利用QTL進(jìn)行植物抗旱基因鑒定的生物信息學(xué)方法和軟件的設(shè)計(jì)與

1、論文名稱 利用QTL進(jìn)行植物抗旱基因鑒定的生物信息學(xué)方法和軟件的設(shè)計(jì)與實(shí)現(xiàn)/Design and Implementation of Bioinformatics Strategy and Software for Identifying Drought Tolerant Genes in Plants Based on QTL Information 作者 曾華宗 <中國> 學(xué)位 博士 答辯日期 培養(yǎng)單位 復(fù)旦大學(xué)023 生命科學(xué)學(xué)院生物信息學(xué) 研究方向 植物生物信息學(xué) 中文關(guān)鍵詞 QTL，水稻，擬南芥，數(shù)據(jù)庫

2、，基因芯片 英文關(guān)鍵詞 QTL,rice,Arabidopsis,database,microarray 指導(dǎo)老師 鐘揚(yáng).生命科學(xué)院 . . 論文總頁碼  共106頁 館藏號(hào)  S07/023/041023019 服務(wù)年限  0 年后 中文摘要  現(xiàn)階段的植物遺傳研究中，對(duì)控制復(fù)雜性狀表達(dá)(如抗旱性狀)基因的研究被認(rèn)為是一項(xiàng)富有挑戰(zhàn)，也十分重要的工作。作為一種研究基因組內(nèi)的遺傳變化和表型變異的有效的方法，數(shù)量性狀位點(diǎn)（Quantitative trait locus , QTL）為控制復(fù)雜性狀的研究提供了一種行之有效的方法。本項(xiàng)研究利

3、用生物信息學(xué)方法，通過對(duì)文獻(xiàn)發(fā)表的QTL相關(guān)的遺傳信息進(jìn)行整合，并在此基礎(chǔ)上提出了一種基于QTL信息進(jìn)行新基因發(fā)掘的策略。同時(shí), 構(gòu)建了一套用于查詢QTL區(qū)間內(nèi)的遺傳信息的數(shù)據(jù)庫系統(tǒng)，以及一套可用于QTL分析的基因芯片數(shù)據(jù)分析軟件，以期為植物數(shù)量性狀相關(guān)基因的發(fā)掘與研究提供一種有效的方法和方便的信息查詢平臺(tái)。 QTL定位的研究為我們提供了豐富的QTL遺傳信息。本研究首先收集了大量文獻(xiàn)中已經(jīng)發(fā)表的QTL信息（以抗逆性為例），構(gòu)建了QTL數(shù)據(jù)庫，并將這些QTL定位到整合的，基于遺傳距離和物理距離的染色體圖譜上，并以此為基礎(chǔ)設(shè)計(jì)了一種利用EST和基因組信息對(duì)QTL相關(guān)候選基因進(jìn)行電子克隆的方法。選取

4、了水稻染色體1，2，4，8和9內(nèi)定位到的QTL對(duì)上述方法進(jìn)行驗(yàn)證，得到QTL相關(guān)的候選基因，結(jié)果經(jīng)實(shí)驗(yàn)驗(yàn)證，證實(shí)了該方法的有效性。為了進(jìn)一步QTL相關(guān)的候選基因進(jìn)行鑒定和功能分析，我們將抗逆QTL數(shù)據(jù)庫及相關(guān)的候選基因發(fā)掘的方法進(jìn)行了整合，并將其擴(kuò)展到所有QTL相關(guān)性狀的研究中。在此基礎(chǔ)上我們構(gòu)建了一個(gè)用于查詢、注釋QTL相關(guān)的基因表達(dá)信息的數(shù)據(jù)庫查詢系統(tǒng)PlantQTL-GE。該數(shù)據(jù)庫整合了大量的基因、基因芯片表達(dá)信息、EST (expressed sequence tags) 和遺傳標(biāo)記數(shù)據(jù)，并通過一個(gè)統(tǒng)一的信息平臺(tái)來對(duì)這些數(shù)據(jù)進(jìn)行管理和查詢。用于幫助研究者找到他們感興趣的QTL內(nèi)部的遺傳

5、信息，并利用這些信息來進(jìn)行QTL相關(guān)的候選基因的篩選和功能分析。該數(shù)據(jù)庫支持用戶通過輸入QTL兩側(cè)的遺傳標(biāo)記名稱、QTL所對(duì)應(yīng)的基因組物理位置兩種方式進(jìn)行檢索，查詢結(jié)果包括了QTL區(qū)間相關(guān)的已知功能的基因、基因芯片數(shù)據(jù)、EST信息，未知功能的候選基因以及其他物種內(nèi)相似的候選基因。其中QTL內(nèi)部的候選基因還進(jìn)一步的利用EST、生物芯片數(shù)據(jù)和預(yù)測的調(diào)控位點(diǎn)信息進(jìn)行了注釋。該數(shù)據(jù)庫目前可以查詢的物種包括水稻和擬南芥，可以通過/qtl2gene/new/網(wǎng)頁來訪問。生物芯片技術(shù)是90年代初才發(fā)展起來的一項(xiàng)新技術(shù)，已經(jīng)在許多領(lǐng)域得到了廣泛的應(yīng)用，但應(yīng)用在植物數(shù)量性狀

6、的研究中還鮮有報(bào)道，相關(guān)的理論和方法還比較匱乏。該項(xiàng)研究對(duì)利用芯片數(shù)據(jù)來進(jìn)行QTL研究進(jìn)行了探索，開發(fā)了一套利用生物芯片數(shù)據(jù)進(jìn)行QTL研究的分析軟件。該軟件用于進(jìn)行植物相關(guān)的芯片數(shù)據(jù)的生物信息學(xué)分析的軟件系統(tǒng)，目的是幫助研究者利用自己的芯片數(shù)據(jù)來進(jìn)行QTL相關(guān)的候選基因的發(fā)掘。該軟件可以整合芯片數(shù)據(jù)和QTL數(shù)據(jù)，并進(jìn)行綜合分析，目前該軟件可以用于進(jìn)行水稻和擬南芥的相關(guān)研究。其功能包括: 1) 將基因芯片差異基因和QTL信息整合到染色體物理圖譜上。 2) 利用BLAST工具對(duì)差異表達(dá)基因進(jìn)行染色體定位。 3) 對(duì)差異表達(dá)基因進(jìn)行GO(gene ontology)分類。   外文摘要 &

7、#160;The discovery of genes controlling complex traits such as drought tolerance is considered to be one of the most important and difficult challenges. Quantitative Trait Locus (QTL) mapping methods were widely applied in recent years to identify candidate genes related to complex traits. In this s

8、tudy, a strategy is described to identify novel gene families based on QTL information derived from published literature. Then, a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information is designed and implemented. A microarray analysis system f

9、or mapping QTL and microarray gene expression data is designed and implemented. QTLs such as drought-related QTL can be readily identified in available databases and literatures. These drought-related QTLs were collected and integrated into a QTL database and summarized in the form of a consensus ma

10、p. An in silico strategy was then deployed to mine for candidate genes associated with QTLs using rice dbEST and rice genome databases. QTLs on rice chromosomes 1, 2, 4, 8, and 9 were selected to test the method. The result showed candidate genes associated with drought tolerance could be readily id

11、entified after experimental detection. In order to facilitate QTL based candidate gene identification and gene function analysis. We have designed and implemented a web-based database system, called PlantQTL-GE, We collected a large number of genes, gene expression information in microarray data and

12、 expressed sequence tags (ESTs) and genetic markers from multiple sources of Oryza sativa and Arabidopsis thaliana. The system integrates these diverse data sources and has a uniform web interface for easy access. It supports QTL queries specifying QTL marker intervals or genomic loci, and displays,

13、 on rice or Arabidopsis genome, known genes, microarray data, ESTs and candidate genes and similar putative genes in the other plant. Candidate genes in QTL intervals are further annotated based on matching ESTs, microarray gene expression data and cis-elements in regulatory sequences. The system is

14、 freely available at /qtl2gene/new/. Microarray is a new technique that has been widely used for plant research. But few research report has beed published to identify candidate genes within QTL interval. In this thesis, we designed and implemented a software system, called PMBA, to facilitate QTL based candidate gene identification using gene expression information in microarray data in rice and Arabidopsis. Its functions include: 1) Construction of a consensus map by integrating difference expression genes in microarray result and QTL information. 2) Identifying chromosom