Phylogenetic Analysis of the Whole mtDNA Genome and Part of D-Loop Sequence of Huaibei Grey Donkey

In order to better protect and utilize the genetic resources of the local breed of Anhui Province, Huaibei Grey Donkeys(HGD), the experiment used PCR and sequencing technology to study the part of the D-loop region of mitochondrial DNA of 60 HGD. In 60 individuals from HGD in Anhui province were analyzed by DNAMAN software, the results showed that 23 polymorphic nucleotide sites. The content of bases A, C, G and T in the mtDNA D-loop sequence are 30.4%, 34.9%, 13.1%, 21.6%, respectively. The complete HGD genome was 16,670 bp in size, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and one non-coding control region. The haplotype diversity and nucleotide diversity of HGD were 0.870 and 0.02115, respectively. Twenty-three variable sites defining11 haplotypes were identified, The most frequent haplotype was Hap 9(23.33%), followed by Hap 4(21.67%), Phylogenetic analysis and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. In conclusion, HGD probably has two maternal lineages. Our results obviously exclude the Asian wild donkey as ancestors of Turkish indigenous donkey populations, and the African wild donkey (W haplotype) is the likely ancestors of HGD.