Abstract：The objective of current study is to identify the genetic resource and phylogenetic relationship of indigenous horses in Gansu based on control region of mitochondrial DNA (D-loop), which was re-sequenced from Equus przewalskii, Mongolian horse , Qilian horse and Maqu horse (Maqu population, Hezuo population and Luqu population). The results revealed that higher proportion of A+T content than that of G+C in all breeds. Fifty-six haplotypes were reconstructed base on 50 polymorphic sites in all populations of Gansu horses. In addition, the nucleotide diversity (π) and haplotyple diversity (Hd) was 0.967±0.004 and 0.01782±0.0076, respectively, which suggested extensive divergence among Gansu horses. Six clusters (A, C, E, F and G) and fifteen sub-clusters(A1-A4, A6, C2, D3-D6, G and F1-F3) were distributed in Gansu horses. Cluster E was identified from Hequ horses merely; Most frequency of Cluster C and Cluster D were filled with Hequ and Qilian, respectively; Cluster A was found from all Gansu horses breeds. Notably, phylogenetic analyses showed Qilian horse share the same haplotype with other population in this study, which implied Qilian horse have the same maternal origin with them. To reveal the relationship between gansu indigenous horses and other breeds in other places of china and all over the world. NJ (Neighbor-Joining) phylogeny tree obtained from phylogenetic analyses compared with other places horses' NJ (Neighbor-Joining) phylogeny tree made based on Vilà C. and Janse T. identified standard cluster. The result suggested E.przewalskii had the same maternal origin, otherwise, E. przewalskii got mutation during their evolution. Mongolian horse, Qilian horse and Hequ horse not only had the same maternal origin with domestic horse (Guanzhong horse, Tibtan horse, Jinjian horse, Datong horse, Debao pony, Lichuan horse, Baise horse) but also had the same maternal origin with horses in East Asia, west Asia , central Europe, Western Europe, North America and Middle East. In addition, Qilian horse and Hequ horse also had the same maternal origin with E. przewalskii, potentially. The study results will be a reference for genetic resources conservation and development and utilization of indigenous horses in Gansu.
