本文選題：山羊 + 基因組重測序�。� 參考：《西南大學》2017年碩士論文

【摘要】：我國有悠久的山羊馴化和養(yǎng)殖歷史,擁有豐富多彩的品種和遺傳資源。山羊為人類提供肉、纖維、皮和奶等產品。然而目前對山羊特征體型體貌、重要的生產和繁殖等經濟性狀的遺傳機理研究多以單基因和候選基因驗證為主,這嚴重忽略了生物的系統(tǒng)性,所以篩選的致因基因的準確度也較低,從而導致山羊經濟性狀遺傳剖分和遺傳機理研究進展緩慢。隨著高通量測序技術的不斷發(fā)展,為從全基因組層面篩選經濟性狀候選基因提供了可能。本研究以飼養(yǎng)在西南大學實驗羊場的大足黑山羊(n=6)和內蒙古絨山羊(n=6)為研究對象,采集頸靜脈全血樣本用于DNA提取,經檢測合格后用于構建350bp雙末端測序文庫,然后采用Illumina HiSeq PE150平臺進行全基因組測序。原始數(shù)據通過BWA軟件進行質檢和過濾接頭等后比對到參考基因組。接著利用SAMtools軟件檢測基因組單核苷酸多態(tài)性(Single Nucletide Polymorphism,SNP)并用ANNOVAR軟件注釋。分別采用Cluster 3.0、ADMIXTURE和MEGA 5.2進行主成分分析、遺傳結構和鄰近進化樹分析;變異比較分析首先篩選每個群體相同的SNPs,然后比較兩個群體差異SNPs,并將外顯子SNPs注釋到基因;其次分別計算群體雜合性(Heterozygosity,Hp)和群體分化(Fst)來篩選候選基因,再分別用Goseq(Bioconductor 2.12)和KOBAS(kobas2.0 20120208)進行GO和KEGG注釋分析初步了解候選基因功能。本研究共產生192.747Gb原始數(shù)據,平均鑒定了500多萬個SNPs。主成分分析、遺傳結構和鄰近進化樹分析均顯示大足黑山羊和內蒙古絨山羊能夠被完全分成結構清晰的兩個不同群體;變異比較分析發(fā)現(xiàn)大足黑山羊和內蒙古絨山羊特有的SNPs各有1,873和1,706個,其中外顯子變異各有21和17個,分別注釋到16和14個基因;雜合性計算在大足黑山羊和內蒙古絨山羊基因組分別篩選到155和294個候選區(qū)域,分別包含86和97個候選基因;Fst統(tǒng)計檢測到368個選擇消除區(qū)域,含有候選基因164個;然后選取低雜合度和高遺傳分化的前1.0%區(qū)域作為受選擇區(qū)域,在大足黑山羊和內蒙古絨山羊基因組內分別篩選到239和176個候選區(qū)域,分別注釋到135和176個候選基因。經過GO和KEGG功能富集、并結合參考文獻報道和試驗驗證分析發(fā)現(xiàn)候選基因與山羊的體貌、生產和繁殖性能相關。如KIT基因(rs647214940)可作為山羊白毛的候選基因,FGF5基因是調控山羊被毛生長的關鍵候選基因;BIRC6基因可能是山羊季節(jié)性繁殖的重要調控基因;EGLN1基因(rs659097694)是內蒙古絨山羊適應性高海拔環(huán)境的候選基因。本研究通過全基因重測序、變異檢測、群體結構、變異比較和選擇信號分析等手段,篩選了系列與山羊經濟表型性狀相關的候選基因,為深度揭示山羊表型性狀的遺傳機理奠定了基礎。
[Abstract]:China has a long history of domestication and breeding of goats, with rich varieties and genetic resources. Goats provide human beings with products such as meat, fiber, skin and milk. However, at present, the genetic mechanism of economic traits such as characteristic body shape, important production and reproduction of goats is mainly verified by single gene and candidate gene, which neglects the systematicness of living things. Therefore, the accuracy of the selected genes is also low, which leads to slow progress in the research of genetic division and genetic mechanism of economic traits in goats. With the development of high throughput sequencing technology, it is possible to screen candidate genes for economic traits from the whole genome level. In this study, Dazu Black Goat (Dazu Black Goat 6) and Inner Mongolia Cashmere Goat (Cashmere Goat No. 6), which were raised in the Experimental Sheep Farm of Southwest University, were studied. The whole blood samples of jugular vein were collected for DNA extraction, and the 350bp double-terminal sequencing library was constructed after the detection. Then the whole genome was sequenced using Illumina HiSeq PE150 platform. The raw data were checked and filtered by BWA software and then compared to the reference genome. SAMtools software was used to detect single Nucletide polymorphism (SNPs) and ANNOVAR software was used to annotate SNPs. Cluster 3.0 and MEGA 5.2 were used for principal component analysis, genetic structure and adjacent phylogenetic tree analysis, variation comparison analysis was used to screen the same SNPs in each population, then the differences between two populations were compared, and the exon SNPs was annotated into the gene. Secondly, population heterozygosity (HP) and population differentiation (FST) were calculated respectively to screen candidate genes, and then go and KEGG annotation analysis were carried out with Goseq(Bioconductor 2.12) and KOBAS(kobas2.0 2010 20208) respectively to understand the function of candidate genes. In this study, the original 192.747Gb data were generated, and more than 5 million SNPs were identified on average. Principal component analysis, genetic structure and adjacent evolutionary tree analysis showed that Dazu Black Goat and Inner Mongolia Cashmere Goat could be divided into two distinct populations. The SNPs of Dazu Black Goat and Inner Mongolia Cashmere Goat were 1873 and 1706 respectively, of which exon variation was 21 and 17 respectively, annotated 16 and 14 genes, respectively. The heterozygosity was estimated to be 155 and 294 candidate regions in the genome of Dazu Black Goat and Inner Mongolia Cashmere Goat, respectively. Fst analysis of 86 and 97 candidate genes detected 368 candidate elimination regions and 164 candidate genes in the genome of Dazu Black Goat and Inner Mongolia Cashmere Goat. Then the first 1.0% region with low heterozygosity and high genetic differentiation was selected as the selected region. 239 and 176 candidate regions were screened in the genome of Dazu Black Goat and Inner Mongolia Cashmere Goat respectively, and 135 and 176 candidate genes were annotated respectively. Through the enrichment of go and KEGG functions, combined with reference reports and experimental verification analysis, it was found that candidate genes were related to goat body appearance, production and reproductive performance. For example, KIT gene rs647214940 can be used as candidate gene for goat white hair, FGF5 gene is the key candidate gene for controlling goat hair growth, and BIRC6 gene may be an important regulating gene for seasonal reproduction of goat. Candidate genes for high altitude environments. In this study, a series of candidate genes related to economic phenotypic traits of goats were screened by means of whole gene resequencing, mutation detection, population structure, variation comparison and selection signal analysis. It lays a foundation for revealing the genetic mechanism of goat phenotypic traits in depth.
【學位授予單位】：西南大學
【學位級別】：碩士
【學位授予年份】：2017
【分類號】：S827

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