| 摘要 | 第6-7页 |
| ABSTRACT | 第7-8页 |
| LIST OF ABBREVIATIONS | 第12-18页 |
| CHAPTER 1 INTRODUCTION | 第18-27页 |
| 1.1 Backound | 第18-19页 |
| 1.2 Anaerobic germination in rice | 第19-21页 |
| 1.2.1 Responses to flooding during germination | 第19页 |
| 1.2.2 Mechanism for anaerobic germination in Rice | 第19-20页 |
| 1.2.3 QTL mapping for anaerobic germination tolerance | 第20-21页 |
| 1.3 Rice seed germination under salt stress | 第21-23页 |
| 1.3.1 Responses to salt stress during germination | 第21页 |
| 1.3.2 Mechanisms of salt tolerance in rice | 第21-22页 |
| 1.3.3 QTL mapping for salinity tolerance | 第22-23页 |
| 1.4 Combined of anaerobic and salt stress in rice | 第23页 |
| 1.5 Genome wide association study (GWAS) and candidate gene | 第23-24页 |
| 1.6 Haplotype analysis for genetic variation in rice | 第24-25页 |
| 1.7 Linkage disequilibrium (LD) and population structure | 第25页 |
| 1.8 Scope and outline of the study | 第25-27页 |
| CHAPTER 2 MATERIALS AND METHODS | 第27-38页 |
| 2.1 Plant materials | 第27-28页 |
| 2.1.1 HHZ IB population | 第27-28页 |
| 2.1.2 Diverse germplasm | 第28页 |
| 2.2 Maintaining seed quality | 第28页 |
| 2.3 Phenotyping of plant materials | 第28-31页 |
| 2.3.1 Phenotyping against anaerobic stress | 第28-30页 |
| 2.3.2 Phenotyping against salt stress at germination stage | 第30-31页 |
| 2.3.3 Phenotyping against combined anaerobic and salt stress | 第31页 |
| 2.4 High throughput genotyping and SNP identification | 第31-32页 |
| 2.5 Statistical analysis | 第32-34页 |
| 2.5.1 Phenotypic data analysis | 第32页 |
| 2.5.2 Population structure and kinship | 第32页 |
| 2.5.3 Linkage Disequilibrium (LD) analysis | 第32-33页 |
| 2.5.4 GWAS and candidate genes identification | 第33-34页 |
| 2.6 Population structure | 第34-38页 |
| 2.6.1 HHZ IB population | 第34-35页 |
| 2.6.2 Diverse germplasm | 第35-38页 |
| CHAPTER 3 RESULTS | 第38-75页 |
| 3.1 Phenotypic performance under anaerobic stress | 第38-42页 |
| 3.1.1 Phenotypic characteristic of the mapping population | 第38-40页 |
| 3.1.2 Correlation among germination related traits in anaerobic stresss | 第40页 |
| 3.1.3 Graphical distribution of phenotypic characters | 第40-41页 |
| 3.1.4 Performance of the best lines against AG | 第41-42页 |
| 3.2 GWAS and candidate gene identification for anaerobic germination | 第42-50页 |
| 3.2.1 QTLs for seedling survival percent in anaerobic stress | 第43页 |
| 3.2.2 QTLs for anaerobic response index in anaerobic stress | 第43-46页 |
| 3.2.3 Functional characterization of candidate genes within QTLs region | 第46-47页 |
| 3.2.4 Identification of candidate genes for QTL (qSP-3.2) on Chromosome 3 | 第47-50页 |
| 3.3 Phenotypic performance under salt stress | 第50-54页 |
| 3.3.1 Phenotypic characteristic of the mapping population | 第50-52页 |
| 3.3.2 Correlation among germination related traits in salt stress | 第52页 |
| 3.3.3 Graphical distribution of phenotypic characters | 第52-53页 |
| 3.3.4 Performance of the best lines against salt stress | 第53-54页 |
| 3.4 GWAS and candidate gene identification for salt tolerance | 第54-65页 |
| 3.4.1 QTL for germination percent in salt stress | 第55-56页 |
| 3.4.2 QTL for root length in salt stress | 第56-57页 |
| 3.4.3 QTL for shoot length in salt stress | 第57-58页 |
| 3.4.4 QTL for biomass in salt stress | 第58-61页 |
| 3.4.5 Functional characterization of candidate genes within QTL | 第61-62页 |
| 3.4.6 Identification of candidate genes for QTL (qGP-9.2) on Chromosome 9 | 第62-65页 |
| 3.5 Phenotypic performance under salt-anaerobic stress | 第65-68页 |
| 3.5.1 Phenotypic characteristic of the mapping population | 第65页 |
| 3.5.2 Correlation among the traits under anaerobic and anaerobic-saline stresses | 第65-66页 |
| 3.5.3 Graphical distribution of phenotypic characters | 第66-67页 |
| 3.5.4 Performance of the best lines against anaerobic-saline stress | 第67-68页 |
| 3.6 GWAS and candidate gene identification for salt-anaerobic germination | 第68-74页 |
| 3.6.1 Functional characterization of candidate genes within QTL | 第70-71页 |
| 3.6.2 Identification of candidate genes for QTL (qASRI-1.1) on Chromosome 1 | 第71-74页 |
| 3.7 Genetic overlapping regions in this study | 第74-75页 |
| CHAPTER 4 DISCUSSION | 第75-83页 |
| 4.1 Genome-wide association study of anaerobic stress tolerance | 第75-77页 |
| 4.2 Genome-wide association study of salt stress tolerance | 第77-80页 |
| 4.3 Genome-wide association study of combined anaerobic and salt stress tolerance | 第80-82页 |
| 4.4 Overall genetic overlapping regions | 第82-83页 |
| CHAPTER 5 SUMMARYAND CONCLUSIONS | 第83-86页 |
| REFERENCES | 第86-100页 |
| APPENDICES | 第100-110页 |
| ACKNOWLEDGEMENT | 第110-111页 |
| RESUME | 第111页 |
