本文選題：種質(zhì)特性　切入點(diǎn)：遺傳多樣性　出處：《中國農(nóng)業(yè)大學(xué)》2017年博士論文　論文類型：學(xué)位論文

【摘要】：畜禽遺傳資源是遺傳改良的基礎(chǔ)素材,是育種工作可持續(xù)發(fā)展的重要保障,因此,對優(yōu)良品種種質(zhì)特性的挖掘以及最大程度地保護(hù)對畜牧業(yè)生產(chǎn)具有非常重要的意義。本研究以中國優(yōu)良地方豬品種的典型代表——太湖豬為例,基于重測序技術(shù)對其分子種質(zhì)特性進(jìn)行挖掘,并針對"高繁殖力"特性進(jìn)行分析驗(yàn)證。而后,基于全基因組標(biāo)記的特點(diǎn),結(jié)合計算機(jī)模擬技術(shù),對豬保種群的保種效果進(jìn)行了評估。論文基于以下兩部分研究:(1)基于全基因組重測序?qū)μi高繁殖力種質(zhì)特性的研究基于全基因組重測序技術(shù)對包括太湖豬在內(nèi)的6個品種4組樣品池進(jìn)行了全基因組重測序。其中以太湖豬為中國高繁殖力組,另外3個對照組分別為中國低繁殖力組(藏豬和滇南小耳豬)、外國高繁殖力組(長白豬)和外國低繁殖力組(杜洛克豬)。通過強(qiáng)選擇和高度分化兩個條件篩選,共鑒定出39個太湖豬分子種質(zhì)特性區(qū)段。進(jìn)一步對等位基因頻率分析,篩選到太湖豬特有的SNP位點(diǎn)132,000個,主要定位在基因的保守非編碼區(qū)內(nèi)。對含有最多的太湖特有SNP位點(diǎn)數(shù)的前1,000個基因進(jìn)行功能富集分析,發(fā)現(xiàn)這些基因主要參與胚胎發(fā)育及外貌表型發(fā)育過程。結(jié)合繁殖性狀QTL數(shù)據(jù),發(fā)現(xiàn)位于8號染色體134.05-134.15Mb的選擇信號區(qū)段是影響繁殖性狀重要的候選區(qū)段,該區(qū)間內(nèi)的候選基因?yàn)楣切螒B(tài)發(fā)生蛋白受體1B(BMPR1B)。比較基因組學(xué)分析發(fā)現(xiàn)在BMPR1B基因第一內(nèi)含子中存在一個哺乳動物保守的雌激素受體反應(yīng)元件。雙螢光素酶結(jié)果表明該位置太湖單倍型結(jié)合雌激素受體(ESR1)的能力顯著高于杜洛克豬,并且梅山豬孕期子宮內(nèi)膜BMPR1B基因的表達(dá)顯著高于杜洛克豬,組織切片結(jié)果也表明梅山豬子宮內(nèi)膜腺體的發(fā)育明顯優(yōu)于杜洛克豬。因此,我們認(rèn)為太湖豬優(yōu)勢單倍型能夠促進(jìn)其與ESR1的結(jié)合能力,順式調(diào)節(jié)BMPR1B基因的表達(dá),進(jìn)而影響豬子宮內(nèi)膜腺體的發(fā)育。(2)利用全基因組SNP標(biāo)記探討豬保種群體遺傳多樣性變化的研究本研究根據(jù)豬全基因組SNP分布特點(diǎn),建立豬全基因組SNP標(biāo)記模擬實(shí)驗(yàn),模擬豬保種群體在現(xiàn)行保種制度下保存50個世代,并在此過程中監(jiān)測保種群體世代間遺傳多樣性的變化�；陂_發(fā)的雙標(biāo)記SNP,首次獲得了 IBD概率的真值來評估群體遺傳多樣性(GD_IBD),同時也利用He、Ho、Ae、Ao、GD_BS和F對該群體的遺傳多樣性進(jìn)行了估計。結(jié)果表明豬保種群體在現(xiàn)行的保種制度下,各指標(biāo)評估的遺傳多樣性在第10個世代丟失了近5%;He、Ho、Pp、GD_IBS在評估遺傳多樣性時在靈敏度和相關(guān)性均表現(xiàn)良好,其中He最為準(zhǔn)確;此外,家系基因組組分結(jié)果表明平均每5個保種世代會有～7.5%的公豬家系,～30%母豬家系基因組信息丟失。因此,如果長期保持保種群處于較高的遺傳多樣性水平,則可以每5個世代向保種群中引入10%同品種的遺傳物質(zhì)(精液、胚胎),以達(dá)到預(yù)期的保種目標(biāo)。綜上所述,本研究采用全基因組重測序技術(shù)鑒定太湖豬種質(zhì)特性相關(guān)的基因組區(qū)段39個,通過比較基因組學(xué)、功能實(shí)驗(yàn)驗(yàn)證了太湖豬"高繁殖力"特性的關(guān)鍵候選基因BMPR1B基因;此外,基于豬保種群體全基因組SNP標(biāo)記模擬實(shí)驗(yàn),分析保種世代間遺傳多樣性的變化模式,為品種種質(zhì)特性的開發(fā)和保護(hù)提供了新思路。
[Abstract]:The genetic resources of livestock and poultry is the basic material for genetic improvement, is an important guarantee for sustainable development of the breeding work therefore, mining the Germplasm Characteristics of fine varieties and maximize the protection of the production of animal husbandry has very important significance. In this study, Chinese excellent local pig varieties typical of Taihu pig: for example, re sequencing technology the molecular characteristics of germplasm mining based on the analysis and verification for the "high fecundity" characteristics. Then, based on the characteristics of whole genome markers, combined with computer simulation technology, the pig conservation population conservation effect is evaluated. The following two parts: (1) based on the research of whole genome sequencing of Germplasm Characteristics Taihu pig high fecundity based on whole genome sequencing of 6 varieties including Taihu pigs, 4 groups of sample cell for whole genome sequencing. The pigs in Taihu For Chinese prolificacy group, the other 3 patients in control group were Chinese group (low fecundity of Tibet pig and pig, Diannan small ear) foreign high fecundity group (Landrace) and low fecundity group (foreign Duroc). The selection is strong and highly differentiated two selected conditions, identified a total of 39 Germplasm Characteristics of Taihu pigs molecular section. Further analysis of the allele frequency of SNP locus in Taihu pigs screened 132000 unique, mainly located in the region of conserved non encoding gene. Functional enrichment analysis of the first 1000 genes containing the most unique Taihu SNP sites, found that these genes mainly involved in embryonic development and the appearance of the phenotypic development process. Combined with the reproductive traits of QTL data, found that the signal section of chromosome 8. 134.05-134.15Mb is an important candidate regions affecting reproductive traits, candidate genes within the interval for bone morphogenetic protein receptor 1 B (BMPR1B). Comparative genomic analysis revealed the presence of a conserved mammalian estrogen receptor response element in the first intron of BMPR1B gene. Dual luciferase results showed that the position of the Taihu haplotype combined estrogen receptor (ESR1) ability was significantly higher than that of Duroc pigs and Meishan pigs, the expression of BMPR1B gene in endometrium during pregnancy was significantly higher than that of Duroc pig, biopsy results also showed that Meishan pig endometrial gland development is obviously better than that of Duroc pigs. Therefore, we believe that the advantages of Taihu pig haplotypes can promote their ability to bind with ESR1, the expression of cis regulatory BMPR1B genes, thereby affecting porcine endometrial gland development. (2) to investigate the conservation of genetic diversity in the population of pigs study on the change of the study according to the characteristics of SNP distribution of the complete genome of swine by whole genome SNP markers, establishment of porcine whole genome SNP markers simulation experiment, simulation Pig conservation population save 50 generations in the current protection system, and in the process of monitoring and conservation of genetic diversity among the population generation changes. Double labeling based on SNP for the first time the true value of IBD probability to assess population genetic diversity (GD_IBD), but also the use of He, Ho, Ae Ao, F, GD_BS and genetic diversity of this group were estimated. The results show that the pig conservation population in the existing conservation system, the evaluation index of genetic diversity in tenth generations lost nearly 5%; He, Ho, Pp, GD_IBS in the assessment of genetic diversity in sensitivity and the correlation was good, in which He is the most accurate; in addition, the family of genome segment results show the average of every 5 ~ 7.5% generations will protect the boar pedigree, ~ 30% sows pedigreed genome information is lost. Therefore, if the population remain at a high level of genetic diversity for a long period of time, you can Each of the 5 generation population of introducing genetic material with 10% varieties (semen, embryos), in order to achieve the desired conservation target. In summary, this study uses genomic regions related to whole genome sequencing technology to identify the characteristics of the 39 Taihu pigs, through comparative genomics, experimental verification of the key function of candidate gene BMPR1B gene of Taihu pig "high fecundity" characteristics; in addition, the pig conservation population of whole genome SNP markers based on the analysis of simulation experiment, and the generation of genetic diversity patterns, provides a new idea for the development and protection of Germplasm Characteristics of 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】：2017
【分類號】：S828

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