山羊群体重测序及GWAS分析

发布时间：2018-11-24 08:20

【摘要】：山羊是人类早期驯化的动物之一,分布广泛且容易饲养,每年为人类提供大量的奶、肉、羊绒等资源,是一种重要的经济型物种。内蒙绒山羊经过长期的自然选择及人工驯化过程,其绒产量和绒质量都世界闻名,已经成为我国一种特有的遗传资源,具有极高的经济价值。然而山羊的育种工作却远远落后于绵羊、猪等动物,之前关于山羊的研究主要集中在采用简单的分子标记,如限制性片段长度多态性(PFLP)、简单重复序列(SSR)等对山羊进行遗传多样的分析,很少涉及到育种层面,导致山羊育种工作进展缓慢。随着新一代测序(NGS)技术的迅猛发展,测序费用不断降低,高通量测序为人们研究工作提供了极大的方便。在有参考基因组的情况下,我们可以对物种进行个体或群体层面的全基因组重测序,鉴定出覆盖度高、密度大的单核苷酸多态性(SNP)等第三代分子标记。借助SNP标记,人们通过全基因组关联分析(GWAS)已经成功鉴定出许多与复杂性疾病相关的位点和基因,为精准医疗带来了极大的帮助。近年来,山羊全基因组图谱构建完成,我们可以采取同样的方法,来鉴定与山羊优良性状相关的变异位点,从而加快山羊的育种进程。本项目采用BGISEQ测序平台对来源于6个群体的258个绒山羊个体进行重测序,平均测序深度为10X。通过使用GATK等软件鉴定出约26M的SNP变异位点。经过SNP质量控制,我们最终使用244个体、约13.8M的SNP进行主成分、系统发生、群体结构和基于绒细度、绒长度进行GWAS等分析,鉴定出了与山羊绒细度紧密相关的SNP位点。并结合山羊基因组数据,得到这些显著关联的SNP所在或紧密连锁的候选基因,最后对这些基因进行功能分析,为山羊育种工作的进行打下良好的基础。
[Abstract]:Goat is one of the early domesticated animals, which is widely distributed and easy to raise. It provides a large amount of milk, meat, cashmere and other resources to human each year. It is an important economic species. After a long period of natural selection and artificial domestication, Inner Mongolia Cashmere Goats have become a special genetic resource of our country and have high economic value. However, goat breeding lags far behind that of sheep and pigs. Previous studies on goats focused on the use of simple molecular markers, such as restriction fragment length polymorphism (PFLP),). The genetic diversity of goat was analyzed by simple repeat sequence (SSR) and few of them were involved in breeding, which resulted in slow progress of goat breeding. With the rapid development of the new generation of sequencing (NGS) technology, the cost of sequencing is decreasing, and high throughput sequencing provides great convenience for the research work. In the case of reference genome we can resequence the whole genome of species at individual or population level and identify the third generation molecular markers such as single nucleotide polymorphism (SNP) with high coverage and density. With the help of SNP markers, many sites and genes related to complex diseases have been successfully identified by genome-wide association analysis (GWAS), which is of great help to accurate medicine. In recent years, the construction of goat whole genome map has been completed. We can use the same method to identify the mutation sites related to goat fine traits, so as to speed up the breeding process of goats. 258 cashmere goat individuals from 6 populations were resequenced by using BGISEQ sequencing platform. The average depth of sequencing was 10X. About 26m of SNP mutation sites were identified by using GATK and other software. After SNP quality control, we finally used 244 individuals, about 13.8M of SNP for principal components, phylogenesis, population structure and GWAS analysis based on cashmere fineness and length, and identified the SNP sites closely related to cashmere fineness. Combined with goat genome data, these candidate genes with significant association of SNP or closely linked genes were obtained. Finally, functional analysis of these genes was carried out, which laid a good foundation for goat breeding.
【学位授予单位】：电子科技大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S827

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