基于高通量测序的绒山羊群体遗传学研究

发布时间：2017-12-28 07:10

本文关键词：基于高通量测序的绒山羊群体遗传学研究　出处：《内蒙古农业大学》2016年硕士论文　论文类型：学位论文

【摘要】：内蒙古绒山羊和辽宁绒山羊是我国特有的动物遗传资源,经过长期的自然和人工选择作用,形成了以绒质量和产量闻名的内蒙古绒山羊和辽宁绒山羊两大品种资源。在群体基因组水平上研究它们的遗传结构和遗传多态性有利于发掘大量的分子标记和本地优良遗传资源的保护。本研究利用Hiseq 2000高通量测序平台并结合生物信息学分析的方法对内蒙古绒山羊的三个类群(二狼山型、阿尔巴斯型和阿拉善型)和辽宁绒山羊共80个个体进行低覆盖度基因组重测序研究。此外,我们还选取12个非产绒山羊品种进一步探索研究绒山羊和非产绒间表型差异的遗传基础。主要研究结果如下：(1)通过遗传变异检测和严格筛选后共检测到6737432个SNPs和194273个InDels;对遗传变异在基因组区分布的注释分析,发现仅有0.77%(3720)的SNP突变分布在外显子区域,基因间区占24.5%和内含子区约占68.79%。InDels分布规律是随着长度的增加而降低。(2)利用连锁不平衡、系统发育树、群体结构、群体杂合度、近交系数等分析方法,对群体遗传结构和多样性分析进行深入分析,发现不同品型和品种的遗传关系及群体之间的存在基因交流现象；内蒙古绒山羊三个品系间有较大的遗传分化和遗传多样性,具有很大的品种选育潜力。(3)通过内蒙古绒山羊(阿拉善、阿尔巴斯)与辽宁绒山羊群体间的全基因组扫描进行的差异分析,共注释出206(5%)个候选基因。GO功能注释分类显示,候选基因主要富集在细胞、细胞部分、催化功能等功能分类上。KEGG代谢通路分析发现,这些基因主要参与Hippo信号通路、黑素生成、WNT信号通路、甲状腺激素合成、cAMP信号通路、糖类消化吸收等16个代谢通路上发生显著富集。可能与绒山羊适应性及绒毛生产相关性状有关。(4)绒山羊与非产绒山羊的遗传关系主成分分析发现,萨能奶山羊和西非矮山羊与绒山羊的遗传关系较近,而其他品种之间遗传关系较远；非产绒中除了萨能奶山羊与西非矮山羊遗传关系较近外,其他各品种间关系较远。(5)通过与12不同品种的非产绒山羊进行基因组扫描分析,共注释出211(5%)个候选基因。GO功能注释分类显示,候选基因主要富集在细胞、细胞部分、催化功能参与生物调控；生物过程主要参与细胞过程、代谢过程等。KEGG代谢通路分析发现候选基因主要参与氨基糖和核苷酸糖代谢、黑素瘤、氧化磷酸化等9个通路上富集。
[Abstract]:Inner Mongolia cashmere goats and Liaoning cashmere goats are endemic animal genetic resources in China. After long-term natural and artificial selection, two major resources of Inner Mongolia cashmere goats and Liaoning cashmere goats are formed, which are famous for their quality and yield. The study of their genetic structure and genetic polymorphism at the population genome level is beneficial to the discovery of a large number of molecular markers and the protection of local excellent genetic resources. This study uses Hiseq 2000 high-throughput sequencing platform and method combined with bioinformatics analysis of three taxa of Inner Mongolia cashmere goats (two Langshan type, Arbas and Alashan type) for coverage of genome sequencing research and low covered a total of 80 individuals in Liaoning cashmere goat. In addition, we also selected 12 non - cashmere goats to further explore the genetic basis of the phenotypic differences between cashmere and non cashmere goats. The main results are as follows: (1) through rigorous testing and screening of genetic variation were detected after 6737432 SNPs and 194273 InDels; the analysis of genetic variation in the genomic distribution of notes, found that only 0.77% (3720) SNP mutation distribution in the exon region, intergenic regions and introns approximately accounted for 24.5% accounted for 68.79%. The distribution of InDels is reduced with the increase of the length. (2) using linkage disequilibrium, phylogenetic tree, inbreeding coefficient analysis of population structure, population heterozygosity, and to analyze the genetic diversity and population structure analysis, found the genetic relationship and genetic exchanges between the groups and different product types and varieties of the phenomenon; three strains of Inner Mongolia cashmere goats there is great genetic differentiation and genetic diversity, variety breeding has great potential. (3) the Inner Mongolia cashmere goat (Alashan, Aerbasi) and difference analysis of whole genome scan in Liaoning cashmere goats between the co injection (5%) released 206 candidate genes. The classification of GO functional annotation shows that the candidate genes are mainly enriched in the functional classification of cells, cell parts and catalytic functions. KEGG metabolic pathway analysis showed that these genes were mainly involved in 16 metabolic pathways, including Hippo signaling pathway, melanogenesis, WNT signaling pathway, thyroid hormone synthesis, cAMP signaling pathway, carbohydrate digestion and absorption. It may be related to the adaptability of cashmere goats and the related traits of villi production. (4) cashmere goats and non genetic relationship between the main components of cashmere goat analysis found that the closer genetic relationship between Saanen dairy goats and West African pygmy goats and cashmere goat, and the genetic relationship between other varieties than non cashmere; in addition to Saanen dairy goats and West African pygmy goats genetic close relationship, other all varieties were obviously different from. (5) a total of 211 (5%) candidate genes were released by genome scanning analysis of non - produced cashmere goats with 12 different varieties. GO functional annotation classification shows that candidate genes are mainly concentrated in cells, cell parts, catalytic functions in biological regulation, and biological processes are mainly involved in cell processes and metabolic processes. KEGG metabolic pathway analysis showed that the candidate genes were mainly involved in the enrichment of 9 pathways, such as amino sugar and nucleotides glucose metabolism, melanoma, and oxidative phosphorylation.
【学位授予单位】：内蒙古农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S827

【相似文献】