Unraveling the Genetic Legacy: Comparative Analysis of Yucatán Black Hairless Pig and Worldwide Indigenous Breeds

Abstract

The Yucatán Black Hairless Pig (YBHP) is a native Mexican breed with cultural and agricultural importance in the Yucatán Peninsula. This study explored the genetic diversity and population structure of YBHP using a genome-wide single-nucleotide polymorphism (SNP) from the porcine GGP 50K chip, comparing it with native and cosmopolitan breeds worldwide. Genetic diversity analyses revealed an observed heterozygosity (HO) of 0.3602 ± 0.032 and an inbreeding coefficient (FIS) of 0.1517 ± 0.076, indicating moderate diversity and a relatively low level of inbreeding for an endangered native breed. ADMIXTURE analyses revealed a predominant and distinctive ancestry component exclusive to YBHP, along with shared ancestry with European breeds, particularly those of presumed Iberian origin. Principal Component Analysis (PCA) and phylogenetic network clustering supported its genomic singularity while confirming ancestral proximity to traditional European pigs. These findings highlight the dual nature of the YBHP: a genetically distinct native breed shaped by local adaptation yet retaining ancestral signals from Old World lineages. This genomic insight provides a scientific basis for conservation planning, supports the breed’s recognition as a unique genetic resource, and promotes its sustainable use in regional production systems.