基于全基因组SNP对猪品种分子种质特性挖掘与保护的研究

发布时间：2018-03-09 08:35

本文选题：种质特性　切入点：遗传多样性　出处：《中国农业大学》2017年博士论文　论文类型：学位论文

【摘要】：畜禽遗传资源是遗传改良的基础素材,是育种工作可持续发展的重要保障,因此,对优良品种种质特性的挖掘以及最大程度地保护对畜牧业生产具有非常重要的意义。本研究以中国优良地方猪品种的典型代表——太湖猪为例,基于重测序技术对其分子种质特性进行挖掘,并针对"高繁殖力"特性进行分析验证。而后,基于全基因组标记的特点,结合计算机模拟技术,对猪保种群的保种效果进行了评估。论文基于以下两部分研究:(1)基于全基因组重测序对太湖猪高繁殖力种质特性的研究基于全基因组重测序技术对包括太湖猪在内的6个品种4组样品池进行了全基因组重测序。其中以太湖猪为中国高繁殖力组,另外3个对照组分别为中国低繁殖力组(藏猪和滇南小耳猪)、外国高繁殖力组(长白猪)和外国低繁殖力组(杜洛克猪)。通过强选择和高度分化两个条件筛选,共鉴定出39个太湖猪分子种质特性区段。进一步对等位基因频率分析,筛选到太湖猪特有的SNP位点132,000个,主要定位在基因的保守非编码区内。对含有最多的太湖特有SNP位点数的前1,000个基因进行功能富集分析,发现这些基因主要参与胚胎发育及外貌表型发育过程。结合繁殖性状QTL数据,发现位于8号染色体134.05-134.15Mb的选择信号区段是影响繁殖性状重要的候选区段,该区间内的候选基因为骨形态发生蛋白受体1B(BMPR1B)。比较基因组学分析发现在BMPR1B基因第一内含子中存在一个哺乳动物保守的雌激素受体反应元件。双萤光素酶结果表明该位置太湖单倍型结合雌激素受体(ESR1)的能力显著高于杜洛克猪,并且梅山猪孕期子宫内膜BMPR1B基因的表达显著高于杜洛克猪,组织切片结果也表明梅山猪子宫内膜腺体的发育明显优于杜洛克猪。因此,我们认为太湖猪优势单倍型能够促进其与ESR1的结合能力,顺式调节BMPR1B基因的表达,进而影响猪子宫内膜腺体的发育。(2)利用全基因组SNP标记探讨猪保种群体遗传多样性变化的研究本研究根据猪全基因组SNP分布特点,建立猪全基因组SNP标记模拟实验,模拟猪保种群体在现行保种制度下保存50个世代,并在此过程中监测保种群体世代间遗传多样性的变化。基于开发的双标记SNP,首次获得了 IBD概率的真值来评估群体遗传多样性(GD_IBD),同时也利用He、Ho、Ae、Ao、GD_BS和F对该群体的遗传多样性进行了估计。结果表明猪保种群体在现行的保种制度下,各指标评估的遗传多样性在第10个世代丢失了近5%;He、Ho、Pp、GD_IBS在评估遗传多样性时在灵敏度和相关性均表现良好,其中He最为准确;此外,家系基因组组分结果表明平均每5个保种世代会有～7.5%的公猪家系,～30%母猪家系基因组信息丢失。因此,如果长期保持保种群处于较高的遗传多样性水平,则可以每5个世代向保种群中引入10%同品种的遗传物质(精液、胚胎),以达到预期的保种目标。综上所述,本研究采用全基因组重测序技术鉴定太湖猪种质特性相关的基因组区段39个,通过比较基因组学、功能实验验证了太湖猪"高繁殖力"特性的关键候选基因BMPR1B基因;此外,基于猪保种群体全基因组SNP标记模拟实验,分析保种世代间遗传多样性的变化模式,为品种种质特性的开发和保护提供了新思路。
[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.

【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】：S828

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