Cytochrome b Genetic Diversity and Maternal Origin of Chinese Domestic Donkey

To clarify the origin of Chinese domestic donkeys, we investigated the mitochondrial Cytb gene from 244 animals from 13 native breeds. We found 55 variable sites in the Cytb gene sequence and subsequently defined 58 haplotypes. Analysis of haplotypes in combination with Cytb sequences revealed two mitochondrial origins in Chinese domestic donkeys, phenotypically expressed by the Somalian and Nubian lineages. The Somalian lineage predominated in Chinese domestic donkey breeds. Five specific Cytb gene SNPs diagnostic of each of the lineages were found in this study: 225(T-C), 237(C-T), 915(C-T), 1014(C-T), and 1134(A-G) mutations. They effectively distinguish the Nubian from the Somalian lineage in the mtDNA Cytb gene. Both lineages are from Africa and thus support the African maternal origins of Chinese domestic donkeys. No obvious geographic structure was found in Chinese domestic donkey breeds, but the population showed abundant genetic diversity.