本文關(guān)鍵詞：水稻耐鹽性機(jī)理的計(jì)算生物學(xué)研究　出處：《吉林大學(xué)》2016年博士論文　論文類型：學(xué)位論文

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【摘要】：土壤鹽堿化引起的非生物脅迫在全世界范圍內(nèi)造成了普遍持續(xù)的農(nóng)作物減產(chǎn)。作為最重要的糧食作物,水稻(Oryza sativa)改良的一個(gè)重要方向就是通過(guò)分子育種的方法使其具備鹽耐受性。然而作為一種由多種基因共同作用決定的復(fù)雜性狀,人們對(duì)水稻耐鹽性的機(jī)理仍然知之甚少。本文采用新的計(jì)算生物學(xué)方法,從系統(tǒng)生物學(xué)角度構(gòu)建了水稻耐鹽的機(jī)理網(wǎng)絡(luò);開(kāi)發(fā)了一種基于機(jī)器學(xué)習(xí)Bootstrap SVM-RFE的改進(jìn)volcano plot方法來(lái)處理基因表達(dá)數(shù)據(jù),并從中選取與水稻耐鹽相關(guān)的基因;通過(guò)構(gòu)建選擇得到基因的蛋白相互作用網(wǎng)絡(luò)獲得若干網(wǎng)絡(luò)模塊。這些模塊所關(guān)聯(lián)的生物過(guò)程包括:磷酸化作用、泛素作用和若干蛋白酶作用,如過(guò)氧化酶、天冬氨酸蛋白酶、葡萄糖基轉(zhuǎn)移酶以及黃酮醇合成。通過(guò)基因本體富集分析,這些被找到的模塊大多與已知的耐鹽機(jī)理相關(guān),如信號(hào)傳導(dǎo)機(jī)制,離子泵,脫落酸調(diào)節(jié),活性氧清除和離子隔離。這些結(jié)果也能夠被數(shù)量性狀位點(diǎn)(QTL),共表達(dá)分析和調(diào)控binding motif分析所驗(yàn)證和評(píng)估。本文還預(yù)測(cè)了一些與耐鹽機(jī)制QTL密切相關(guān)蛋白的三維結(jié)構(gòu),并從拓?fù)湫再|(zhì)上探索其在機(jī)理網(wǎng)絡(luò)中的作用。同時(shí),針對(duì)不斷涌現(xiàn)的二代測(cè)序數(shù)據(jù),本文提出了一種貝葉斯劃分算法,以發(fā)掘全基因組關(guān)聯(lián)分析中基因型與表現(xiàn)型的高維相互作用,為從序列層面挖掘生物的分子機(jī)理提供數(shù)據(jù)挖掘和分析工具。本研究中的計(jì)算生物學(xué)研究在一定程度上揭示了水稻的耐鹽機(jī)理,提供了研究一般植物性狀的系統(tǒng)生物學(xué)計(jì)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.
【學(xué)位授予單位】：吉林大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：S511;TP181

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本文編號(hào)：1398041