# Exploring the Genetic Heritage of the Yucatán Black Hairless Pig: A Comparative Worldwide ROH Study

## TL;DR

This study uses genetic data to explore the inbreeding and genetic heritage of the Yucatán Black Hairless Pig, comparing it to other pig breeds worldwide.

## Contribution

The study provides new insights into the genomic homozygosity and shared genetic regions of the Yucatán Black Hairless Pig compared to indigenous and commercial breeds.

## Key findings

- The Yucatán Black Hairless Pig has moderate genomic inbreeding with ROH segments mainly in the 5–20 Mb range.
- The breed shares more ROH segments with indigenous populations than with commercial breeds.
- Genes within ROH regions include FGF5, BMP2K, PAQR3, RASGEF1B, and ANTXR2, involved in developmental pathways.

## Abstract

The Yucatán Black Hairless Pig is an indigenous Mexican breed adapted to tropical conditions. This study characterized its homozygosity using genome-wide SNP data and compared its runs of homozygosity (ROH) with those of indigenous and commercial pig populations worldwide. The results indicate moderate genomic inbreeding and the presence of conserved homozygous regions shared mainly with other indigenous breeds. These findings provide complementary genomic information useful for the characterization and conservation of this local breed. Protecting this genetic heritage is important for biodiversity conservation and for promoting sustainable livestock production in tropical regions of México.

The Yucatán Black Hairless Pig (YBHP) is an indigenous Mexican breed shaped by tropical environments and traditional management systems. This study aimed to characterize its runs of homozygosity (ROH) and compare its ROH patterns with those of indigenous and commercial pig breeds worldwide using the GGP Porcine 50K SNP array. After applying standard quality-control filters, ROH were identified, classified by length, and evaluated for shared homozygous regions across populations. The YBHP showed intermediate levels of genomic homozygosity (FROH = 0.09), with most ROH segments falling within the 5–20 Mb range. Comparative analyses indicated that the YBHP shared a higher number of ROH segments with indigenous populations than with cosmopolitan breeds. Gene annotation within ROH regions revealed SNPs located in genes previously reported in indigenous populations, including FGF5, BMP2K, PAQR3, RASGEF1B and ANTXR2, which participate in developmental and regulatory biological pathways. Overall, these results provide a detailed description of ROH distribution in the YBHP and offer complementary information to previous studies on its genetic characterization, supporting future conservation and management strategies.