基于全基因组重测序技术对太湖猪分子种质特性的研究

发布时间：2018-03-03 06:07

本文选题：种质特性　切入点：基因组测序　出处：《西南大学》2017年硕士论文　论文类型：学位论文

【摘要】：太湖猪是中国著名的地方猪品种,具有独特的种质特性,主要表现在高繁殖性能,以及肉质好、耐粗饲等,特别是其繁殖性能,享誉世界,因此太湖猪被誉为我国“国宝”,并受到了国内外养猪生产者和遗传育种研究者们高度关注。然而太湖猪特有种质特性的遗传机制目前并不清楚,相关的研究也比较少,其中也包括重要表型种质特征和高繁生产性能的功能基因、或基因组区域等方面都有待进一步的解析和验证。本研究应用全基因组重测序技术对4个组别的猪品种群体进行了测定分析,即无血缘关系的12头太湖猪(6头二花脸猪和6头枫泾猪)、12头杜洛克猪、12头长白猪、以及12头其他中国地方猪种(6头滇南小耳猪和6头藏猪),获得了测序深度达10X,有效数据总量为119Gb的全基因组重测序数据。经过与猪参考基因组序列(Sus scrofa 10.2.75)的对比分析,共获得2100万多个SNPs和260万余个InDels变异信息,发现其中的2511464个SNP和362974个InDel是太湖猪独有的变异。对4个测定组之间的基因组变异信息进行比对分析,该方法采用的选择窗口大小为100 kb,滑动步长为50 kb的滑动窗口,应用杂合度和群体固定指数等参数进行了选择性清除的研究,获得了与太湖猪种质特性相关的候选基因360个。经过GO富集分析和KEGG通路分析,发现了这些基因主要涉及到繁殖过程、牙齿发育、油脂代谢、胶原蛋白代谢以及神经发育负调节等生物过程以及卵巢类固醇生成代谢通路,特别值得关注的是发现了太湖猪高繁殖性能相关的重要功能基因,如BMPR1B和BMP15等,这为进一步解析和完善了太湖猪高繁力种质特性的分子机制提供了一个新途径。经过mapping分析,确定了与太湖猪种质特性关联的43个候选区域在染色体的位置。本研究从基因组水平揭示了43个特有区域是太湖猪种质特性的分子基础,360个功能基因是主要控制太湖猪种质特性的分子机制。
[Abstract]:Taihu pig is a famous local pig breed in China. It has unique germplasm characteristics, mainly manifested in its high reproductive performance, good meat quality and forage tolerance, etc., especially its breeding performance. Therefore, Taihu pig is regarded as the "national treasure" of our country, and has been highly concerned by domestic and foreign pig producers and researchers of genetics and breeding. However, the genetic mechanism of specific germplasm characteristics of Taihu pig is not clear, and the related research is relatively few. It also includes important phenotypic germplasm characteristics and functional genes for high propagation performance. In this study, the whole genome sequencing technique was used to determine and analyze the four groups of pig breeds. That is, 12 unrelated Taihu pigs, 6 Erhualian pigs and 6 Fengjing pigs, 12 Duroc pigs and 12 Landrace pigs. And 12 other Chinese local pig breeds, 6 Diannan small ear pigs and 6 Tibetan pigs, obtained the whole genome re-sequencing data with a depth of 10X and a total effective data of 119Gb. The results were compared with the reference genomic sequence Sus scrofa 10.2.75. More than 21 million SNPs and more than 2.6 million InDels variants were obtained, of which 2511464 SNP and 362974 InDel were found to be unique to Taihu pigs. In this method, the selected window size is 100kb, the sliding step is 50kb, and the parameters such as heterozygosity and population fixed index are used to study the selective clearance. 360 candidate genes related to the characteristics of Taihu pig germplasm were obtained. Through go enrichment analysis and KEGG pathway analysis, it was found that these genes were mainly involved in reproduction, tooth development and lipid metabolism. Biological processes such as collagen metabolism, negative regulation of nerve development and ovarian steroid production metabolic pathway are of particular interest in the discovery of important functional genes related to high reproductive performance in Taihu pigs, such as BMPR1B and BMP15. This provides a new way to further analyze and improve the molecular mechanism of the high fertility germplasm of Taihu pig. The location of 43 candidate regions associated with the characteristics of Taihu pig germplasm was determined. This study revealed from the genomic level that 43 specific regions were the molecular basis of the characteristics of Taihu pig germplasm, and 360 functional genes were the main control. Molecular Mechanism of Germplasm characteristics of Taihu Pig.
【学位授予单位】：西南大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S828

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