| 题名 | 品种犬系统地理结构与家犬SNP数据库构建研究 |
| 作者 | 白冰 |
| 学位类别 | 博士 |
| 答辩日期 | 2015-05 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 张亚平 |
| 关键词 | 家犬驯化 SNP 系统地理结构 二代测序 数据库 |
| 其他题名 | The Studies of Breed Dog Phylogeographic Structure and Construction of Dog SNP Database |
| 中文摘要 | 家犬（Canis familiaris）的驯化研究一直是遗传学研究中的热点，由于其与人类经过上万年形成的密切关系，家犬一直备受国内外生物学者的重视。从被驯化开始，家犬从行为、食性、外型等方面表现出了和其祖先灰狼(Canis lupus)较大的差异，品种化过程进一步丰富了家犬的表型。家犬是人类研究家养动物的驯化过程、理解各种表型的遗传基础、与人类共同疾病的形成原因、甚至是自身的进化过程的绝佳遗传学研究材料。 第一章主要对家犬驯化研究工作进行了介绍，范围覆盖了家犬起源、家犬二段式驯化、品种犬丰富的表型及疾病研究。并在现有研究的基础上提出了两个本论文要探讨及解决的问题。一、我们通过分析家犬在东亚、中东、欧洲地区的系统地理结构，来研究家犬早期在欧亚地区的扩散方式；二、近年来，家犬/灰狼重测序数据呈增长态势。丰富的数据，给了我们弥补家犬单核苷酸多态性（SNP）参考集（dbSNP139）缺陷的契机，也对如何合理的组织运用大量的家犬、灰狼重测序数据向我们提出了要求，因此，我们构建了第一个家犬/灰狼SNP数据库。 第二章主要通过分析品种犬在东亚、中东、欧洲地区的系统地理结构来探讨家犬的扩散问题。在目前的家犬驯化研究中，对于家犬驯化后，如何在世界范围内扩散的问题还没有较为清晰的回答，唯有一个前期的全基因组SNP研究表明，品种犬在东亚、中东、欧洲地区有清晰的系统地理结构。该结构可能暗示着家犬是以有遗传差异的群体为基础扩散到各地的，为了检验这个假设，我们分析了上述三地品种犬的线粒体控制区及Y染色体的非重组区的系统地理结构。结果表明这三个地区的品种犬在父系及母系遗传上有很高遗传相似性，缺乏清晰的系统地理结构。这个结果可能是由于单亲遗传标记缺乏选择信号、辨析度较低造成的，也说明了这三个地区品种犬的祖先即土狗存在着基因交流。 第三章主要介绍了第一个家犬SNP数据库(DoGSD：http://dogsd.big.ac.cn)。家犬SNP参考集是家犬遗传学研究中广泛运用的基础数据集，但是目前的参考数据集（dbSNP139），存在着数量少、测序及采样覆盖度偏差大、用户界面不够友好等缺陷。随着二代测序技术的进步，家犬、灰狼的全基因组重测序数据在近几年来呈增长态势，为了更加合理的组织管理日益增加的家犬、灰狼重测序数据、弥补现有家犬SNP参考数据集的缺陷及减少用户处理二代测序数据的计算资源花费，我们构建了第一个家犬全基因组SNP数据库。该数据库提供了高质量、高密度的SNP数据集、友好的用户界面及两个重要的遗传学参数，为家犬的种上及种间遗传学分析等提供了高质量的数据平台。 |
| 英文摘要 | 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 appearance. The breeding process enriched dogs’ phenotypes 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 analyzing 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 of 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 analyzing the currently phylogeographic structure of breed dogs from East-Asia, Middle East and Europe areas. Until now, questions concerning dog dispersal after 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 analyzed 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 provides 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. |
| 语种 | 中文 |
| 内容类型 | 学位论文 |
| 源URL | [http://159.226.149.26:8080/handle/152453/10175]  |
| 专题 | 昆明动物研究所_分子进化基因组学 |
| 推荐引用方式 GB/T 7714 | 白冰. 品种犬系统地理结构与家犬SNP数据库构建研究[D]. 北京. 中国科学院研究生院. 2015. |
| 个性服务 |
| 查看访问统计 |
| 相关权益政策 |
| 暂无数据 |
| 收藏/分享 |
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。
修改评论