The Studies Of East-Asian, Middle-Eastern And European Breed Dog Phylogeographic Structure And Construction Of Dog SNP Databsse

The demostication of dogs(Canis familiaris) has always been a hot point in genetic research field. Being closely related to human made them the focus of worldwide biologists. From the beginning of the domestication, dogs demonstrated large differences to their wild ancestor grey wolf(Canis lupus) in terms of behavior, feeding habit and phenotype. The breeding process enriched dogs’ phenotypies even more. Dogs provide us great opportunities to gain a better understanding of the animal domestication process, the genetic basis of their tremendously diverse phenotypes, the causing factors underlying human mutual diseases and even the evolution process of ourselves.In the first chapter, we summarized the current state of dog domestication studies, which include researches concern dog origin, two-phase domestication process and their diverse phenotypes and illnesses. Then, we proposed two research points we would discuss and solve in this dissertation. The first one:we investigated the early dispersal history of domestic dogs by analysing the phylogeographic structure of breed dogs from East-Asia, Middle East and Europe; the second one:the dog/wolf resequencing data increase fast in recent years. These abundant data is not only an opportunity to compensate for the drawbacks of the current dog single nucleotide polymorphism (SNP) reference dataset (dbSNP139), but also a requirement to reasonable and effective data organization. So, we constructed the first dog/wolf SNP database.In the second chapter, we discussed the early dispersal history of domestic dogs by analysing the currently phylogeographic structure of breed dogs from East-Asia, Middle East and Europe areas. Until now, questions concerning the dispersal of dogs after its East-Asia origin have not been clearly answered. According to a former research of breed dog’s whole genome SNP, there is a clear phylogeographic pattern between the three former mentioned places. This structure implied early dogs might disperse based on populations with genetic differences. In order to test this hypothesis, we analysed the phylogeographic structures of mtDNA control region and Y chromosome non-recombination region of breed dogs from these three places. The result shows the genetic similarities of mtDNA and Y chromosome markers were high in the three places. This result might due to lack of selection signals and the relatively low resolution of uniparental markers. And the highly similar genetic basis of these two uniparental markers might suggest the existence of gene flow between the ancestors of breed dogs (village dogs) in the three areas.In the third chapter, we introduced the first dog specific whole genome SNP database(DoGSD:http://dogsd.big.ac.cn). Dog SNP reference dataset is a widely used and basic dataset in dog genetic researches, however the current reference dataset has many drawbacks, such as scarcity of SNP data, big biases in sampling location and sequencing coverage, un-friendly or easy access, etc. With the advancement of next generation sequencing (NGS), dog/wolf whole genome resequencing data increased dramatically. In order to better organize the ever growing dog/wolf resequencing data, compensate for the drawbacks of current dog reference SNP list and reduce the cost of computing resources of NSG data processing, we constructed the first dog whole genome SNP database(DoGSD), which provide high-quality and high-density SNP data, user-friendly interfaces and two important genetic statistics. The DoGSD severs as a high-quality platform for dog’s within or between species genetic analyses.