本文關(guān)鍵詞：利用混池測序檢測不同雞種的全基因組結(jié)構(gòu)變異　出處：《中國農(nóng)業(yè)大學(xué)》2016年博士論文　論文類型：學(xué)位論文

  更多相關(guān)文章： 混池測序 結(jié)構(gòu)變異 遺傳多樣性 進化和選擇

【摘要】：雞是最早被人類馴化的禽類之一,雞蛋和雞肉都是現(xiàn)代人類重要的蛋白質(zhì)來源。經(jīng)過漫長的進化和選擇過程,雞逐漸形成了現(xiàn)在豐富多樣的品種。對雞的遺傳多樣性和群體進化的研究有相當(dāng)重要的生物學(xué)意義,多個研究表明結(jié)構(gòu)變異在這些方面具有重要的作用。隨著生物芯片技術(shù)以及第二代測序技術(shù)的發(fā)展,給基因組中結(jié)構(gòu)變異的研究帶來了極大的便利和革新�，F(xiàn)在通常意義所指的結(jié)構(gòu)變異是基因組中變異的堿基數(shù)大于50bp的變異,主要包括插入、缺失、倒位、轉(zhuǎn)座和拷貝數(shù)變異。雖然結(jié)構(gòu)變異的絕對數(shù)量沒有單核苷酸變異以及短的插入缺失多,但是由于結(jié)構(gòu)變異影響的堿基總數(shù)更多,所以對于全基因組來講,結(jié)構(gòu)變異帶來的影響可能會更大。對人類的研究發(fā)現(xiàn),結(jié)構(gòu)變異所影響堿基總數(shù)最大可能占到人類基因組的5%。近年來,由于人們漸漸意識到結(jié)構(gòu)變異對群體多樣性以及重要性狀等方面具有重要作用,使得結(jié)構(gòu)變異的研究越來越受到廣大科研工作者的廣泛關(guān)注。本研究利用第二代測序技術(shù)結(jié)合基因組混池的方法,對4個具有代表性的雞種各選擇了20只雞基因組混池之后進行全基因組混池測序。這種方法通過降低每個個體基因組的代表性,達到高效且低成本的對群體進行測序,進而獲得大量的多態(tài)性信息。這4個品種分別選擇了肉雞(科寶)、蛋雞(白來航)、中國地方雞種(烏雞)和原雞品種(德宏原雞),這樣的選擇保證了實驗材料選擇的多樣性和差異性。我們利用得到的測序數(shù)據(jù)結(jié)合多種方法對全基因組的結(jié)構(gòu)變異進行檢測,然后通過嚴(yán)格的篩選和合并過程將結(jié)果進行整合得到最終的全基因組結(jié)構(gòu)變異集合。檢出的結(jié)構(gòu)變異包括了缺失、插入、倒位和拷貝數(shù)變異等多種類型。4個品種中均檢出大量的結(jié)構(gòu)變異,覆蓋了全基因組1.75%至2.29%的區(qū)域,其中數(shù)量最多的是缺失,最大的變異是倒位,有部分結(jié)構(gòu)變異與外顯子區(qū)域或者基因調(diào)控區(qū)有重疊。利用檢出的結(jié)構(gòu)變異,繪制了所研究品種高分辨率的全基因組結(jié)構(gòu)變異圖譜,我們發(fā)現(xiàn)基因組上結(jié)構(gòu)變異的分布并不是隨機的而是存在一定的分布熱點。之后對各個品種的結(jié)構(gòu)變異檢出進行了比較,發(fā)現(xiàn)有4422個缺失變異在4個品種中都被檢出,此外每個品種平均有近20%的結(jié)構(gòu)變異是品種特有的。經(jīng)過和QTL的關(guān)聯(lián)、GO和KEGG分析,發(fā)現(xiàn)這些結(jié)構(gòu)變異可能在品種的形成過程中起到了重要的作用。綜上所述,本研究利用一種高效而且低成本的測序手段一混池測序?qū)哂写硇缘?個雞種進行了全基因組結(jié)構(gòu)變異的檢測,并且為利用混池測序檢測雞的結(jié)構(gòu)變異的提供了良好的參考。首先,利用檢出結(jié)果構(gòu)建了高分辨率的全基因組結(jié)構(gòu)變異圖譜,分析了結(jié)構(gòu)變異的分布特點和可能的生物學(xué)作用。發(fā)現(xiàn)結(jié)構(gòu)變異的分布可能跟重復(fù)序列有關(guān)系,而且SNP的分布和缺失的分布存在一定的關(guān)聯(lián)性。其次,利用品種間結(jié)構(gòu)變異的差異,結(jié)合遺傳學(xué)和生物信息學(xué)研究手段,我們發(fā)現(xiàn)結(jié)構(gòu)變異對科寶肉雞的生長速度可能產(chǎn)生了影響,對不同品種的表型性狀的差異也有一定的貢獻。
[Abstract]:Chicken is one of the earliest domesticated poultry, egg and chicken are an important source of protein for modern humans. After a long process of evolution and selection of chicken, and gradually formed the rich and diverse varieties. There is very important to study the biological significance of chicken genetic diversity and population evolution, a number of studies show that structural variation has an important role in these aspects. With the development of the bio chip technology and the second generation sequencing technology, has brought great convenience to the research and innovation of structural variation in the genome. It usually refers to the significance of structural variation is the variation in the genome variation base of more than 50bp, mainly including insertion, deletion, inversion transposition, and copy number variation. Although the absolute number of structure variation and no single nucleotide variation in short insertions and deletions, but due to structural variability affects more total bases So much for the whole genome, affect the structure with the variation may be greater. The discovery of human studies, the influence of base structure variation may account for the largest number of human genome 5%. in recent years, as people gradually realized that the structure variation plays an important role on the diversity and importance of shape, which makes the research structure variation has attracted extensive attention of researchers. The research method of the second generation sequencing technology combined with genomic mixed pool, after the 4 chicken representative of each selected 20 chicken genome mixed whole genome sequencing mixed pool pool. This method by reducing the representative of each individual genome. To achieve high efficiency and low cost of sequencing groups, and then get a lot of information. The polymorphism of the 4 cultivars were selected broilers (Ke Bao), chickens (White Leghorn), China Local chicken (chicken) and fowl varieties (Dehong, gallus) this choice ensures experimental material selection diversity and difference. We use the sequencing data obtained by using various methods to detect structure variation on the whole genome, and then through the screening and merging process strictly will integrate the whole set of results obtained genomic structure variation. The final structure variation detection including deletion, insertion, inversion and copy were detected in the number of variation of structure variation and other types of.4 species, covering the area of 1.75% to 2.29% of the whole genome, which is the largest number of missing, the biggest variation is inversion, some structural variation and the explicit regulatory region of sub region or gene overlap. Using mutation detection, whole genome structural variation map of varieties of high resolution rendering, we found that the gene structure of group And the same distribution is not random but there is a distribution of hot spots. After the structure variation of each variety were compared, found that 4422 deletion mutations were detected in 4 varieties, each variety in addition average structure variation is nearly 20% varieties. The unique association and QTL analysis. GO and KEGG found the structural variation in the formation process of varieties may play an important role. In conclusion, an efficient and low cost sequencing means mixed pool sequencing of 4 chicken representative of the gene detection group structure variation in this paper, and for the use of the structure the variation of mixing pool sequencing chicken to provide a good reference. Firstly, the detection results of constructing genomic structural variation map with high resolution, analyzes the distribution characteristics of structure variation and possible biological role. Distribution structure variation may have a relationship with repeat sequence, and there is a certain correlation between the distribution and the loss of SNP. Secondly, the differences between the varieties structure variation, the combination of genetics and bioinformatics research methods, we found that the structure of the mutation rate on growth of chicken meat cobio may have had an impact, also have certain the difference of phenotypic traits of different varieties.

【學(xué)位授予單位】：中國農(nóng)業(yè)大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：S831

【相似文獻】

相關(guān)期刊論文 前10條

1 劉朋虎;林冬梅;林占q，

本文編號：1399500