水稻耐盐性机理的计算生物学研究

发布时间：2018-01-08 17:30

本文关键词：水稻耐盐性机理的计算生物学研究　出处：《吉林大学》2016年博士论文　论文类型：学位论文

【摘要】：土壤盐碱化引起的非生物胁迫在全世界范围内造成了普遍持续的农作物减产。作为最重要的粮食作物,水稻(Oryza sativa)改良的一个重要方向就是通过分子育种的方法使其具备盐耐受性。然而作为一种由多种基因共同作用决定的复杂性状,人们对水稻耐盐性的机理仍然知之甚少。本文采用新的计算生物学方法,从系统生物学角度构建了水稻耐盐的机理网络;开发了一种基于机器学习Bootstrap SVM-RFE的改进volcano plot方法来处理基因表达数据,并从中选取与水稻耐盐相关的基因;通过构建选择得到基因的蛋白相互作用网络获得若干网络模块。这些模块所关联的生物过程包括:磷酸化作用、泛素作用和若干蛋白酶作用,如过氧化酶、天冬氨酸蛋白酶、葡萄糖基转移酶以及黄酮醇合成。通过基因本体富集分析,这些被找到的模块大多与已知的耐盐机理相关,如信号传导机制,离子泵,脱落酸调节,活性氧清除和离子隔离。这些结果也能够被数量性状位点(QTL),共表达分析和调控binding motif分析所验证和评估。本文还预测了一些与耐盐机制QTL密切相关蛋白的三维结构,并从拓扑性质上探索其在机理网络中的作用。同时,针对不断涌现的二代测序数据,本文提出了一种贝叶斯划分算法,以发掘全基因组关联分析中基因型与表现型的高维相互作用,为从序列层面挖掘生物的分子机理提供数据挖掘和分析工具。本研究中的计算生物学研究在一定程度上揭示了水稻的耐盐机理,提供了研究一般植物性状的系统生物学计算流程。
[Abstract]:Abiotic stress caused by soil salinization has caused widespread and sustained crop yield reduction worldwide. It is the most important food crop. An important direction of rice Oryza sativa improvement is to make it salt-tolerant through molecular breeding. However, it is a complex trait determined by the interaction of many genes. Little is known about the mechanism of salt tolerance in rice. In this paper, a new computational biology method is used to construct the mechanism network of salt tolerance in rice from the point of view of systems biology. An improved volcano plot method based on machine learning Bootstrap SVM-RFE is developed to process gene expression data. The genes related to salt tolerance in rice were selected. A number of network modules were obtained by constructing the protein-interaction network of selected genes. The biological processes associated with these modules include phosphorylation, ubiquitin and protease, such as peroxidase. Aspartate protease, glucosyltransferase and flavonol synthesis. Through gene enrichment analysis, most of these modules are related to known mechanisms of salt tolerance, such as signal transduction mechanism, ion pump. Abscisic acid regulates reactive oxygen species scavenging and ion isolation. These results can also be identified by quantitative trait loci (QTL). Coexpression analysis and regulation binding motif analysis were validated and evaluated. Three dimensional structures of some proteins closely related to salt tolerance mechanism QTL were also predicted. At the same time, this paper proposes a Bayesian partitioning algorithm for the emerging second-generation sequencing data. To explore the high dimensional interaction between genotypes and phenotypes in genome-wide association analysis. In order to provide data mining and analysis tools for the molecular mechanism mining of organisms at the sequence level, the research of computational biology in this study reveals the salt tolerance mechanism of rice to a certain extent. A systematic biological calculation process for the study of general plant traits is provided.
【学位授予单位】：吉林大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S511;TP181

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