| The molecular phylogeny of horse populations was analysised based on the genetic variation of cytochrome b gene to study the relationship and genetic diversity of twelve horse populations of eastern Asia.The complete cytochrome b gene of Mongolia horse, Przewalskii'horse A and B strain, together with horse sequences of Xinihe, Sanhe, Cheju, Japan, Wuzhumuqin, Baerhu, Wushen, Pony and Thoroughbreed horse in GenBank, was sequenced to study DNA polymorphism and phylogenetic relationships. Analysis of the sequence variation of cytochrome b gene indicated that there was no insertion/deletion found in cytb sequences (1,140bp). The 1,140bp cytochrome b alignment contained 52 variable sites, of which 33 were parsimony informative sites with the strongest variable in the third codon positions and less variable in the first and second codon positions. The base composition of the cytochrome b sequences was highly biased. The average percent value of G+C (45.4%) was less than that of A+T (54.6%). There was a bias of the content of A and T in the second codon position, coming up to 61.5%. The content of nucleotide G at the third position was the lowest, the average was only 5.2%, and divergence among species is 4.7～5.5%. Sequence variation analysis exhibited high transition (Si) to transversion (Sv) substitution ratios (Si/Sv=14.2), and transitions and transversions were unsaturated in the sequence of cytochorrne b gene. The transition occured between G and A, T and C. Using a structural model of the cytochrome b protein as a template, we divided cyt b sequence data for horse populations into three functional domains. There was more variance within transmembrane domain of cytochrome b. The N-terminal end of cytb gene had more informative for phylogeny analysis.Phylogenetic tree of these horse populations were reconstructed by three methods: Neighbor-joining, UPGMA and Most Parsimonious methods. We supported the opinion that Przewalskii'horse and Mongolia horse were the kins and had the...
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