| 摘要 | 第8-11页 |
| ABSTRACT | 第11-14页 |
| LIST OF ABBREVIATIONS | 第15-22页 |
| CHAPTER Ⅰ INNTRODUCTION | 第22-27页 |
| 1.1 COTTON GENUS | 第22-23页 |
| 1.2 COTTON FIBER | 第23-24页 |
| 1.3 COTTON FIBER MUTANTS | 第24-27页 |
| CHAPTER Ⅱ CHARACTERIZATION OF THE EARLY FIBER DEVELOPMENTGENE,LIGON-LINTLESS-1(LI1),USING MICROARRAY | 第27-49页 |
| 1 INTRODUCTION | 第27-29页 |
| 2 MATERIALS AND METHODS | 第29-32页 |
| 2.1 Plant materials | 第29页 |
| 2.2 RNA extraction and microarray hybridization | 第29页 |
| 2.3 Data acquisition, statistical analysis and clustering | 第29-30页 |
| 2.4 Semi-quantitative RT-PCR and quantitative reverse tran scription PCR(qRT-PCR) validation | 第30-31页 |
| 2.5 Bioinformatics Analysis | 第31-32页 |
| 3 RESULTS | 第32-42页 |
| 3.1 Nature of Lil mutant fiber during initiation and early elongation | 第32-33页 |
| 3.2 Identification of differentially expressed genes during the early elongationstage between the Lil mutant and wild-type using microarrays | 第33-35页 |
| 3.3 Gene ontology(GO)categories associated with differentially expressedgenes | 第35-37页 |
| 3.4 Cluster analysis of differentially expressed genes during early fiberdevelopment | 第37-39页 |
| 3.5 Validation of microarray data by RT-PCR and qRT-PCR | 第39-42页 |
| 4 DISCUSSION | 第42-47页 |
| 5 CONCLUSION | 第47-49页 |
| CHAPTER Ⅲ GENOME-WIDE CHARACTERIZATION AND EXPRESSIONANALYSIS OF MYB TRANSCRIPTION FACTORS IN GOSSYPIUM HIRSUTUM | 第49-80页 |
| 1 INTRODUCTION | 第49-52页 |
| 2 MATERIAL AND METHODS | 第52-56页 |
| 2.1 Identification of MYB gene family in upland cotton | 第52-53页 |
| 2.2 Mapping MYB genes on chromosomes | 第53页 |
| 2.3 Phylogenetic analysls | 第53-54页 |
| 2.4 Gene structure analysis and identified motifs | 第54页 |
| 2.5 Plant materials,RNA extraction and qRT-PCR analysis | 第54-56页 |
| 2.6 RNA-seq data analysis | 第56页 |
| 3 RESULTS AND DISCUSSION | 第56-79页 |
| 3.1 Genome-wide identification of upland cotton GhMYB transcription factors | 第56-60页 |
| 3.2 Chromosomal distribution and annotation MYB genes | 第60-65页 |
| 3.3 Phylogenetic analysis of MYB transcription factors genes in upland cotton | 第65-66页 |
| 3.4 MYB gene structure analysis and conserved motif identification | 第66-73页 |
| 3.5 Upland cotton MYB family relationships with other plant | 第73-74页 |
| 3.6 Expression profiles of MYB genes in G. hirsutum | 第74-76页 |
| 3.7 Expression verification of GhMYB genes involved in cotton fiberdevelopment | 第76-79页 |
| 4 CONCLUSION | 第79-80页 |
| CHAPTER IV COMPREHENSIVE ANALYSIS OF COTTON C2H2-ZINCFINGER TRANSCRIPTION FACTORS FAMILY AND THEIR EXPRESSIONANALYSIS DURING FIBER DEVELOPMENT | 第80-115页 |
| 1 INTRODUCTION | 第80-82页 |
| 2 MATERIALS AND METHODS | 第82-86页 |
| 2.1 Identification of C2H2-zine finger gene family in cotton | 第82-83页 |
| 2.2 Phylogenetic analysis of upland C2H2-zinc finger proteins | 第83-84页 |
| 2.3 Exon/intron structure analysis and conserved motif identification | 第84页 |
| 2.4 Chromosomal localization and gene duplication | 第84-85页 |
| 2.5 Plant materials,RNA extraction and qRT-PCR analysis | 第85页 |
| 2.6 Gene expression analysis using the publicly available RNA-seq data | 第85-86页 |
| 3 RESULTS | 第86-108页 |
| 3.1 Identification of C2H2-zinc finger protein family in cotton | 第86-88页 |
| 3.2 Chromosomal distribution of cotton C2H2-zine finger genes | 第88-89页 |
| 3.3 Gene duplication events of upland cotton C2H2-zine finger genes | 第89-93页 |
| 3.4 Relation between C2H2-zinc finger proteins cotton with other plants | 第93-97页 |
| 3.5 Phylogenetic tree,gene structure analysis and conserved motif identificationof the upland cotton C2H2-zinc finger gene family | 第97-102页 |
| 3.6 Expression Profiles of upland cotton C2H2-zinc finger genes at differentdevelopmental stages | 第102-105页 |
| 3.7 C2H2-zine finger genes and their involvement in cotton fiber mutation | 第105-106页 |
| 3.8 Verification of C2H2-zine figer gene expression by qRT-PCR | 第106-108页 |
| 4 DISCUSSION | 第108-113页 |
| 5 CONCLUSIONS | 第113-115页 |
| CHAPTER V LONG NON-CODING RNAS ANALYSIS AND THEIRFUNCTIONS IN LIGON-LINTLESS-1 MUTANT COTTON DURING FIBERDEVELOPMENT | 第115-149页 |
| 1 INTRODUCTION | 第115-118页 |
| 2 MATERIALS AND METHODS | 第118-125页 |
| 2.1 Plant material and RNA extraction | 第118-119页 |
| 2.2 Library preparation for lncRNA sequencing | 第119-120页 |
| 2.3 Bioinformatic identification of upland cotton LncRNAs | 第120-121页 |
| 2.4 Gene expression analysis | 第121页 |
| 2.5 Target gene prediction | 第121页 |
| 2.6 Differential expression analysis | 第121-122页 |
| 2.7 GO and KEGG enrichment analysis | 第122页 |
| 2.8 Small RNA sequencing and processing | 第122-123页 |
| 2.9 Identification of conserved and novel microRNAs | 第123页 |
| 2.10 Interaction determination between miRNAs and lncRNAs | 第123-124页 |
| 2.11 RT-qPCR analysis | 第124-125页 |
| 3 RESULTS | 第125-144页 |
| 3.1 Identification of long noncoding RNAs in Ligon-lintless-1 and wild-type | 第125-128页 |
| 3.2 The distribution of LncRNAs and mRNAs in the upland cotton genome 1073.3 Differentially expressed LncRNAs at different stage of cotton fiberdevelopment | 第128-129页 |
| 3.3 Differentially expressed LncRNAs at different stage of cotton fiber development | 第129-132页 |
| 3.4 Common differentially expressed LncRNAs in cotton fiber development | 第132-134页 |
| 3.5 Functional analysis of differentially expressed LncRNAs | 第134-139页 |
| 3.6 Interaction determination between miRNAs and LncRNAs | 第139-142页 |
| 3.7 Expression verification of candidate LncRNAs involved in cotton fiberdevelopment | 第142-144页 |
| 4 DISCUSSION | 第144-149页 |
| SUMMARY AND OUTLOOK | 第149-151页 |
| REFERENCES | 第151-178页 |
| APPENDICES | 第178-234页 |
| Supplementary table 1.Location and annotation of MYB genes in upland cottongenome.The positive(+) and negative(-) symbols following each gene representforward and reverse orientations,respectively, on the chromosome | 第178-190页 |
| Supplementary Table 2.Location,annotation and protein domains of 386C2H2-zinc finger genes identified in upland cotton and their proteins sequencecharacteristics including,proteins length,molecular weight and subcellular position | 第190-200页 |
| Supplementary table 3.Synonymous (Ks)and non-synonymons(Ka)substitution rates are represented for each orthologous gene pairs between G.arboreum(A2)and upland cotton G.hirsutum(At),as well as those between G.raimondii(D5) | 第200-208页 |
| Supplementary table 4.Differentially expressed LncRNAs,their positions andtarget predictions involved in cotton fiber development during initiation stage(0DPA) | 第208-216页 |
| Supplementary table 5.Differentially expressed LncRNAs,their positions andtarget predictions involved in cotton fiber development during elongation stage(8DPA) | 第216-228页 |
| Supplementary table 6.LncRNAs were predicted as miRNA targets using thepsRNATarget | 第228-234页 |
| PUBLICATIONS | 第234-235页 |
| ACKNOWLEDGEMENTS | 第235-236页 |
