| 摘要 | 第7-9页 |
| ABSTRACT | 第9-10页 |
| LIST OF ABBREVIATIONS | 第14-20页 |
| CHAPTER 1 INTRODUCTION | 第20-40页 |
| 1.1 GENERAL INTRODUCTION | 第20-23页 |
| 1.2 LITERATURE REVIEW | 第23-31页 |
| 1.2.1 What is grain size | 第24页 |
| 1.2.2 Genetic analysis of grain size and weight | 第24-25页 |
| 1.2.3 What are quantitative trait loci(QTL) | 第25-26页 |
| 1.2.4 Genetic mapping of quantitative trait loci in rice | 第26页 |
| 1.2.5 Identification of QTL | 第26-27页 |
| 1.2.6 QTL mapping/linkage analysis | 第27-29页 |
| 1.2.7 Association mapping/marker-trait association analysis | 第29页 |
| 1.2.8 Genome-wide association mapping | 第29-31页 |
| 1.2.9 Candidate gene association mapping | 第31页 |
| 1.3 MAJOR GRAIN SIZE REGULATORS AND QTL | 第31-37页 |
| 1.3.1 GS3 and DEP | 第32-33页 |
| 1.3.2 MAPK signaling pathway functions in grain size | 第33页 |
| 1.3.3 Ubiquitin-proteasome pathways(UPP) | 第33-34页 |
| 1.3.4 Phytohormones control grain size | 第34-35页 |
| 1.3.5 Auxin | 第35页 |
| 1.3.6 Cytokinin | 第35-36页 |
| 1.3.7 Grain size control by transcriptional regulatory factors | 第36-37页 |
| 1.4 LIMITATIONS,CHALLENGES AND PROSPECT OF QTL MAPPING OF GRAIN SIZE | 第37-40页 |
| CHAPTER 2 Rapid Identification Of Major Quantitative Trait Loci Associated With Grain Size Using Advance Backcross Generation In Rice | 第40-53页 |
| 2.1 INTRODUCTION | 第40-42页 |
| 2.2 MATERIALS AND METHODS | 第42-44页 |
| 2.2.1 Plant materials | 第42-43页 |
| 2.2.2 Field trial and phenotypic evaluation | 第43页 |
| 2.2.3 Statistical analysis | 第43-44页 |
| 2.2.4 Marker development and bulk sergeant analysis method | 第44页 |
| 2.2.5 Identification of QTL and linkage map construction | 第44页 |
| 2.2.6 DNA extraction and genotyping | 第44页 |
| 2.3 RESULTS | 第44-50页 |
| 2.3.1 Phenotypic performance of two parents and introgression line | 第44-48页 |
| 2.3.2 Genetic map and QTL analysis | 第48-50页 |
| 2.3.3 QTL environmental interaction analysis and stability of QTL for grain size | 第50页 |
| 2.4 Discussion | 第50-53页 |
| CHAPTER 3 Association mapping of quantitative trait loci affecting grain size in advance backcross-generation derived by Oryza rufipogon griff | 第53-73页 |
| 3.1 INTRODUCTION | 第53-55页 |
| 3.2 MATERIALS AND METHODS | 第55-58页 |
| 3.2.1 Plant materials construction | 第55-56页 |
| 3.2.2 Field trial and phenotypic evaluation | 第56页 |
| 3.2.3 Statistical analysis | 第56页 |
| 3.2.4 DNA extraction and SNP genotyping | 第56页 |
| 3.2.5 Genome-wide association mapping and allele mining | 第56-57页 |
| 3.2.6 DNA sequence analysis | 第57页 |
| 3.2.7 Gene expression analysis | 第57-58页 |
| 3.3 RESULTS | 第58-69页 |
| 3.3.1 Phenotypic evaluation of parents and introgression line | 第58-62页 |
| 3.3.2 Basic statistics of SNP markers | 第62-63页 |
| 3.3.3 Genome-wide association analysis | 第63-66页 |
| 3.3.4 Pleiotropy or gene linkage | 第66-67页 |
| 3.3.5 DNA sequence and haplotype analysis | 第67-68页 |
| 3.3.6 Gene expression analysis | 第68-69页 |
| 3.4 DISCUSSION | 第69-73页 |
| CHAPTER 4 Rna-Seq/Next-Generation Sequencing Of Young Panicles Of Rice | 第73-101页 |
| 4.1 INTRODUCTION | 第73-74页 |
| 4.2 MATERIALS AND METHODS | 第74-79页 |
| 4.2.1 Plant material | 第74-75页 |
| 4.2.2 RNA extraction and quality control | 第75页 |
| 4.2.3 Library preparation | 第75页 |
| 4.2.4 Mapping of reads | 第75-76页 |
| 4.2.5 Gene expression analysis | 第76页 |
| 4.2.6 Gene expression statistics | 第76页 |
| 4.2.7 Repeat sample correlation analysis | 第76页 |
| 4.2.8 Differential gene expression analysis and expression level | 第76-77页 |
| 4.2.9 Significant differentially expressed gene DEG screening | 第77页 |
| 4.2.10 Differentially expressed gene analysis | 第77页 |
| 4.2.11 Gene ontology(GO)function and enrichment analysis and classification | 第77页 |
| 4.2.12 DEG GO function,classification and GO enrichment | 第77-78页 |
| 4.2.13 Functional analysis of DEG,KEGG pathway and enrichment analysis | 第78页 |
| 4.2.14 Cluster analysis of differential gene expression | 第78页 |
| 4.2.15 Variable splicing analysis | 第78页 |
| 4.2.16 New transcription predictive analysis, | 第78页 |
| 4.2.17 Point mutation(SNP)analysis | 第78-79页 |
| 4.3 RESULTS AND DISCUSSION | 第79-101页 |
| 4.3.1 Sequencing data statistics | 第79页 |
| 4.3.2 Gene expression analysis of DEGs | 第79-81页 |
| 4.3.3 Significant differentially expressed gene DGE screening | 第81-83页 |
| 4.3.4 Grouping of DEGs | 第83-84页 |
| 4.3.5 Gene ontology(GO)annotation and enrichment analysis | 第84-92页 |
| 4.3.6 Cluster analysis | 第92-96页 |
| 4.3.7 Variable splicing analysis | 第96-97页 |
| 4.3.8 Point mutation(SNP)analysis | 第97-100页 |
| 4.3.9 New transcript prediction analysis | 第100-101页 |
| CHAPTER 5 SUMMARY AND RECOMMENDATIONS | 第101-105页 |
| 5.1 SUMMARY | 第101-103页 |
| 5.2 MAJOR FINDINGS | 第103-104页 |
| 5.3 FUTURE DESIGN | 第104-105页 |
| REFERENCE | 第105-117页 |
| APPENDICES | 第117-129页 |
| LIST OF PUBLICATIONS DURING PH.D.STUDY | 第129-130页 |
| ACKNOWLEDGEMENT | 第130-132页 |
| AUTHOR RESUME | 第132页 |
