified German and Serbian breeds, with potential connections to Asian lineages. Mitogenomic variability was concentrated in the control region and RNA genes, while protein-coding genes showed signatures of purifying selection. To complement the reference resources, we genotyped 143 PPH individuals from southern Peru (Arequipa, Ica, and Lima) using the Illumina Equine SNP70K BeadChip; after quality control, diversity indices indicated moderate genetic variation (Ho = 0.348; Hs = 0.345; Ht = 0.352) and low regional differentiation (Fst = 0.021), consistent with substantial gene flow, although PCA and phylogenetic clustering suggested subtle sub-structuring, including a recognizable cluster of individuals from Ica. Genomic inbreeding estimated from runs of homozygosity showed considerable inter-individual variation (fROH = 0.011-0.260; mean = 0.085), with most horses showing moderate inbreeding (fROH ≈ 0.05-0.12) and ~10% showing high values (fROH > 0.15), indicative of recent consanguinity. Overall, these results establish the first comprehensive genomic framework for the PPH and provide a foundation for implementing genomic tools to monitor diversity and inbreeding, identify potentially at-risk lineages, and inform long-term breeding and conservation planning for this culturally and economically important Peruvian breed.

Keywords: 2026

How to Cite:

Saldaña, C., Vásquez, H., Bardales, W., Murga Valderrama, L., Maicelo, J. & Arbizu, C., (2026) “Peruvian Equine Genomics: Application of Third-Generation Sequencing (TGS) and High-Density SNP Genotyping in the Peruvian Paso Horse”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287365. doi: https://doi.org/10.31274/wcgalp.24276

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