Abstract：At present, there are few studies on sheep (Ovis areis) populations in Southwest regions. To analyze genetic variability, population structure and evolutionary relationships of Chinese indigenous sheep in Southwest regions, the complete sequences of mitochondrial DNA (mtDNA) cytochrome (Cytb) gene of 183 individuals in 10 sheep populations were determined with primer pairs which were designed by Oligo 6.0 based on the sheep mitochondrial genome. We analyzed the genetic diversity and population structure of 8 local breeds and 2 imported breeds using softwares of MEGA 5.2, DnaSP 5, Phylip 3.695 and Network 4.0. Results of genetic diversity showed that 62 haplotypes were defined by 153 polymorphic sites. The mean haplotype diversity, the average nucleotide diversity and the average number of nucleotide differences were 0.792, 0.002 43 and 5.054, respectively. The range of the nucleotide diversity (Pi) among 10 sheep breeds was from 0.001 28 (Zhaotong sheep) to 0.006 55 (Guidehei sheep). The haplotype diversity (Hd) varied from 0.582 (Tengchong sheep) to 0.924 (Xizang sheep). The results showed that 3 sheep populations in Yunnan Province had a relatively lower level of genetic diversity, while the genetic diversity level of several other sheep populations was higher. From the results of analysis of molecular variance (AMOVA) analysis, selected 10 sheep populations in China had maintained a high level of within-population genetic differentiation (87%), with remainder explained by differentiation among populations (13%). The neighbor-joining tree and network analysis indicated that there were 3 main branches in Chinese indigenous sheep, however, lineages A and B were still main lineages of Chinese indigenous sheep in southwest China. These results may provide theoretical reference for developing a scheme of preservation and utilization of sheep genetic resources in Southwest China.
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