| LIST OF ABBREVIATIONS | 第1-11页 |
| 摘要 | 第11-14页 |
| ABSTRACT | 第14-18页 |
| CHAPTER 1 REVIEW OF LITERATURE | 第18-36页 |
| ·Epigenetic regulation in living organisms | 第18-19页 |
| ·Transcriptional gene silencing(TGS) | 第19页 |
| ·Post-transcriptional gene silencing(PTGS) | 第19页 |
| ·DNA methylation(CG,CHG and CHH)and its importance | 第19-22页 |
| ·RNA directed DNA methylation(RdDM) | 第22-24页 |
| ·Histone modification | 第24-26页 |
| ·DNA methyltransferases,the source of DNA methylation in plants | 第26-29页 |
| ·Methyltransferase 1(MET1) | 第27-28页 |
| ·Chromo-methyltransferases(CMT) | 第28页 |
| ·Domains rearranged methyltransferase(DRM) | 第28-29页 |
| ·DNA methylation and repression of transcription | 第29-30页 |
| ·Plant stress response | 第30页 |
| ·A genome-wide correlation between DNA methylation and salt and osmotic stress regulation in rice | 第30-33页 |
| ·Model of DNA methylation regulation in rice under abiotic stresses | 第33-34页 |
| ·Aims and Perspectives | 第34-36页 |
| CHAPTER 2 GENOME-WIDE CHARACTERIZATION AND EXPRESSION ANALYSIS OF DNAMTASE GENES IN RICE | 第36-50页 |
| ·Introduction | 第36-37页 |
| ·Materials and Methods | 第37-40页 |
| ·Plant materials and growth conditions | 第37页 |
| ·Application of stresses and preparation of samples | 第37页 |
| ·Identification and phylogenetic analysis of DNA MTase genes family | 第37-38页 |
| ·RNA extraction and RT-PCR | 第38页 |
| ·Quantitative Real-time PCR | 第38页 |
| ·Statistical analysis | 第38-40页 |
| ·Results | 第40-48页 |
| ·Characterization and phylogeny of MTases in rice | 第40-42页 |
| ·Expression profiles of DNA MTase genes in various tissues | 第42-44页 |
| ·Expression of cytosine DNA-MTases with hormone treatments | 第44-45页 |
| ·Expression of cytosine DNA-MTase in root and shoot under two stress conditions | 第45-47页 |
| ·Distinct expression of DNA-MTases in 2 rice subspecies under stress conditions | 第47-48页 |
| ·Discussion | 第48-50页 |
| CHAPTER 3 GENOME-WIDESPREAD DYNAMIC DNA METHYLATION IN RESPONSE TOSALT AND OSMOTIC STRESSES IN RICE | 第50-92页 |
| ·Introduction | 第50-51页 |
| ·Materials and Methods | 第51-60页 |
| ·Plant material and growth conditions | 第51页 |
| ·Stresses application and preparation of samples | 第51-52页 |
| ·Flow chart of methodology | 第52-53页 |
| ·Genome-wide MeDIP library generation and sequencing | 第53-55页 |
| ·Peak based analysis of three samples(CK,NaCl and PEG) | 第55-56页 |
| ·Bisulfite sequencing | 第56-57页 |
| ·RNA-sequencing library generation and gene-chip sequencing | 第57页 |
| ·MeDIP-on-gene chip hybridization | 第57-58页 |
| ·PCR and Real-Time qRT-PCR Assay | 第58页 |
| ·Gene ontology(GO)analysis | 第58页 |
| ·KEGG pathway analysis | 第58-59页 |
| ·Statistical tools | 第59-60页 |
| ·Results | 第60-86页 |
| ·Genome-wide mapping of DNA methylation in rice samples | 第60-62页 |
| ·Distribution of DNA methylation in different gene elements(Global patterns of methylation) | 第62-65页 |
| ·Validation of MeDIP-sequencing(bisulfite sequencing) | 第65-67页 |
| ·DNA methylation in CpG Island,gene body and repetitive elements | 第67-70页 |
| ·Distribution of MeDIP-sequencing reads and gene chip data | 第70-72页 |
| ·Correlation between DNA methylation and gene expression | 第72-75页 |
| ·Promoter and gene body based methylation changes | 第75-78页 |
| ·Identification of differentially methylated genes of abiotic stresses responsive families | 第78-80页 |
| ·Validation of some novel genes | 第80-81页 |
| ·qPCR analysis of candidate bed-up and bed-down genes in root and shoot | 第81-84页 |
| ·Gene ontology(Go)enrichment analysis and pathways annotation | 第84-86页 |
| ·Discussion | 第86-92页 |
| CHAPTER 4 GENOME-WIDE IDENTIFICATION OF ZFP FAMILY,ITS CLASSIFICATION,EXPRESSION AND CORRELATION ANALYSIS WITH DNA METHYLATION FOR ABIOTIC-STRESSE REGULATION | 第92-108页 |
| ·Introduction | 第92-94页 |
| ·Materials and methods | 第94-95页 |
| ·Plant materials and growth condition | 第94页 |
| ·Application of stresses and preparation of samples | 第94-95页 |
| ·DNA and RNA extraction and preparation of cDNA | 第95页 |
| ·MeDIP-on-chip assay | 第95页 |
| ·Quantitative Real-timePCR | 第95页 |
| ·Gene ontology(GO)analysis | 第95页 |
| ·KEGG pathway analysis | 第95页 |
| ·Results | 第95-105页 |
| ·Genome-widespread DNA methylation facts and its correlation with specific ZFP-genes expression in rice under stresses | 第95-96页 |
| ·Genome-wide identification,classification and characterization of candidate ZFP genes | 第96-98页 |
| ·Chromosomal distribution and segmental duplication of genes | 第98-99页 |
| ·Quantitative expression profile of genes under two stresses | 第99-103页 |
| ·Gene Ontology(GO)and KEGG-pathway of some important ZFP-gene | 第103-105页 |
| ·Discussion | 第105-108页 |
| CHAPTER 5 FINAL DISCUSSION AND FUTURE WORK | 第108-116页 |
| ·The role of DNA MTase gene family for plant stress regul ation | 第108-110页 |
| ·Genome-widespread DNA methylation for abiotic stresses regulation | 第110-114页 |
| ·Future Planning | 第114-116页 |
| SUMMARY | 第116-118页 |
| INNOVATIONS | 第118-120页 |
| APPENDIX | 第120-158页 |
| 1. Primers used for bisulfite sequencing (BS-seq) | 第120-121页 |
| 2. Primers used for qPCR in chapter 3 | 第121-122页 |
| 3. Primers used for RT-PCR for the expression analysis of 14-genes of ZFP family | 第122-123页 |
| 4. A sample of all differential up and down regulated genes on chrl Primers | 第123-138页 |
| 5. Genome coverage distribution across sequencing depth | 第138-140页 |
| 6. Distribution of CpG bases vary with sequencing depth | 第140-142页 |
| 7. Distribution of CHG sites vary with sequencing depth | 第142-144页 |
| 8. Distribution of CHH sites vary with sequencing depth | 第144-146页 |
| 9. Distribution of peaks varies with peaks length in three samples (CK, NaCl and PEG 6000) | 第146-150页 |
| 10. Distribution of MeDIP-seq and gene signals on the chromosomes | 第150-151页 |
| 11. GO pathway of some selected genes under CK vs. NaCl (Downstream2k bed-down genes) | 第151-152页 |
| 12. Pathway analysis of selected genenes from CK vs. NaCl (CDS bed-up genes) | 第152-153页 |
| 13. GO pathway of some selected genes under CK vs. PEG (Upstream2k bed-up genes) | 第153-154页 |
| 14. KEGG pathway of some selected genes under CK vs. PEG (CDS bed-up genes) | 第154-155页 |
| 15. Pathway analysis of selected genes under CKvs. PEG | 第155-156页 |
| 16. GO pathway of some selected genes under CK vs. PEG (Upstream2k bed-down genes) | 第156-157页 |
| 17. Bisulfite-seq results of randomly selected six loci | 第157-158页 |
| REFERENCES | 第158-172页 |
| PUBLICATIONS | 第172页 |
| PAPER PRESENTED IN INTERNATIONAL CONFERENCES | 第172-174页 |
| ACKNOWLEDGEMENTS | 第174-175页 |
