| ABSTRACT | 第13-16页 |
| ABBREVIATIONS | 第17-18页 |
| CHAPTER ONE:GENERAL INTRODUCTION | 第18-22页 |
| 1.1 Background Information | 第18-19页 |
| 1.2 Statement of problem | 第19-20页 |
| 1.3 Justification of study | 第20-21页 |
| 1.4 Objective of the study | 第21-22页 |
| CHAPTER TWO:HIGH THROUGHPUT SEQUENCING ADVANCEMENTS AND FUTURE CHALLENGES | 第22-38页 |
| 2.2 Introduction | 第23-25页 |
| 2.3 Key HTS Platforms and applications | 第25-33页 |
| 2.3.1 Sanger capillary sequencing | 第25-26页 |
| 2.3.2 De novo sequencing | 第26-27页 |
| 2.3.3 Metagenomics | 第27-28页 |
| 2.3.4 Whole genome/targeted re-sequencing | 第28-29页 |
| 2.3.5 Targeted region specific sequencing | 第29页 |
| 2.3.6 Exome sequencing | 第29-30页 |
| 2.3.7 RNA sequencing | 第30-31页 |
| 2.3.8 miRanalyzer | 第31-32页 |
| 2.3.9 Whole transcriptome | 第32页 |
| 2.3.10 Bioinformatics Data Analysis tools | 第32-33页 |
| 2.4 Bioinformatic challenges | 第33-34页 |
| 2.4.1 Ethical challenges | 第33-34页 |
| 2.5 Future prospective | 第34-35页 |
| 2.5.1 Third-generation sequencing technology | 第34-35页 |
| 2.5.2 Sequencing in diagnostics | 第35页 |
| 附图 | 第35-38页 |
| CHAPTER THREE: TRANSCRIPTOMIC ANALYSIS OF BIOLOGICAL NETWORKS INVOLVING IN GRAPEVINE (cv. SUMMER BLACK) LEAF DEVELOPMENT | 第38-82页 |
| 3.2 Introduction | 第39-42页 |
| 3.3 Material and Methods | 第42-44页 |
| 3.3.1 Leaf Sample collection | 第42页 |
| 3.3.2 RNA extraction, cDNA library construction and Illumina deep sequencing | 第42-43页 |
| 3.3.3 Analysis of gene expression level | 第43页 |
| 3.3.4 Pathway enrichment analysis of DEGs | 第43页 |
| 3.3.5 qRT-PCR Validation | 第43-44页 |
| 3.4 Results and discussion | 第44-58页 |
| 3.4.1 Sequence quality control and Illumina HiSeq RNA sequencing | 第44-45页 |
| 3.4.2 Global transcriptome analysis, functional classification, and metabolic pathway analysis by KEGG of all detected transcripts | 第45-47页 |
| 3.4.3 Quality control, filtering of raw reads and analysis of base composition and quality | 第47页 |
| 3.4.4 Quality Control of alignment Statistics and alignment analysis | 第47-48页 |
| 3.4.5 Distribution of reads on reference genes | 第48-49页 |
| 3.4.6 Gene expression distribution of gene's coverage and gene expression difference analysis during leaf growth and development | 第49-50页 |
| 3.4.7 SNP analysis | 第50页 |
| 3.4.8 Prediction and Annotation of Novel Transcripts | 第50-51页 |
| 3.4.9 Alternative Splicing Analysis | 第51-52页 |
| 3.4.10 Identification of Expressed Genes Responding to Leaf Developmental Stages | 第52-53页 |
| 3.4.11 Leaf Growth and Development Alter Photosynthesis and Chlorophyll Metabolic Pathway in Grapevine | 第53-55页 |
| 3.4.12 Genes Related to Secondary Metabolism Biosynthetic Pathways | 第55-56页 |
| 3.4.13 Genes Related to Plant Hormone Signal Transduction Pathways During Leaf Developmental Stages | 第56-58页 |
| 3.5 Discussion | 第58-62页 |
| 3.6 Conclusion | 第62页 |
| 附图表 | 第62-82页 |
| CHAPTER FOUR: TRANSCRIPTOMIC ANALYSIS OF BIOLOGICAL NETWORKS INVOLVING IN GRAPEVINE FRUIT DEVELOPMENT | 第82-110页 |
| 4.2 Background | 第83-85页 |
| 4.3 Materials and methods | 第85-86页 |
| 4.3.1 Grape berry sampling and development | 第85页 |
| 4.3.2 RNA extraction, cDNA library construction and Illumina deep sequencing | 第85页 |
| 4.3.3 Differential Gene Expression Analysis | 第85页 |
| 4.3.4 qRT-PCR Validation | 第85-86页 |
| 4.3.5 Real time RT-PCR validation | 第86页 |
| 4.4 Results and discussion | 第86-98页 |
| 4.4.1 Sequence quality control and Illumina HiSeq RNA sequencing | 第86-87页 |
| 4.4.2 Global transcriptome analysis, networks analysis by KEGG of all detected transcripts and functional classification | 第87-88页 |
| 4.4.3 Differential expressed aroma-related genes during berry development | 第88-89页 |
| 4.4.4 Differential expressed transcripts during Organic acid metabolism | 第89-90页 |
| 4.4.5 Color expression patterns related transcripts | 第90-93页 |
| 4.4.6 Differential expression transcripts related to Sucrose-metabolism networks | 第93-95页 |
| 4.4.7 Differential Expression of Cell Wall Degradation and Softening Related Transcripts | 第95-98页 |
| 附图表 | 第98-110页 |
| CHAPTER FIVE:COMPARISON OF GENES AND BIOLOGICAL NETWORKS INVOLVING IN FRUIT AND LEAF DEVELOPMENT | 第110-124页 |
| 5.1 Background | 第111-112页 |
| 5.2 MATERIAL AND METHOD | 第112页 |
| 5.2.1 Leaf and fruit samples | 第112页 |
| 5.2.2 cDNA library construction and Illumina deep sequencing and Analysis of gene expression level | 第112页 |
| 5.3 Results and discussion | 第112-115页 |
| 5.3.1 Sequence quality control and Illumina HiSeq RNA sequencing | 第112-113页 |
| 5.3.2 Global transcriptomic analysis of metabolic networks and functional classification | 第113-114页 |
| 5.3.3 Expressed Genes Responding to Leaf and fruit Development | 第114-115页 |
| 5.4 Differential expressed genes in developmental networks and metabolic pathways | 第115-119页 |
| 5.4.1 Genes expression related to Photosynthetic network | 第115-116页 |
| 5.4.2 Differentially expressed genes related to flavonoid-related metabolic network | 第116-117页 |
| 5.4.3 Pigmentation patterns in growth networks altered by Genes | 第117页 |
| 5.4.4 Genes regulation and expression related to plant hormone signaling networks | 第117-118页 |
| 5.4.5 Genes related to secondary metabolites biosynthetic networks | 第118-119页 |
| 附图表 | 第119-124页 |
| CHAPTER SIX: CHLOROPLAST BASED GENETIC DIVERSITY AMONG GRAPE GENOTYPES | 第124-134页 |
| 6.2 Background | 第124-126页 |
| 6.3 Material and Methods | 第126-127页 |
| 6.3.1 Plant Materials | 第126页 |
| 6.3.2 Organelle DNA Extraction and PCR Amplification | 第126-127页 |
| 6.3.3 Statistical Analysis | 第127页 |
| 6.4 Results | 第127-128页 |
| 6.5 Discussion | 第128-131页 |
| 附图表 | 第131-134页 |
| CHAPTER SEVEN: ASSOCIATION BETWEEN CHLOROPLAST AND MITOCHONDRIAL DNA SEQUENCES IN CHINESE PRUNUS GENOTYPES (PRUNUS PERSICA, PRUNUS DOMESTICA,AND PRUNUS AVIUM) | 第134-150页 |
| 7.2 Back ground | 第135-137页 |
| 7.3 Results | 第137-140页 |
| 7.3.1 Phylogenetic analysis | 第137-138页 |
| 7.3.2 Nature of the polymorphism based on sequencing Alignment | 第138-139页 |
| 7.3.3 Sequence comparison between and among mt and cpDNA | 第139-140页 |
| 7.4 Materials and Methods | 第140-141页 |
| 7.4.1 Plant Materials | 第140页 |
| 7.4.2 Total DNA Extraction and PCR Amplification | 第140页 |
| 7.4.3 Organelle DNA extraction from PAGE | 第140-141页 |
| 7.4.4 TA cloning and sequencing | 第141页 |
| 7.5 Discussion | 第141-144页 |
| 7.6 Conclusion | 第144页 |
| 附图表 | 第144-150页 |
| MAJOR FINDINGS | 第150-152页 |
| REFERENCES | 第152-178页 |
| PUBLICATIONS AND SUBMITTED MANUSCRIPTS | 第178-180页 |
| ACKNOWLEDGEMENT | 第180-182页 |
| APPENDICES | 第182-187页 |
