不同尾型绵羊全基因组关联分析、拷贝数变异及选择信号检测

发布时间：2018-06-29 04:18

本文选题：全基因组关联分析 + 拷贝数变异检测　；参考：《中国农业大学》2017年博士论文

【摘要】：我国的绵羊品种按尾形分类可以分为长脂尾、短脂尾、脂臀尾、长瘦尾和短瘦尾五种。脂尾型和脂臀尾型绵羊是由野生的瘦尾绵羊经过人工驯化和自然选择而来,在驯化和选择过程中,气候环境和人类的需求及不同的选择方式都对不同尾型的形成产生了重要影响。同时,绵羊的尾型也是一个重要的经济性状,一直受到育种学者的关注,在过去,绵羊尾部脂肪对绵羊自身和人类都有重要作用,但目前,随着消费观念的改变和牧区饲养条件的改善,绵羊尾部脂肪的作用己经不重要且给生产带来经济压力。因此,利用SNP芯片对不同尾型的绵羊品种开展全基因组遗传变异分析,探索不同品种绵羊尾型差异的遗传基础对绵羊分子育种具有重要意义。本研究利用Illumina OvineSNP600 BeadChip高密度商业化芯片对三个不同尾型的绵羊品种31进行全基因组关联分析、拷贝数变异和选择信号检测,并对候选基因进行了富集分析。本论文具体研究内容如下:1、大尾寒羊、阿勒泰羊和藏羊尾型性状全基因组关联分析本研究在山东聊城、新疆阿勒泰和甘肃天祝分别采集大尾寒羊、阿勒泰羊和藏羊各40只,利用Illumina OvineSNP600 BeadChip高密芯片进行基因分型,质量控制后,剩余119只个体和538762个SNP,利用广义线性模型(GLM),使用Tassel软件对大尾寒羊、阿勒泰羊和藏羊的尾型性状进行全基因组关联分析。结果在全基因组范围内检测到与尾型显著关联的31个显著SNP位点,这些位点分别位于1、2、7、10、13、15和19号染色体上。对于显著的SNP位点,确定其物理位置,并在该区域内筛选候选基因。通过基因功能注释和参考前人研究结果,将SPAG17,Tbx15,VRTN,NPC2,BMP2和PDGFD等基因作为控制尾型的关键候选基因。2、大尾寒羊、阿勒泰羊和藏羊全基因组拷贝数变异检测应用PennCNV软件对三个品种共计120只个体进行拷贝数变异(CNV)检测。结果显示,在大尾寒羊、阿勒泰羊和藏羊上分别检测到了 371、201和66个CNV区域,长度分别是71.35 Mb、51.65 Mb和10.56 Mb。合并在基因组位置上重叠的拷贝数后,得到490个拷贝数变异区域(CNVRs),其中90个重复,390个缺失,7个重复缺失共存;根据CNVRs在26条常染色体上的位置,绘制出绵羊全基因组拷贝数变异图谱;随机选取10个CNVRs进行qPCR验证,结果10个区域中有8个得到验证;对不同品种间CNVRs的数目分布进行分析,结果发现大尾寒羊和阿勒泰羊基因组中的拷贝数变异高于藏羊;对CNVRs区域内的基因进行了 GO和KEGG分析,结果发现了与脂肪代谢、气候环境相适应的候选基因。3、大尾寒羊、阿勒泰羊和藏羊全基因组选择信号检测用固定指数(FST)和杂交群体扩展单倍型纯合度(XPEHH)两种方法对三个品种两两之间进行选择信号检测。FST方法发现脂尾-瘦尾和脂臀尾-瘦尾之间受到的选择信号比大尾-脂臀尾之间的多,只在大尾-瘦尾之间受到选择的SNP位点有67个,44个选择区域,总长度为10.10Mb,平均长度为0.233Mb,通过基因注释和富集分析发现,在这些区域内找到了脂肪相关的候选基因,如JAZF1,GEM,PRNP,BMP2,PPP1CC,PDGFD,MC4R,GPR124 和 ADRB3。XPE分析对将藏羊怍为参考群体,将大尾寒羊和阿勒泰羊分别作为实验群体,结果发现,在大尾寒羊和阿勒泰羊中分别有231和179个SNP位点受到正向选择,将每个显著的SNP位点向上下游个扩展50kb作为一个受选择的区域,通过基因注释和富集分析发现这些受选择区域CPT1A,CA4,CLPS,BMP2,KLF3,RETN,WNT,INSR,IRS1,CPT1A,SLC27A2,SLC27A4,PRKAG1,JAZF1,MC4R,BMP8B,CPT2,FABP3,SLC27A4,KLF11,PRKAG2,BMPR1B,SLC27A6,FOXP1,FGFR1基因与脂肪相关。通过这两种方法检测选择信号,结果发现这两种方法有重叠的选择区域,这些重叠区域内JAZF1,BMP2,MC4R基因与脂肪形成相关。
[Abstract]:The sheep breeds in our country can be classified into five types: long fat tail, short fat tail, fat buttock tail, long thin tail and short tail. The fat tail type and fat buttock tail sheep are domesticated and natural selection by the wild thin tail sheep. In the course of domestication and selection, the climate environment and human needs and different choice methods are different. The formation of tail type has an important influence. At the same time, the tail type of sheep is also an important economic character, which has been paid attention to by the breeding scholars. In the past, sheep tail fat has an important effect on both the sheep and the sheep. But at present, with the change of the consumption concept and the improvement of the feeding conditions in the pasture area, the effect of sheep tail fat has passed through the sheep. It is not important and brings economic pressure to production. Therefore, it is important for sheep molecular breeding to carry out genome genetic variation analysis of different tail type sheep by SNP chip and explore the genetic basis of different breed of sheep tail type for sheep molecular breeding. This study uses Illumina OvineSNP600 BeadChip high density commercial chip to three The whole genome association analysis, copy number variation and selection signal detection were carried out for 31 sheep varieties with different tail type, and the candidate genes were enriched and analyzed. The specific contents of this thesis are as follows: 1, the whole genome association analysis of tail cold sheep, Aletai sheep and Tibetan sheep tail type in Liaocheng, Altai and Gansu in Xinjiang, Xinjiang 40 sheep and 40 sheep of Aletai sheep and Tibetan sheep were collected for genotyping by using Illumina OvineSNP600 BeadChip high density chip. After quality control, the remaining 119 individuals and 538762 SNP were used to use the generalized linear model (GLM), and the tail type traits of big tail Han sheep, Aletai sheep and Tibetan sheep were analyzed by Tassel software. Results 31 significant SNP loci associated with the tail type were detected in the whole genome. These sites were located on the 1,2,7,10,13,15 and chromosome 19. For the significant SNP loci, their physical location was identified and the candidate genes were screened in the region. SPAG17, Tbx15, by genetic functional annotation and reference to previous research results. VRTN, NPC2, BMP2 and PDGFD as the key candidate gene for controlling tail type.2, large tail Han sheep, Aletai sheep and Tibetan sheep whole genome copy number variation detection application PennCNV software for three varieties totalling 120 individuals with copy number variation (CNV) detection. The results showed that 37 were detected in big tail Han Sheep, Aletai sheep and Tibetan sheep respectively. 1201 and 66 CNV regions, which are 71.35 Mb, 51.65 Mb and 10.56 Mb., are combined to overlap the number of copies of the genome, and get 490 copy number variation region (CNVRs), of which 90 repeat, 390 missing, and 7 repeating deletion coexist, and the whole genome copy number variation of sheep is drawn according to the position of CNVRs in 26 regular chromophore. A random selection of 10 CNVRs was selected for qPCR validation, and 8 of the 10 regions were verified. The number distribution of CNVRs in different varieties was analyzed. The results showed that the copy number variation in the genome of the big tail Han sheep and Aletai sheep was higher than that of the Tibetan sheep; the GO and KEGG analysis of the genes in the CNVRs region were carried out, and the results were found to be with the fatty substitute. Xie, a candidate gene for climatic and environmental adaptation,.3, large tail Han sheep, Aletai sheep and Tibetan sheep, two methods of selection signal detection using FST and hybrid population extended haplotype homozygosity (XPEHH) were selected for the selection signal detection between three varieties and 22, and found between fat tail and fat tail and fat rump tail and thin tail. The selected signal is more than the big tail fat hip tail. There are 67 selected SNP loci between the big tail and the thin tail, 44 selected regions, the total length is 10.10Mb, the average length is 0.233Mb. The fat related candidate genes, such as JAZF1, GEM, PRNP, BMP2, PPP1CC, PDGFD, MC4R, are found in these regions by gene annotation and enrichment analysis. GPR124 and ADRB3.XPE analyzed the Tibetan sheep as a reference group, taking the big tail Han sheep and Aletai sheep as the experimental group respectively. The results showed that 231 and 179 SNP loci were positively selected in the big tail Han sheep and Aletai sheep, and each significant SNP site was extended to the upper and lower reaches of 50kb as a selected area, through the base. CPT1A, CA4, CLPS, BMP2, KLF3, RETN, WNT, INSR, IRS1, CPT1A, SLC27A2, SLC27A4, WNT, INSR, WNT, WNT, WNT, INSR, BMP2 The JAZF1, BMP2 and MC4R genes in these overlapping regions are related to fat formation.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S826

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