多组学分析揭示恩施黑猪经济性状相关的遗传信号和分子通路

发布时间：2018-07-20 13:05

【摘要】：大量报道表明,驯化物种的受选择基因组区域或者基因与遗传育种程序高度相关,能用于辅助产生新的或者期望的表型性状,此外基因的甲基化水平和表达水平也与这些受选择信号高度相关。恩施黑猪是一种典型的肉脂兼用型猪种,它具有肉质好、适应性强、蓄脂能力强以及抗病性强等优良性状。为了研究其驯化过程中这些优良性状的遗传调控机制,本研究对来自三个不同地方的恩施黑猪群体的DNA分别进行了混池测序,并获得了约72倍猪参考基因组大小的重测序数据。此外,本研究还分别对90日龄的恩施黑猪、大白猪以及中国野猪进行了全基因组甲基化测序、mRNA测序以及小RNA测序。最后对四种数据进行了整合分析,主要获得以下结果:(1)获得了属于三个不同亚群的5头恩施黑猪的全线粒体DNA序列,长度约为16.7kb,发现三种不同体型的恩施黑猪具有较近的遗传关系。(2)三个亚群恩施黑猪以及野猪群体重测序共产生266.30Gb数据,在四个群体中都发现了大约14M的SNP,恩施黑猪与中国野猪见共享了60.92%的SNP,而恩施黑猪群体之间则共享75.56%的SNP。基于全基因组SNP信息位点的系统发育分析结果显示,恩施黑猪遗传距离较小,且大型猪和中型猪具有更近的遗传距离。(3)在恩施黑猪基因组中鉴定出417个受到强烈选择的基因,这些受选择的基因主要与新陈代谢、免疫应答以及生长发育相关。其中RPS10、GSK3A、INSL6、TBX19以及VASN5个基因在恩施黑猪中呈现极强的正向选择信号,这些基因的功能涉及到免疫、肥胖、体型大小以及繁殖力等方面,与恩施黑猪的优良性状高度相关。(4)首次构建了恩施黑猪肝脏组织的全基因组单碱基分辨率DNA甲基化图谱,结果表明,绝大多数甲基化位点出现在CpG二核苷酸处,CHG和CHH三核苷酸中甲基化位点较少且甲基化水平较低。(5)恩施黑猪与大白猪以及中国野猪之间的差异甲基化基因主要富集于转录、细胞分化以及免疫相关通路。恩施黑猪与大白猪以及中国野猪之间的差异表达基因主要富集于能量代谢以及免疫相关通路。恩施黑猪与大白猪以及中国野猪之间的差异表达miRNA的靶基因主要富集于新陈代谢以及生长发育相关通路。四种组学数据都能展示恩施黑猪优良性状相关的分子通路,且各组学的调控过程不是一个独立的过程,而是以某种复杂的方式共同发挥作用的。(6)启动子区域高甲基化的基因表达水平较低,低甲基化水平的基因表达水平较高,受这种调控模式的差异表达基因占了总差异表达的基因的50%,说明这仅是甲基化对基因表达调控的主要模式之一。同理,启动子区域高甲基化的miRNA表达水平较低,低甲基化水平的miRNA表达水平较高,但只有极少数miRNA受到这种机制的调控,miRNA受甲基化调控的机制和mRNA具有较大的不同。此外,受选择基因在以上三个不同猪种中都具有高表达低甲基化的特点,说明这些基因可能对维持猪的生命功能发挥着重要的作用。综上,本研究对恩施猪进行线粒体DNA测序、重测序、DNA甲基化测序、mRNA测序、mi RNA测序等多层次的功能基因组学分析,鉴定出恩施黑猪基因组中受自然选择的区域或基因,阐明了部分重要功能基因表达调控规律,揭示各组学的调控关系。这些发现有助于理解恩施黑猪重要优良经济性状的起源和发展,能够为进一步开发利用我国这一宝贵遗传资源提供基础理论。
[Abstract]:A large number of reports indicate that the selected genome area or gene of the domesticated species is highly related to the genetic breeding program, and can be used to assist in the production of new or expected phenotypic traits. In addition, the level of methylation and expression of the gene is highly correlated with these selected signals. The Enshi black pig is a typical type of meat fat concurrently type pig. In order to study the genetic regulation mechanism of these excellent characters in the course of domestication, the DNA of the Enshi black pig population from three different places was sequenced, and the retest number of about 72 times the size of the pig's reference genome was obtained. In addition, the whole genome methylation, mRNA sequencing and small RNA sequencing of 90 day old Enshi black pigs, big white pigs and Chinese wild boars were carried out. Finally, four data were integrated and analyzed, and the following results were obtained: (1) the whole mitochondrial DNA sequence of 5 Enshi black pigs belonging to three different subgroups was obtained. The length of the three Enshi black pigs of three different types had a close genetic relationship. (2) the weight sequencing of three subgroups of Enshi black pigs and the wild boar group produced a total of 266.30Gb data, the SNP of about 14M was found in the four population, and the Enshi black pig shared 60.92% SNP with the Chinese wild boar, while the Enshi black pig population shared 7. 5.56% SNP. based on the phylogenetic analysis of the whole genome SNP information sites showed that the genetic distance of Enshi black pigs was smaller, and the large and medium pigs had closer genetic distance. (3) 417 strongly selected genes were identified in the Enshi black pig genome, and these selected genes were mainly associated with metabolism, immune response and Growth and development related. Among them, RPS10, GSK3A, INSL6, TBX19 and VASN5 genes are very strong positive selection signals in Enshi black pigs. These genes are related to immunity, obesity, size and fecundity, and are closely related to the excellent characters of Enshi black pigs. (4) the whole gene of the liver tissue of Enshi black pig was first constructed. The single base resolution DNA methylation map showed that most methylation sites appeared at CpG dinucleotide, CHG and CHH trinucleotides were less methylation sites and lower methylation levels. (5) the difference methylation genes between Enshi black pig and big white pig and Chinese wild boar were mainly enriched in transcription, cell differentiation and immunity. The differential expression genes between the Enshi black pig and the big white pig and the Chinese wild boar are mainly enriched in energy metabolism and immune related pathways. The differential expression of miRNA between Enshi black pig and big white pig and Chinese wild boar is mainly enriched in metabolism and growth related pathways. The four types of data can be displayed. The molecular pathways related to the excellent characters of Enshi black pigs are shown, and the regulation process of each group is not an independent process, but in a complex way. (6) the gene expression level of hypermethylation in the promoter region is low, the level of the low methylation level is higher, and the differential expression base of this regulation mode is different. 50% of the genes expressed in the total difference show that this is only one of the main modes of regulation of gene expression by methylation. Similarly, the miRNA expression level of hypermethylation in promoter region is low, and the level of miRNA expression at low methylation level is higher, but only a few miRNA are regulated by this mechanism, and the mechanism of miRNA regulation by methylation is the mechanism and the regulation of methylation. MRNA has a large difference. In addition, the selected genes have high expression of low methylation in all three different pigs. It shows that these genes may play an important role in maintaining the life function of pigs. In this study, the mitochondrial DNA sequencing, sequenced, DNA sequencing, mRNA sequencing, MI RNA sequencing of Enshi pigs were carried out in this study. In order to identify the regions or genes selected naturally in the genome of Enshi black pig, the regulation regularity of some important functional gene expression is clarified and the regulation relationship of each group is revealed. These discoveries help to understand the origin and development of the important and excellent economic traits in Enshi black pigs, and can be further developed for the benefit of further development. The basic theory of this precious genetic resource in China is provided.
【学位授予单位】：华中农业大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S828

【参考文献】