| Abstract | 第9-12页 |
| 摘要 | 第13-16页 |
| List of Abbreviations | 第16-19页 |
| CHAPTER ONE: Literature Review | 第19-48页 |
| 1.1 Rice importance and history | 第19页 |
| 1.2 Rice viruses | 第19-26页 |
| 1.2.1 Rice stripe virus (RSV) | 第20-21页 |
| 1.2.2 Rice black-streaked dwarf virus (RBSDV) | 第21-26页 |
| 1.2.2.1 Rice black-streaked dwarf disease (RBSDD) symptoms | 第21页 |
| 1.2.2.2 RBSDV transmission and epidemiology | 第21-22页 |
| 1.2.2.3 RBSDD occurrence and incidence | 第22-23页 |
| 1.2.2.4 RBSDV particle and protein functions | 第23-26页 |
| 1.2.2.5 RBSDV resistance | 第26页 |
| 1.3 RNA silencing and plant viral diseases | 第26-30页 |
| 1.3.1 RNA-silencing pathways in plants | 第27页 |
| 1.3.2 Suppression of RNA silencing and viral counter defense | 第27-28页 |
| 1.3.3 RNA silencing-mediated resistance to plant viruses | 第28-30页 |
| 1.4 Agrobacterium-mediated transformation in rice | 第30-32页 |
| 1.4.1 Advantages of Agrobacterium-mediated transformation | 第30-31页 |
| 1.4.2 Choice of rice tissues | 第31页 |
| 1.4.3 Selectable marker genes | 第31-32页 |
| 1.4.4 Regeneration of transgenic plants | 第32页 |
| 1.5 Transcriptome analysis using RNA sequencing | 第32-36页 |
| 1.5.1 RNA-Seq for understanding plant-pathogen interactions | 第32-33页 |
| 1.5.2 Transcriptome alteration in response to rice viruses | 第33页 |
| 1.5.3 Attempts to study responses of rice to RBSDV infection | 第33-36页 |
| 1.6 Aims and objectives of present study | 第36-37页 |
| References | 第37-48页 |
| CHAPTER TWO:Transcriptional Changes of Rice in Response to Rice Black-Streaked DwarfVirus Infection | 第48-83页 |
| 2.1 Introduction | 第49-52页 |
| 2.2 Materials and methods | 第52-58页 |
| 2.2.1 Plant materials | 第52-53页 |
| 2.2.2 Samples preparation | 第53-54页 |
| 2.2.2.1 Total RNA extraction and cDNA synthesis | 第53页 |
| 2.2.2.2 Verification of healthy and RBSDV-infected rice plants | 第53-54页 |
| 2.2.2.3 Library preparation for RNA-Seq | 第54页 |
| 2.2.3 Mapping reads to the reference genome and annotated genes | 第54页 |
| 2.2.4 Evaluation of genes from RNA-Seq and Gene Ontology (GO) analysis | 第54-55页 |
| 2.2.5 Identification of differentially expressed genes (DEGs) and pathway analysis | 第55页 |
| 2.2.6 Validation of RNA-Seq results by quantitative real-time PCR (qRT-PCR) | 第55-58页 |
| 2.3 Results | 第58-73页 |
| 2.3.1 Confirmation of RBSDV infection in rice plants by RT-PCR | 第58页 |
| 2.3.2 Transcriptome profiles | 第58-63页 |
| 2.3.3 Identification of DEGs | 第63页 |
| 2.3.4 Functional annotation of DEGs | 第63-64页 |
| 2.3.5 KEGG enrichment analysis of DEGs | 第64页 |
| 2.3.6 The RBSDV-responsive transcriptome in rice | 第64-65页 |
| 2.3.7 Validation of RNA-Seq data by quantitative real-time PCR (qRT-PCR) | 第65-73页 |
| 2.4 Discussion | 第73-76页 |
| 2.5 Conclusion | 第76-77页 |
| References | 第77-83页 |
| CHAPTER THREE:Time-Course Gene Expression Analysis of Rice Plants Infected With RiceBlack-Streaked Dwarf Virus | 第83-110页 |
| 3.1 Introduction | 第84-86页 |
| 3.2 Materials and methods | 第86-91页 |
| 3.2.1 Virus resources and insect vector | 第86页 |
| 3.2.2 Virus inoculation via SBPHs | 第86-87页 |
| 3.2.3 Samplings of seedlings, RNA extraction and cDNA synthesis | 第87-88页 |
| 3.2.4 Verification of RBSDV infection in rice plants | 第88页 |
| 3.2.5 Quantitative real-time PCR(qRT-PCR) | 第88页 |
| 3.2.6 Statistical analysis | 第88-91页 |
| 3.3 Results | 第91-100页 |
| 3.3.1 Confirmation of RBSDV infection in rice plants by RT-PCR | 第91页 |
| 3.3.2 Altered expression of some genes related to dwarf symptoms | 第91-94页 |
| 3.3.3 Different expression of some defense and stress response-related genes | 第94-98页 |
| 3.3.4 Altered expression of some chloroplast and photosynthesis related genes | 第98-100页 |
| 3.4 Discussion | 第100-104页 |
| References | 第104-110页 |
| CHAPTER FOUR: Overexpression of Rice Black-Streaked Dwarf Virus Non-Structural ProteinsP7-1 and P9-1 Altered Expression of Some Rice Genes Targeted By Virus-ResponsiveMicroRNAs | 第110-138页 |
| 4.1 Introduction | 第111-115页 |
| 4.2 Materials and methods | 第115-120页 |
| 4.2.1 RBSDV RNA extraction and cDNA synthesis | 第115页 |
| 4.2.2 Construction of plasmids for overexpression of RBSDV P7-1 and P9-1 in rice | 第115-116页 |
| 4.2.3 Transformation of rice calli | 第116页 |
| 4.2.4 Detection of inserted genes via PCR | 第116-117页 |
| 4.2.5 Verification of trangene expression by reverse-transcription PCR (RT-PCR) | 第117页 |
| 4.2.6 Gene expression analysis by quantitative real-time PCR (qRT-PCR) | 第117-118页 |
| 4.2.7 Statistical analysis | 第118-120页 |
| 4.3 Results | 第120-129页 |
| 4.3.1 Overexpression constructs and rice transformation | 第120-121页 |
| 4.3.2 Accumulation of overexpression constructs in transgenic plants | 第121-124页 |
| 4.3.3 Expression of RBSDV-responsive miRNAs target genes in RBSDV P7-1 and P9-1-overexpressed transgenic rice | 第124-129页 |
| 4.3.3.1 qRT-PCR analysis of RBSDV-responsive miRNAs target genes | 第125-128页 |
| 4.3.3.2 Overexpression of RBSDV P7-1 and P9-1 altered gene expression of two SCLgenes in transgenic rice plants | 第128-129页 |
| 4.4 Discussion | 第129-132页 |
| References | 第132-138页 |
| CHAPTER FIVE: RNAi-mediated Resistance to Rice Black-Streaked Dwarf Virus in TransgenicRice | 第138-167页 |
| 5.1. Introduction | 第139-141页 |
| 5.2 Materials and methods | 第141-148页 |
| 5.2.1 RBSDV RNA extraction and reverse transcription | 第141-142页 |
| 5.2.2 Construction of plasmids | 第142-144页 |
| 5.2.3 Transformation of rice calli | 第144页 |
| 5.2.4 Detection of inserted genes via PCR | 第144-145页 |
| 5.2.5 Selection of selectable marker free transgenic plants | 第145页 |
| 5.2.6 Homozygous selection and zygosity determination | 第145-146页 |
| 5.2.7 Assessment of transgene expression by qRT-PCR | 第146页 |
| 5.2.8 Assessment of resistance to RBSDV | 第146-147页 |
| 5.2.9 RBSDV detection by qRT-PCR | 第147-148页 |
| 5.3 Results | 第148-159页 |
| 5.3.1 RNAi constructs and rice transformation | 第148页 |
| 5.3.2 Accumulation of target gene-specific RNAi constructs in T_0 generation | 第148-150页 |
| 5.3.3 Segregation of the selectable marker and RNAi construct in the progeny | 第150页 |
| 5.3.4 Homozygous selection and zygosity determination | 第150-154页 |
| 5.3.5 High level resistance against RBSDV in T5 generation of transgenic rice plants thatharbored either S7-2- or S8-specific RNAi | 第154-159页 |
| 5.4 Discussion | 第159-161页 |
| References | 第161-167页 |
| Conclusions | 第167-169页 |
| List of Publications | 第169-170页 |
| Acknowledgements | 第170-171页 |
