本文選題：全基因組關(guān)聯(lián)分析 + 拷貝數(shù)變異檢測��； 參考：《中國農(nóng)業(yè)大學(xué)》2017年博士論文

【摘要】：我國的綿羊品種按尾形分類可以分為長脂尾、短脂尾、脂臀尾、長瘦尾和短瘦尾五種。脂尾型和脂臀尾型綿羊是由野生的瘦尾綿羊經(jīng)過人工馴化和自然選擇而來,在馴化和選擇過程中,氣候環(huán)境和人類的需求及不同的選擇方式都對不同尾型的形成產(chǎn)生了重要影響。同時(shí),綿羊的尾型也是一個(gè)重要的經(jīng)濟(jì)性狀,一直受到育種學(xué)者的關(guān)注,在過去,綿羊尾部脂肪對綿羊自身和人類都有重要作用,但目前,隨著消費(fèi)觀念的改變和牧區(qū)飼養(yǎng)條件的改善,綿羊尾部脂肪的作用己經(jīng)不重要且給生產(chǎn)帶來經(jīng)濟(jì)壓力。因此,利用SNP芯片對不同尾型的綿羊品種開展全基因組遺傳變異分析,探索不同品種綿羊尾型差異的遺傳基礎(chǔ)對綿羊分子育種具有重要意義。本研究利用Illumina OvineSNP600 BeadChip高密度商業(yè)化芯片對三個(gè)不同尾型的綿羊品種31進(jìn)行全基因組關(guān)聯(lián)分析、拷貝數(shù)變異和選擇信號檢測,并對候選基因進(jìn)行了富集分析。本論文具體研究內(nèi)容如下:1、大尾寒羊、阿勒泰羊和藏羊尾型性狀全基因組關(guān)聯(lián)分析本研究在山東聊城、新疆阿勒泰和甘肅天祝分別采集大尾寒羊、阿勒泰羊和藏羊各40只,利用Illumina OvineSNP600 BeadChip高密芯片進(jìn)行基因分型,質(zhì)量控制后,剩余119只個(gè)體和538762個(gè)SNP,利用廣義線性模型(GLM),使用Tassel軟件對大尾寒羊、阿勒泰羊和藏羊的尾型性狀進(jìn)行全基因組關(guān)聯(lián)分析。結(jié)果在全基因組范圍內(nèi)檢測到與尾型顯著關(guān)聯(lián)的31個(gè)顯著SNP位點(diǎn),這些位點(diǎn)分別位于1、2、7、10、13、15和19號染色體上。對于顯著的SNP位點(diǎn),確定其物理位置,并在該區(qū)域內(nèi)篩選候選基因。通過基因功能注釋和參考前人研究結(jié)果,將SPAG17,Tbx15,VRTN,NPC2,BMP2和PDGFD等基因作為控制尾型的關(guān)鍵候選基因。2、大尾寒羊、阿勒泰羊和藏羊全基因組拷貝數(shù)變異檢測應(yīng)用PennCNV軟件對三個(gè)品種共計(jì)120只個(gè)體進(jìn)行拷貝數(shù)變異(CNV)檢測。結(jié)果顯示,在大尾寒羊、阿勒泰羊和藏羊上分別檢測到了 371、201和66個(gè)CNV區(qū)域,長度分別是71.35 Mb、51.65 Mb和10.56 Mb。合并在基因組位置上重疊的拷貝數(shù)后,得到490個(gè)拷貝數(shù)變異區(qū)域(CNVRs),其中90個(gè)重復(fù),390個(gè)缺失,7個(gè)重復(fù)缺失共存;根據(jù)CNVRs在26條常染色體上的位置,繪制出綿羊全基因組拷貝數(shù)變異圖譜;隨機(jī)選取10個(gè)CNVRs進(jìn)行qPCR驗(yàn)證,結(jié)果10個(gè)區(qū)域中有8個(gè)得到驗(yàn)證;對不同品種間CNVRs的數(shù)目分布進(jìn)行分析,結(jié)果發(fā)現(xiàn)大尾寒羊和阿勒泰羊基因組中的拷貝數(shù)變異高于藏羊;對CNVRs區(qū)域內(nèi)的基因進(jìn)行了 GO和KEGG分析,結(jié)果發(fā)現(xiàn)了與脂肪代謝、氣候環(huán)境相適應(yīng)的候選基因。3、大尾寒羊、阿勒泰羊和藏羊全基因組選擇信號檢測用固定指數(shù)(FST)和雜交群體擴(kuò)展單倍型純合度(XPEHH)兩種方法對三個(gè)品種兩兩之間進(jìn)行選擇信號檢測。FST方法發(fā)現(xiàn)脂尾-瘦尾和脂臀尾-瘦尾之間受到的選擇信號比大尾-脂臀尾之間的多,只在大尾-瘦尾之間受到選擇的SNP位點(diǎn)有67個(gè),44個(gè)選擇區(qū)域,總長度為10.10Mb,平均長度為0.233Mb,通過基因注釋和富集分析發(fā)現(xiàn),在這些區(qū)域內(nèi)找到了脂肪相關(guān)的候選基因,如JAZF1,GEM,PRNP,BMP2,PPP1CC,PDGFD,MC4R,GPR124 和 ADRB3。XPE分析對將藏羊怍為參考群體,將大尾寒羊和阿勒泰羊分別作為實(shí)驗(yàn)群體,結(jié)果發(fā)現(xiàn),在大尾寒羊和阿勒泰羊中分別有231和179個(gè)SNP位點(diǎn)受到正向選擇,將每個(gè)顯著的SNP位點(diǎn)向上下游個(gè)擴(kuò)展50kb作為一個(gè)受選擇的區(qū)域,通過基因注釋和富集分析發(fā)現(xiàn)這些受選擇區(qū)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基因與脂肪相關(guān)。通過這兩種方法檢測選擇信號,結(jié)果發(fā)現(xiàn)這兩種方法有重疊的選擇區(qū)域,這些重疊區(qū)域內(nèi)JAZF1,BMP2,MC4R基因與脂肪形成相關(guān)。
[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.
【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】：2017
【分類號】：S826

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