Maternal Origin And Genetic Diversity Of Chinese Domestic Donkeys

All 126 mtDNA D-loop sequences of 12 Chinese domestic donkey breeds were analyzed to reseach their origin and genetic diversity. These donkey breeds includes Beiyang donkey, Dezhou donkey, Guanzhong donkey, Huaibei donkey, Jiami donkey, Menggu donkey, Liangzhou donkey, Qingyang donkey, Taihang donkey, Xiji donkey, Xinjiang donkey and Yunnan donkey. The main results in this study are as follows:(1) There is high level of genetic diversity in Chinese domestic donkeys. All 126 sequences defined 36 different haplotypes with 37 variable sites defined. The haplotype diversity and the nucleotide diversity were 0.4667~0.9778 and 0.0012~0.0285 respectively, of which Liangzhou donkey displayed the lowest level, while Xinjiang donkey held the highest. The mean haplotype diversity and the mean nucleotide diversity in all breeds were 0.9055 and 0.0228.(2) The maternal origin of Chinese domestic donkeys was Somali and Nubian wild ass in Africa. A Neighbor-Joining tree with Kimura-2-parameter model was constructed using 36 haplotypes of Chinese domestic donkeys, 3 sequences from Nubian wild ass, 3 sequences from Somali wild ass and 6 sequences belonging to Asian wild ass, which clearly demonstrated that there were 15 haplotypes representing 76 samples in lineage Somali, and 21 haplotypes representing 50 samples in lineage Nubian. The reduced median networks also revealed two lineages and showed star-like phylogeny, in which two large haplotypes CD1 and CD5 were located in the center of lineages Somali and Nubian, respectively. so,the networks further support the N-J tree.The Chinese donkey sequences didn't clustered together with the Asian wild ass sequenses,so this study excluded the Asian wild ass as progenitor of Chinese donkeys.(3) There is poor population structure among Chinese donkey breeds. The donkeys of large, medium and small type belonged to the mixture of lineages Somali and Nubian except LZ breed, which only appeared in Lineage Somali.And all of the three donkey types were presented in the four high-frequency haplotypes CD1, CD2, CD3 and CD4. AMOVA analysis estimated that only 3.09% of the variation was among breeds and the left was within breeds. These results indicated that there was no correspondence between the geographic regions, body types and maternal origin among Chinese donkey breeds.Interpopulation Net Nucletide Diversity (Da). Interpopulation Nucletide Diversity (Dxy) and Fst values among Chinese donkey breeds were all quite low,which possiblely indicated the high gene flow.(4) There happened population expansion events in Chinese domestic donkeys. Mismatch distributions of lineages Somali and Nubian both showed one peak, and Fs values were -7.64(P<0.01) and -13.12(P<0.01),respectively, which suggested Chinese donkeys both lineages Somali and Nubian underwent population expansion events, and lineage Nubian did a larger one.(5) We discussed the spread routes of Chinese donkeys. It's approved that when an ancestral population and a derived population of the ancestral population are compared, genetic loci from the ancestral population are expected to show higher haplotype diversity and nucleotide diversity. Our results supported that the earliest domestic donkeys in China were raised in Xinjiang region, and the possible spread routes were:â—‹1 from Xinjiang via Gansu, Ningxia, Yan'an Shannxi to Guanzhong plain of Shaanxi province, then to Shanxi, Hebei, Henan, Anhui, Shandong and so on where donkeys were domesticated adaptable to the local climate and geographic conditions;â—‹2 meanwhile, from Xinjiang via Yan'an Shannxi, the Great Wall, Horqin Plain to northeastern China and Inner Mongolian plain where Northeastern donkey and Menggu donkey were domesticated, respectively;â—‹3 Finally, from North China via Sichuan to Yunnan province. The hypothesis is almost consistent with the history records. But more reseach is necessary to confirm these results.To further study maternal origin and genetic diversity of Chinese donkeys, it is necessary to do reseach on mtDNA D-loop region with more samples, or on microsatellite loci and Y chromosome so as to provide more proof.