功能基因与QTL数据整合分析软件开发及应用

发布时间：2018-05-31 19:54

本文选题：功能基因组学 + 生物信息学　；参考：《山东农业大学》2017年硕士论文

【摘要】：功能基因组学利用结构基因组学的信息,系统的研究生物体内多个基因和蛋白质,阐述DNA序列的功能,它代表了基因组分析的新阶段。转录组的研究可以揭示生物体的基因表达、研究结构变异及发现新基因等,转录组测序技术(RNA-seq)利用下一代测序技术,为转录组的研究提供了一种新的研究手段。数量性状与其他生物性状一样,受染色体上基因的控制,从基因水平上研究畜禽的数量性状已经成为动物研究领域的热点。单核苷酸多态性(SNP)是基因组中发生频率最高的变异种类,研究SNP对探究基因组结构,基因进化历史及疾病发生根源具有很重要的指导作用。功能基因组学、控制数量性状的QTL定位分析以及SNP分析,在阐述基因序列的功能方面,提高畜禽产品经济价值,探索与生物进化及疾病相关的基因方面具有重大的意义。在他们不断发展前提下,产生大量生物学数据,需要进行采集、归类及分析,目前为止,没有一款工具将这几类数据有效的整合在一起。在本研究中,我们采用开发R包的方式,将RNA-seq数据、QTL数据、SNP数据快速的整合起来,实现相互查询的功能,以及辅助功能。本研究的AnimalGene2QTL包运行在RStudio或R中,可以查看Vignette文档和示例文档。通过测试查询10000行数据量的用时,结果显示用时为47.90秒,结果说明本研究的R包操作非常简便、快速。在结果准确上,我们对本研究的R包与ensembl、Animalgenome网站两种查询方式进行比对,分别查询100个ensembl基因对应的QTL,通过统计查看,结果显示查询的QTL没有任何差别,R包与网站的查询结果完全一样,结果显示本研究的R包查询结果非常准确,具有很高的有效性。在应用方面,本研究中,我们用AnimalGene2QTL包分别对家禽的肠炎沙门氏菌感染相关基因和空肠弯曲杆菌感染相关基因进行QTL查询,肠炎沙门氏菌感染相关的数据为10000个高质量靶基因,通过对查询得到的35942个QTL统计筛选直接相关性状,再对直接相关性状筛选,确定了 369个与试验数据研究相关的QTL,通过统计369个QTL对应的基因,最终我们确定了与肠炎沙门氏菌感染直接相关的基因359个。空肠弯曲杆菌感染的数据为101个ensembl基因,通过对查询得到的1437个QTL进行统计筛选直接相关性状,在对直接相关性状筛选,最终确定了直接相关的基因39个。我们可以结合原基因数据对这些基因进行GO、pathway预测功能分析,不仅可以在结果上更加精确,同时可以增加对结果的可靠性。
[Abstract]:Functional genomics makes use of the information of structural genomics to systematically study many genes and proteins in organisms and explain the function of DNA sequence which represents a new stage of genome analysis. Transcriptome research can reveal gene expression, study structural variation and find new genes, etc. RNA-seq) provides a new research method for transcriptome research using next generation sequencing technology. Quantitative traits, like other biological traits, are controlled by genes on chromosomes, so the study of quantitative traits of livestock and poultry at the gene level has become a hot spot in animal research field. Single nucleotide polymorphisms (SNPs) are the most frequent mutations in genomes. The study of SNP plays an important role in exploring the genome structure, gene evolution history and the origin of disease. Functional genomics, QTL mapping and SNP analysis for quantitative traits are of great significance in explaining the function of gene sequences, improving the economic value of livestock and poultry products, and exploring genes related to biological evolution and disease. Under the premise of their continuous development, a large number of biological data need to be collected, classified and analyzed. So far, there is no tool to effectively integrate these kinds of data together. In this study, we use R package to integrate RNA-seq data quickly, and realize the function of mutual query and auxiliary function. The AnimalGene2QTL package in this study runs in RStudio or R, and you can view Vignette documents and sample documents. The test results show that the time of 10000 rows of data is 47.90 seconds. The results show that the R packet operation is very simple and fast. As to the accuracy of the results, we compared the R package of this study with the two query methods of the Animalgenome website, and queried the QTLs corresponding to 100 ensembl genes respectively, and checked the QTLs by statistical analysis. The results show that there is no difference between the QTL of the query and the query results of the website. The results show that the R packet query results of this study are very accurate and highly effective. In the aspect of application, in this study, we used AnimalGene2QTL bag to inquire the genes related to Salmonella enteritidis infection in poultry and Campylobacter jejuni infection genes respectively. The data of salmonella enteritidis infection was 10 000 high quality target genes. Three hundred and thirty-nine hundred and ninety-two QTLs related to the experimental data were identified by the 35942 QTL statistical screening and then the direct correlation traits were screened, and the corresponding genes of 369 QTL were counted. Finally, we identified 359 genes directly associated with Salmonella enteritis infection. The data of Campylobacter jejuni infection was 101 ensembl genes. Through the statistical screening of 1 437 QTL obtained from the query, 39 directly related genes were identified in the screening of the direct correlation traits of Campylobacter jejuni (Campylobacter jejuni). We can analyze the prediction function of these genes by combining proto gene data, which can not only improve the accuracy of the results, but also increase the reliability of the results.
【学位授予单位】：山东农业大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q811.4;S852.61

【参考文献】