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To obtain a full understanding of the genetic diversity of the cytochrome oxidase III gene  (COX-III)  and its association with high altitude adaptation in Tibetan chickens, we sequenced  COX-III  in 12 chicken populations (155 Tibetan chickens and 145 other domestic chickens). We identified a total of 11 single nucleotide polymorphisms (SNPs) and 12 haplotypes (Ha1–Ha12). Low genetic diversity (haplotype diversity = 0.531 ± 0.087, nucleotide diversity = 0.00125) was detected for  COX-III , and haplotype diversity of Tibetan chicken populations (0.750 ± 0.018) was markedly higher than lowland chicken populations (0.570 ± 0.028). Obvious genetic differentiation (nucleotide divergence = 0.092~0.339) and conspicuous gene communication (gene flow = 0.33~32.22) among 12 populations suggested that Tianfu black-bone fowl (white feather) was possibly introduced from Tibetan chicken. SNP m.10587 T>C affects the specific functions of the COX enzyme. Haplotype Ha3 was found in Tibetan chickens, and SNP m.10115G>A caused an amino acid substitution (Val62Ile) associated with phospholipid binding, while mutations m.10017C>A and m.10555G>A and the previously reported SNP m.10065T>C reduced the hydropathy index to some extent. Together, this indicates that the mitochondrial membrane is more hydrophobic in Tibetan chickens.

A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens