| When, why and how were the sheep domesticated by Human? The purposes to answer these questions didn't only satisfy the scientists' curiosity, but also provided useful information for protecting ovine genetic resources and elucidating the history of human migration.Based on mitochondrial DNA study, domestic sheep were derived from many domestication events. At least, three lineages of wild sheep contributed to the gene pool of domestic sheep (another two lineages identified recently require further evidence).At present, it was B lineage that could be digged out complete mitochondrial genome from GenBank. For A lienage, only parts of coding region and control region sequence could be found in GenBank. For C lineage, only control region sequence could be found. In this study, one of the purposes was to search for SNPs among sheep lineages. Therefore, we collected 12 samples which contained all lineages from ChangPing Farm. Mitochondrial DNA was extracted and purified with Biovision Kit. Eleven paires of primers overlapping in mitochondrial DNA were designed with Premair Primer 5.0. Afer cloning and sequencing, we assembled fragments into one complete mitochondrial genome. Then, we predicted the structure of mitochondrial RNA and protein in order to analyze the effect in fitness among lineages. We carried out positive selection test in coding region with PALM and DNA SR In final, we estimated the divergation time with Penalized Likelihood methods.To uncover Chinese sheep population structure and demography, we constructed a data set, which included sequences accumulated in our laboratory and mined from GenBank. We reconstructed phylogenetic tree in Neighbor-Joint method with MEGA 3.0. To obtain optimal nucleotide substitution model, we scanned the data set with PAUP* and Modeltest 3.7. Sequentially, we reconstructed the Maximum likelihood tree with the optimal nucleotide substitution model. Then, we analyzed the data set with Network 4.1.1.1. At last, we tested population expansion with Arlequin 3.0.In this study, our conclusions were as follows:â…°. 144 SNPs were found among three lineages.In region for coding tRNA and rRNA, 24 nucleotide substitutions were found. SNPs occurred in loops or unstructured single strand, therefore, we inferred these substitution could not change secondary structure of RNAs.Eight amino acid substitutions were found in region encoding mitochondrial protein. Based on results of multi-alignment and strucfure prediction, these nonsynonymous mutations did not affect protein function.â…±. Based on the results from PALM and DNA SP, there were no positive selection on the ovine mitochondrial coding region.â…²Divergation time among three lineages was caculatedThe A mtDNAs had a TMRCA of 0.21 MYA; The TMRCA of B mtDNAs was 0.32 MYA; C mtDNAs was 0.32 MYA. We observed the origin of A lineage was slightly more recent than the appearance of B and C lineages. The divergation times we obtained were geared with speciation radiation among large herbivores during the Pleistocene.â…³According to Fu's test and mismatch distribution analysis, each lineage had been population expension.In sequence, B lineage was the first, then A lineage, C lineage was the last.Based on results from mismatch distribution, each lineage originated from a very small ewe population.â…´We found introgression from Agarli sheep, which requires further evidence.â…µLineage D was proved in Chinese sheep.â…¶Complete sequences of A and C mtDNA were revealed, B mtDN'A was proofreaded.Based on the results in Chapter Two, we discussed the impact of introduced breeds on local ones in national sheep breeding plan. We proposed that mtDNA from introduced sheep could not fixed in improved population. In Chapter Three, we inferred sheep speciated procession. We proposed that lineage C was derived from wild sheep in central Asian. At the end of each chapter, we provided some suggestions for future study. |
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