Endothelial PAS domain protein 1（EPAS1）, also called hypoxia-inducible factor-2, is a key regulatory factor of hypoxic responses and plays an essential role in high-altitude adaptation in mammalian species. In this study, polymorphisms of EPAS1 were detected in 217 individuals from 2 Tibetan pig populations and 3 low-altitude pig breeds by DNA pooling, PCR-SSCP, PCR-RFLP and DNA sequencing methods. A total of 14 synonymous polymorphisms were identified in the coding region. The analysis suggested that SNP1（G963A）, SNP7（C1632T）, SNP10（G1929A） and SNP11（G1947A） showed potential association with high-altitude environment because of their particular variation patterns in Tibetan pigs. Linkage disequilibrium（LD） of these SNPs was analyzed. One common LD block including 5 SNPs clustering in exon 12 was identified in all studied pig populations. Haplotype H1（AGGTC） in LD block was dominant in Tibetan pigs（76.6 and 74.2% in Linzhi（LZ） and Chayu（CY） pigs, respectively） and segregated at higher frequency than that in low-altitude pig breeds（52.3, 58.7 and 56.2% in Wuzhishan（WZS）, Min（M） and Laiwu（LW） pigs, respectively）, indicating that H1 may relate to adaptation to high altitude in Tibetan pigs. These findings raise hope that EPAS1 gene can be a candidate gene that involved in adaptation of high altitude in Tibetan pigs.
