| 摘要 | 第5-6页 |
| Abstract | 第6-7页 |
| List of abbreviations | 第13-14页 |
| Chapter1:Background | 第14-22页 |
| 1.1 Introduction | 第14页 |
| 1.1.1 Overview of plant innate immunity | 第14页 |
| 1.2 Bacterial virulence factors | 第14-16页 |
| 1.2.1 Secreted proteins | 第14-15页 |
| 1.2.2 Small molecules as virulence factors | 第15-16页 |
| 1.3 Plant Immunity | 第16-18页 |
| 1.3.1 PAMP-triggered immunity | 第16页 |
| 1.3.2 Effector-triggered immunity | 第16-18页 |
| 1.4 Bacterial blight:a devastating disease in rice growing regions | 第18-19页 |
| 1.4.1 Importance of rice | 第18页 |
| 1.4.2 History of BB disease | 第18页 |
| 1.4.3 Breeding strategies to overcome BB | 第18-19页 |
| 1.4.4 Overview of BB resistance genes | 第19页 |
| 1.5 RNA-Seq:a kick in omics technology | 第19-21页 |
| 1.5.1 Advantages of RNA-Seq technology | 第19-20页 |
| 1.5.2 Limitations of traditional sequencing technology | 第20-21页 |
| 1.6 Objectives of the study | 第21-22页 |
| Chapter2:Comparative Transcriptome Profiling of CBB23 and JG30 Genotypes Under Infection of PXO99~A Strain | 第22-40页 |
| 2.1 Summary | 第22页 |
| 2.2 Introduction | 第22-23页 |
| 2.3 Materials and Methods | 第23-25页 |
| 2.3.1 Plant Material and Growth Conditions | 第23-24页 |
| 2.3.2 Inoculation of Rice Plants with PXO99A and Collection of Leaf Samples | 第24页 |
| 2.3.3 RNA Extraction and Library Preparation for Illumina Sequencing | 第24页 |
| 2.3.4 Data Analysis | 第24-25页 |
| 2.3.5 Gene Enrichment Analysis | 第25页 |
| 2.3.6 Validation of RNA-Seq Data | 第25页 |
| 2.4 Results | 第25-36页 |
| 2.4.1 RNA-Sequencing of Different Samples and Data Analysis | 第25-26页 |
| 2.4.2 Identification of DEGs in Response to PXO99A in CBB23 and JG | 第26-27页 |
| 2.4.3 Response of Differentially Expressed TFs to PXO99A Infection | 第27-28页 |
| 2.4.4 Response of Different Kinase Responsive Genes to PXO99A Infection | 第28-30页 |
| 2.4.5 GO Based Analysis of the DEGs | 第30-31页 |
| 2.4.6 MapMan Overview of DEGs Related to Plant-Pathogen Interaction | 第31-32页 |
| 2.4.7 KEGG Pathway | 第32-33页 |
| 2.4.8 Validation of RNA-Seq Results by qRT-PCR | 第33-36页 |
| 2.5 Discussion | 第36-40页 |
| Chapter3:Transcriptome analysis of CBB23 Genotype Under infection of PXO99~A and P99M2 Strains | 第40-60页 |
| 3.1 Summary | 第40页 |
| 3.2 Introduction | 第40-41页 |
| 3.3 Materials and Methods | 第41-43页 |
| 3.3.1 Plant materials and Growth Conditions | 第41-42页 |
| 3.3.2 Bacterial inoculation and leaf sampling | 第42页 |
| 3.3.3 RNA extraction and construction of cDNA library for Illumina sequencing | 第42页 |
| 3.3.4 Data analysis of Illumina sequencing | 第42-43页 |
| 3.3.5 Functional classification of DEGs and co-expression analysis | 第43页 |
| 3.3.6 Validation of RNA-Seq data | 第43页 |
| 3.4 Results | 第43-56页 |
| 3.4.1 Illumina sequencing of rice leaves inoculated with PXO99A and P99M | 第43-44页 |
| 3.4.2 Identification of DEGs in PXO99A vs P99M2 inoculated leaves at different time points | 第44-45页 |
| 3.4.3 Identification of differentially expressed TFs | 第45-47页 |
| 3.4.4 Identification of peroxidases related DEGs | 第47-48页 |
| 3.4.5 GO analysis of DEGs | 第48-49页 |
| 3.4.6 Pathway analysis | 第49-52页 |
| 3.4.7 Co-expression network analysis | 第52-53页 |
| 3.4.8 Data validation | 第53-56页 |
| 3.5 Discussion | 第56-60页 |
| Chapter 4:RNA-Seq Analysis of Gene Expression Changes Triggered by PXO99~A and PH Strains in the Susceptible Rice Genotype,JG30 | 第60-76页 |
| 4.1 Summary | 第60页 |
| 4.2 Introduction | 第60-62页 |
| 4.3 Materials and Methods | 第62-63页 |
| 4.3.1 Plant materials and growth conditions | 第62页 |
| 4.3.2 Inoculation of different Xoo strains | 第62页 |
| 4.3.3 RNA extraction and Illumina sequencing | 第62-63页 |
| 4.3.4 Analysis of the RNA-Seq data | 第63页 |
| 4.3.5 Functional classification and pathway enrichment analysis | 第63页 |
| 4.3.6 Validation of RNA-Seq data | 第63页 |
| 4.4 Results | 第63-72页 |
| 4.4.1 Transcriptome profiling of JG30 genotype for DEGs | 第63-65页 |
| 4.4.2 Identification of the differentially expressed TFs | 第65-66页 |
| 4.4.3 Identification of the kinase and peroxidase responsive genes in RNA-Seq data | 第66-67页 |
| 4.4.4 Pathway enrichment analysis | 第67-70页 |
| 4.4.5 GO enrichment analysis | 第70-71页 |
| 4.4.6 RNA-Seq data validation | 第71-72页 |
| 4.5 Discussion | 第72-76页 |
| Conclusion | 第76-77页 |
| References | 第77-91页 |
| Supplementary data | 第91-92页 |
| Acknowledgement | 第92-93页 |
| Curriculum Vitae | 第93-94页 |
