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.
Vet.