本文關鍵詞：水稻耐鹽性機理的計算生物學研究　出處：《吉林大學》2016年博士論文　論文類型：學位論文

  更多相關文章： 特征選擇 機器學習 計算生物學 系統(tǒng)生物學 機理網(wǎng)絡 水稻耐鹽性

【摘要】：土壤鹽堿化引起的非生物脅迫在全世界范圍內造成了普遍持續(xù)的農作物減產。作為最重要的糧食作物,水稻(Oryza sativa)改良的一個重要方向就是通過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雜性狀,人們對水稻耐鹽性的機理仍然知之甚少。本文采用新的計算生物學方法,從系統(tǒng)生物學角度構建了水稻耐鹽的機理網(wǎng)絡;開發(fā)了一種基于機器學習Bootstrap SVM-RFE的改進volcano plot方法來處理基因表達數(shù)據(jù),并從中選取與水稻耐鹽相關的基因;通過構建選擇得到基因的蛋白相互作用網(wǎng)絡獲得若干網(wǎng)絡模塊。這些模塊所關聯(lián)的生物過程包括:磷酸化作用、泛素作用和若干蛋白酶作用,如過氧化酶、天冬氨酸蛋白酶、葡萄糖基轉移酶以及黃酮醇合成。通過基因本體富集分析,這些被找到的模塊大多與已知的耐鹽機理相關,如信號傳導機制,離子泵,脫落酸調節(jié),活性氧清除和離子隔離。這些結果也能夠被數(shù)量性狀位點(QTL),共表達分析和調控binding motif分析所驗證和評估。本文還預測了一些與耐鹽機制QTL密切相關蛋白的三維結構,并從拓撲性質上探索其在機理網(wǎng)絡中的作用。同時,針對不斷涌現(xiàn)的二代測序數(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理提供數(shù)據(jù)挖掘和分析工具。本研究中的計算生物學研究在一定程度上揭示了水稻的耐鹽機理,提供了研究一般植物性狀的系統(tǒng)生物學計算流程。
[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.
【學位授予單位】：吉林大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：S511;TP181

【參考文獻】

相關期刊論文 前2條

1 湯鳳蘭;李敏;朱長波;武守君;;鹽堿地水稻開發(fā)及技術措施[J];黑龍江農業(yè)科學;2011年03期

2 胡時開;陶紅劍;錢前;郭龍彪;;水稻耐鹽性的遺傳和分子育種的研究進展[J];分子植物育種;2010年04期

，

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