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

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.