Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima’s D and Fu’s F_S tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.

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.