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研究生： 陳麗如
Li-Ru Chen
論文名稱： 綠豆幼苗在低溫逆境基因表現的比較性分析
Comparative gene expression profiles of mungbean, Vigna radiata (L.) Wilczek, seedlings in response to cold
指導教授： 林彩雲
Tsai-Yun Lin
口試委員:
學位類別： 博士
Doctor
系所名稱： 生命科學暨醫學院 - 生命科學系
Department of Life Sciences
論文出版年： 2008
畢業學年度： 96
語文別： 中文
論文頁數： 196
中文關鍵詞： 生物晶片 、幼苗 、低溫敏感性 、綠豆 、即時定量PCR 、扣減 、耐寒性
外文關鍵詞： cDNA microarray □, seedling, susceptibility to cold □, Vigna radiata □, Relative quantification in real-time PCR (qRT-PCR), Expressed sequence tags □ □, Motif, Subtraction, Cold tolerance
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    • 綠豆 (Vigna radiata (L.) Wilczek)是高營養價值的熱帶豆科作物，也是農業上常用來恢復土壤肥力的輪作植物。低溫逆境嚴重影響熱帶及亞熱帶作物的產量及品質。為了在環境逆境下生存，植物必須改變生理及代謝條件來對抗逆境。許多溫帶植物在冷馴化，低溫處理一段時間，觸發一連串低溫調控基因的轉錄變化而增加凍害抗性，然而大部分的熱帶作物，都對低溫敏感且不具冷馴化的能力。目前可利用的綠豆基因組資源非常少，相關的冷逆境研究也非常有限。本論文分為二部分，第一部分是綠豆幼苗早期發育及冷逆境相關的基因，第二部分是對二種具有不同冷逆境敏感性的綠豆變異種，進行基因表現的比較性分析。
    綠豆變異種，NM94及VC1973A在幼苗期具有不同的冷逆境敏感性，在4　degree C下，NM94幼苗的葉片較VC1973A可維持較好的膜完整性。為了進一步了解這種內生冷逆境敏感性的分子機制，本研究應用生物晶片技術，比較NM94及VC1973A幼苗在4 degree C冷逆境下，735個綠豆基因的轉錄變化。並比較在冷逆境處理後，回復到正常生長環境的基因表現。結果顯示冷逆境趨使NM94及VC1973A表現相同的一群基因，這些基因轉錄的蛋白質與蛋白質合成裝置重組、運移、降解及逆境保護子的合成相關。光合作用能力及數個冷逆境保護子可能是NM94變異種較能忍受冷逆境的重要調節者。除此之外，脂質運輸蛋白可能同時扮演冷逆境保護及在冷逆境處理後幫助回復正常生長的角色。

    Mungbean (Vigna radiata (L.) Wilczek) is commonly used as human food. However, the genomic resources of this species available in databases are limited. This study has two sections, the expressed sequence tags (EST) related to early seedling development and chilling response are developed in the first part. Two mungbean varieties NM94 and VC1973A were obtained from the Asian Vegetable Research and Development Center-The World Vegetable Center (AVRDC). They differ in disease resistance and susceptibility to chilling temperatures. NM94 can maintain a better membrane integrity than VC1973A during seedling stage exposed to 4 degree C. To investigate the molecular mechanisms of the inherent chilling-susceptibility, the gene expression patterns in young seedlings of NM94 and VC1973A were compared in the second part of this thesis. A cDNA microarray containing 735 uniESTs was employed to profile the transcriptional changes during chilling stress and after recovery from chilling. The results show that a chilling exposure triggered the expression of a common set of CORs (cold regulated genes) in both NM94 and VC1973A. These CORs encode proteins that are involved in restructuring the protein synthesis apparatus, participating in protein trafficking and degradation, and synthesizing the stress protectants. The comparative expression profile indicates that the photosynthetic capacity and the cryoprotective proteins may be the key regulators of comparative toler55ance to chilling in NM94. Our data support the role of LTPs (lipid transfer proteins) in cryoprotection during chilling stress and resumption of plant growth after recovery from chilling.

    Table of Contents Page 摘要----------------------------------------------------------------------------------------------------------i Abstract-----------------------------------------------------------------------------------------------------ii 謝誌--------------------------------------------------------------------------------------------------------iii Table of Contents-----------------------------------------------------------------------------------------iv List of Tables----------------------------------------------------------------------------------------------ix List of Figures----------------------------------------------------------------------------------------------x Abbreviations---------------------------------------------------------------------------------------------xi Part I: Early developmental and stress responsive ESTs from mungbean, Vigna radiata (L.) Wilczek, seedlings--------------------------------------------------------------------------1 I.1 Abstract-----------------------------------------------------------------------------------------------2 I.2 Introduction-------------------------------------------------------------------------------------------3 I.3 Materials and methods I.3.1 Plant materials----------------------------------------------------------------------------5 I.3.2 Electrolyte leakage measurement------------------------------------------------------5 I.3.3 Electron microscopy---------------------------------------------------------------------6 I.3.4 RNA isolation----------------------------------------------------------------------------7 I.3.5 Construction of cDNA library----------------------------------------------------------8 I.3.6 Construction of PCR-select cDNA subtraction libraries---------------------------8 I.3.7 ESTs generation and DNA sequencing-----------------------------------------------9 I.3.8 Sequence processing and contig assembly------------------------------------------10 I.4 Results and discussion I.4.1 Mungbean seedling development and response to cold temperature------------11 I.4.2 Mesophyll cells of mungbean suffered ultrastructural injury after cold--------12 I.4.3 Platform of mungbean ESTs----------------------------------------------------------14 I.4.4 Functional annotation of mungbean uniESTs--------------------------------------15 I.4.5 Mungbean uniESTs related to early seedling development----------------------16 I.4.6 Mungbean uniESTs response to cold------------------------------------------------18 I.4.7 Transcript abundance of mungbean uniESTs---------------------------------------22 I.4.8 Motif analysis---------------------------------------------------------------------------22 I.4.9 Conclusion------------------------------------------------------------------------------23 I.5 References-------------------------------------------------------------------------------------------25 I.6 Tables and figures----------------------------------------------------------------------------------32 Part II: Comparative gene expression profiling of two mungbean varieties during seedling stage in response to cold--------------------------------------------------------51 II.1 Abstract-----------------------------------------------------------------------------------------------52 II.2 Introduction------------------------------------------------------------------------------------------53 II.3 Materials and methods-----------------------------------------------------------------------------56 II.3.1 Plant materials--------------------------------------------------------------------------56 II.3.2 RNA isolation---------------------------------------------------------------------------56 II.3.3 DNA microarray fabrication and hybridization------------------------------------56 II.3.4 Analysis of microarray data-----------------------------------------------------------58 II.3.5 Relative quantification real-time PCR (qRT-PCR)--------------------------------59 II.4 Results II.4.1 Gene expression profiling of mungbean seedlings upon exposure to cold-----61 II.4.1.1 Identification of CORs in NM94 and VC1973A seedlings-----------------61 II.4.1.2 Comparison of the expression profiles of CORs between NM94 and VC1973A seedlings-----------------------------------------------------------------------------63 II.4.1.3 Recovery responsive CORs-----------------------------------------------------65 II.4.2 Verification of microarray data with qRT-PCR------------------------------------66 II.4.2.1 Cold stress changes gene expression involved in photosynthesis, polyamines biosynthesis and proteasome-ubiquitin protein degradation pathway-----67 II.4.2.2 Cold stress raises the mRNA levels of stress protectants and enzymes involved in metabolic process and localization---------------------------------------------68 II.5 Discussion II.5.1 Putative CORs contribute to different susceptibility of VC1973A and NM94------------------------------------------------------------------------------------------------70 II.5.1.1 The NM94 seedlings could still maintain a high photosynthetic capacity under cold stress---------------------------------------------------------------------------------70 II.5.1.2 Activation of stress genes in NM94 may result in a better cold tolerance------------------------------------------------------------------------------------------71 II.5.1.3 Cold stress may trigger remodeling and synthesizing stress protectants----------------------------------------------------------------------------------------72 II.5.1.4 Post-transcriptional and post-translational regulation might be critical for cold tolerance in mungbean----------------------------------------------------------------74 II.5.2 Some recovery responsive CORs may function for the resumption of plant growth-----------------------------------------------------------------------------------------------75 II.5.3 Conclusion------------------------------------------------------------------------------77 II.6 References-------------------------------------------------------------------------------------------78 II.7 Tables and figures----------------------------------------------------------------------------------84 Appendix------------------------------------------------------------------------------------------107 Appendix I-1. ESTs clustering results. 523 ESTs were assembled into 136 contigs----------108 Appendix I-2. UniESTs that can not be categorized into biological processes according to gene ontology annotation------------------------------------------------------------110 Appendix I-3. Contigs of the most abundant mungbean ESTs-----------------------------------113 Appendix I-4. Motif analysis of uniESTs without significant homologs in GeneBank-------114 Appendix II-1. Microarray protocol------------------------------------------------------------115 Appendix II-2. A total of 159 CORs of NM94 were grouped into three sets based on the duration of upregulation or downregulation-------------------------------------122 Appendix II-3. A total of 92 CORs of VC1973A were grouped into three sets based on the duration of upregulation or downregulation-----------------------------------128 Appendix II-4. Highly induced CORs showing no significant similarity to known genes---131 Appendix II-5. qRT-PCR validation in mungbean seedlings-------------------------------------132 Paper published: MeJA-induced transcriptional changes in adventitious roots of Bupleurum kaoi Paper in press: Early developmental and stress responsive ESTs from mungbean, Vigna radiata (L.) Wilczek, seedlings Paper in press: Rapid authentication of Bupleurum species using an array of immobilized sequence-specific oligonucleotide probes List of Tables Table I-1. Singletons and contig statistics of mungbean ESTs----------------------------------32 Table I-2. UniESTs were categorized into biological processes according to gene ontology------------------------------------------------------------------------------------33 Table II-1. Primer sequences designed for qRT-PCR----------------------------------------------84 Table II-2. CORs in NM94 seedlings----------------------------------------------------------------85 Table II-3. CORs in VC1973A seedlings------------------------------------------------------------89 Table II-4. CORs shared by NM94 and VC1973A varieties--------------------------------------92 Table II-5. CORs specific to NM94 variety---------------------------------------------------------94 Table II-6. CORs specific to VC1973A variety-----------------------------------------------------97 Table II-7. Recovery responsive CORs in NM94 seedlings--------------------------------------98 Table II-8. Recovery responsive CORs in VC1973A seedlings---------------------------------100 List of Figures Fig. I-1 Development of mungbean seedlings-----------------------------------------------------41 Fig. I-2 Cold stress effect on electrolyte leakage of mungbean seedlings----------------------43 Fig. I-3 Cross-section of mungbean leaves a 3-dai exposed to 4□C or 25□C for 24 h--------45 Fig. I-4 Cellular structure of mungbean palisade and spongy mesophylls---------------------47 Fig. I-5 Ultrastructural changes in mungbean chloroplasts upon exposure to cold-----------49 Fig. II-1 Kinetic expression patterns of CORs by cold and after recovery from cold--------101 Fig. II-2 Transcript profiles of CORs encoding proteins involved in photosynthesis, polyamines synthesis and proteasome-ubiquitin protein degradation pathway seedlings under cold and recovery after cold-------------------------------------------103 Fig. II-3 Transcript levels of other CORs in NM94 and VC1973A seedlings induce by 4□C and recovery after cold stress-------------------------------------------------------------105 Abbreviations □L microliter ABA abscisic acid ACC 1-aminocyclopropane-1-carboxylate AVRDC Asian Vegetable Research and Development Center-The World Vegetable Center BLAST Basic Local Alignment Search Tool bp base pair CBF C-repeat binding factor cDNA complementary deoxyribonucleic acid CLS cercospora leaf spot contig contiguous sequence CORs cold regulated genes CTAB hexadecyltrimethylammonium bromide CU gene up-regulated by chilling in 1-72 h dai day after imbibition DEPC diethyl-pyrocarbonate DMSO dimethyl sulfoxide DTT dithiothreitol EDTA ethylenediamine tetraacetic acid EST expressed sequenced tag EU gene up-regulated by chilling only in 1-4 h EU/LD gene early up-regulated by chilling only in 1-4 h and late down-downregulated in 24-72 h h hour HSP heat shock protein ICE1 inducer of CBF expression 1 LD gene down-regulated by chilling only in 24-72 h LEA late embryogenesis abundant LOX lipoxygenase LTP lipid transfer protein LU gene up-regulated by chilling only in 24-72 h mg milligram min minute mL milliliter mM millimolar MMLV Moloney murine leukemia virus mRNA messenger ribonucleic acid MYMV mungbean yellow mosaic virus NCBI National Center for Biotechnology Information PCR polymerase chain reaction PDF plant defensin pg picogram PVP polyvinylpyrrolidinone qRT-PCR relative quantification with real-time PCR r correlation coefficient RNA ribonucleic acid ROS reactive oxygen species s second SAM S-adenosylmethionine SAMDC S-adenosylmethionine decarboxylase SD standard deviation SDS sodium dodecyl sulfate SRC Soybean gene regulated by cold SSC saline-sodium citrate TAIR the Arabidopsis Information Resource TEM transmission electron microscopy U unit

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