Mitochondrial diversity and phylogeographic structure of native cattle breeds from Yunnan, Southwestern China

Little is so far known about genetic diversity and phylogeographic structure of native cattle breeds from Yunnan in Southwestern China, a frontier zone that connects China with South and Southeast Asia. Herein we analyzed a 910-bp fragment of mitochondrial DNA (mtDNA) D-loop region sequences of 280 individuals from 6 Yunnan native cattle breeds, of which 251 sequences were newly determined. There were 93 variable sites that defined 117 haplotypes among all sequences. Phylogenetic analysis of all haplotypes revealed that Yunnan native cattle had two distinct mtDNA lineages - taurine and zebu. The taurine sequences fell into four haplogroups T1a, T2, T3 and T4, whereas the zebu sequences grouped into two haplogroups I1 and I2. In addition, our results revealed patterns of gradient changes in frequencies of taurine and zebu mtDNA lineages across different geographic regions of Yunnan. Furthermore, three kinds of methods (haplotype network, analysis of molecular variance, and Mantel tests) consistently showed no significant phylogeographic structuring among Yunnan native cattle breeds. This might be attributed to historical strong gene flow and genetic admixture among native cattle breeds in different geographic regions.