Genetic Diversity, Origin And Genetic Differentiation Of Ten Sheep Breeds Using Mitochondrial DNA D-loop Region

The whole sequence of D-loop of mitochondrial DNA (mtDNA) from 133 individuals representing 10 sheep breeds was analyzed to determine the origin and genetic diversity of domestic sheep. Phylogenetic analyses revealed that there were two mtDNA lineages (A and B) identified in 10 sheep breeds. Population genetic structure and population expansion were carried out. The conclusions were as follows:1.The results showed that the length of mtDNA D-loop in domestic sheep was 1106～1182 bp. It could be concluded that the length of D-loop be 1181bp. Besides insertion or deletion of several nucleotide sites, the length variation of mtDNA D-loop sequences of sheep individuals mainly resulted from the different times of 75 bp tandem repeats motif. Continuous 4 bases deletion existed in three sequences of 1176bp besides single insertion/deletion. The percentage of A, T, G, C were 33.0%,29.7%,14.4%,22.9%,A+T was 62.7%,G+C was 32.3%. Obviously, the content of A+T was higher than that of G+C. There were 155 polymorphic sites, with 53 singleton polymorphic sites and 102 parsimony informative polymorphic sites. There are 143 transitions and 16 transversions within 155 variable sites, of which 4 sites simultaneous existed transition and transversion. The main substitution was transition.2. 103 haplotypes were defined by 155 polymorphic sites. Lanzhou big sheep and Sunite sheep had one shared haplotype (Hap₃0 and Hap₈1). The mean nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02015±0.00076 and 0.9937±0.0022, respectively, and the average number of nucleotide differences (k) was 20.532. The results showed an abundant genetic diversity in ten domestic sheep. The range of the mean nucleotide diversity among ten sheep breeds were 0.00697⁰.02209, of which the highest and lowest sheep breed were Bashibai sheep (0.02209) and Zhaotong sheep (0.00697), respectively. The range of haplotype diversity among breeds was 0.803¹.000, of which the highest and the smallest breed was Tashikuergan sheep and Hanzhong sheep respectively. The result shows the genetic diversity of domestic sheep breeds was abundant, but the genetic diversity of Zhaotong sheep was low. 3. The genetic distance was caculated by MEGA 4.0 using Kimura 2- parameter model. Genetic distance among 10 sheep breeds was calculated with 0.011 0.031. Zhaotong sheep had rather small distances with Tashikuergan sheep and had rather big distances with imported sheep breeds. Genetic distance within breeds was from 0.007 to 0.023. And it was smallest within breeds Zhaotong sheep, 0.007, on the other hand, it was biggest within Bashibai, 0.025. Genetic variations of populations were mainly resulted from variation within populations under the analysis of molecular variance. From the result of genetic differentiation of ten sheep breeds, genetic differentiation between populations was obvious, but genetic differentiation between introduced breeds and local breeds was significant.4. The NJ tree of 103 haplotypes and 5 sequences from NCBI were constructed by MEGA 4.0 software using Kimura 2-parameter model. The NJ tree indicated that there were two main branches in Chinese domestic sheep, thereinto, one branch was clustered with O. musimon, while O. vignei and O. ammon was clustered together, Haplotypes A and haplotype B are clustered two lineages respectively. Further median-joining network ananlysis also showed two lineages were determined in ten domestic sheep breeds. The NJ tree was constructed using 133 haplotypes and some sheep sequences downloaded from GenBank, thereinto, 103 haplotypes appeared within first and second clades while did not appear within third clades. All these evidences show that domestic sheep populations may at least have two mother lineages. Some modern domestic sheep derive from O. musimon, while O. vignei and O. ammon have no contribution to modern domestic sheep.5. Analysis of mismatch distribution showed unimodal distribution of two lineages. And Fu's test of selective neutrality revealed that two lineages were in departure from the neutrality, which the difference were significant (P<0.01). It implies two lineages of ten sheep breeds ever experienced population expansion possibly.