【摘要】：植物基因型與表型間復(fù)雜的相互關(guān)系涉及到細(xì)胞內(nèi)多種組分間的時(shí)空調(diào)控和代謝產(chǎn)物在不同細(xì)胞器或組織中的分布,一直是研究人員關(guān)注的熱點(diǎn)和難點(diǎn)。傳統(tǒng)的研究方法有數(shù)量性狀基因定位(QTL)和全基因組關(guān)聯(lián)分析(GWAS)。然而,QTL和GWAS沒(méi)有考慮到分子間的調(diào)控關(guān)系,不能很好地解釋性狀與基因間相互作用關(guān)系的分子機(jī)制。整合多種組分間的調(diào)控關(guān)系包括代謝調(diào)控網(wǎng)絡(luò),蛋白質(zhì)互作網(wǎng)絡(luò),基因調(diào)控網(wǎng)絡(luò)等,構(gòu)建多層次調(diào)控網(wǎng)絡(luò),探索定量研究復(fù)雜生物網(wǎng)絡(luò)的新途徑,能夠?yàn)楦玫睦斫夂脱芯恐参锘蛐秃捅憩F(xiàn)型之間的相互關(guān)系提供一種可能。本項(xiàng)目以水稻為研究對(duì)象,首先,從水稻基因組注釋信息出發(fā),擬利用一個(gè)半自動(dòng)化的流程對(duì)現(xiàn)有生物學(xué)公共數(shù)據(jù)庫(kù)的信息進(jìn)行整合,完成水稻基因組尺度的代謝網(wǎng)絡(luò)進(jìn)行初步構(gòu)建。我們開(kāi)發(fā)了一種新的基于內(nèi)共生學(xué)說(shuō)的代謝網(wǎng)絡(luò)空缺填補(bǔ)的方法(DEF),用于高精度的代謝網(wǎng)絡(luò)空缺填補(bǔ)。然后,通過(guò)系統(tǒng)生物學(xué)的方法和實(shí)驗(yàn)手段對(duì)網(wǎng)絡(luò)進(jìn)行精細(xì)的修正和評(píng)估,包括化合物胞內(nèi)價(jià)態(tài)的計(jì)算,反應(yīng)方程式的配平,反應(yīng)可逆性的預(yù)測(cè),空缺的查找及填補(bǔ)。試圖構(gòu)建出第一個(gè)目前數(shù)據(jù)水平上最為完整的高質(zhì)量的水稻基因組尺度的代謝網(wǎng)絡(luò)。在此基礎(chǔ)上,整合蛋白互作網(wǎng)絡(luò)、轉(zhuǎn)錄調(diào)控網(wǎng)絡(luò)的實(shí)驗(yàn)驗(yàn)證數(shù)據(jù)與預(yù)測(cè)數(shù)據(jù),完成水稻多層次調(diào)控網(wǎng)絡(luò)的初步構(gòu)建。為了將構(gòu)建好的基因組尺度多層次調(diào)控網(wǎng)絡(luò)注釋到亞細(xì)胞器中,我們還開(kāi)發(fā)了一種新的高精度的用于植物蛋白質(zhì)亞細(xì)胞定位預(yù)測(cè)的整合算法(PSI)�；赑SI的預(yù)測(cè)結(jié)果,我們將水稻組學(xué)尺度多層次生物調(diào)控網(wǎng)絡(luò)注釋到10個(gè)亞細(xì)胞器中。最后,完成水稻多層次基因調(diào)控網(wǎng)絡(luò)數(shù)據(jù)庫(kù)(RiceNetDB)及多層次生物調(diào)控網(wǎng)絡(luò)3D展示工具的開(kāi)發(fā),期望本研究能夠?yàn)樗旧锓肿娱g調(diào)控機(jī)制的研究提供參考,有助于水稻基因型與表現(xiàn)型間關(guān)系的研究。
[Abstract]:The complex relationship between plant genotypes and phenotypes involves the temporal and spatial regulation of various components in cells and the distribution of metabolites in different organelles or tissues. Traditional research methods include quantitative trait gene mapping (QTL) and genome-wide association analysis (GWAS). However, QTLs and GWAS did not take into account the intermolecular regulatory relationship and could not explain the molecular mechanism of the interaction between traits and genes. Integrating the regulation and control relationships among various components, including metabolic regulation network, protein interaction network, gene regulation network and so on, to construct a multi-level regulatory network, and to explore new ways to quantitatively study complex biological networks. It provides a possibility to better understand and study the relationship between genotypes and phenotypes of plants. This project takes rice as the research object. First of all, from the rice genome annotation information, we plan to integrate the information of the existing public biological database by a semi-automatic process. The metabolic network of rice genome was constructed. A new metabolic network vacancy filling method based on INTERGROWTH theory (DEF),) is developed. Then, the network is revised and evaluated by the methods of system biology and experiment, including the calculation of the intracellular valence state of compounds, the balance of the reaction equation, the prediction of the reversibility of the reaction, and the searching and filling of the vacancy. This paper attempts to construct the first high quality genome scale metabolic network of rice at present data level. On this basis, the integrated protein interaction network, transcriptional regulatory network experimental verification data and prediction data, completed the preliminary construction of the multi-level regulatory network of rice. In order to annotate the constructed genome scale multilevel regulatory network into suborganelles, we have also developed a new integration algorithm, (PSI)., which can be used to predict the subcellular localization of plant proteins. Based on the prediction results of PSI, we annotated the multi-level biological regulatory network of rice genome into 10 suborganelles. Finally, the development of (RiceNetDB) and 3D display tool of multi-level biological regulation network is completed. It is expected that this study can provide a reference for the study of the mechanism of rice biomolecular regulation. It is helpful to study the relationship between genotypes and phenotypes of rice.
【學(xué)位授予單位】：浙江大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類(lèi)號(hào)】：Q943.2;Q811.4

【參考文獻(xiàn)】

相關(guān)期刊論文 前1條

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本文編號(hào)：2178034