| 摘要 | 第6-8页 |
| abstract | 第8-10页 |
| LIST OF ABBREVIATIONS | 第17-18页 |
| DEDICATIONS | 第18-19页 |
| CHAPTER ONE INTRODUCTION | 第19-32页 |
| 1.1 Cotton and Challenges in Cotton Production | 第19-20页 |
| 1.1.1 Drought and Salt Stress Coping Strategies in Cotton | 第19页 |
| 1.1.2 Plant’s Transcription Factors and Gene Functions in Plants Under Drought and Salt Stress Conditions | 第19-20页 |
| 1.2.Morpho‐physiological Mechanism of Cotton Plants in Responses to Drought Stress | 第20-21页 |
| 1.3.Biochemical and Molecular Mechanism of Drought Tolerance in Cotton | 第21-22页 |
| 1.4.Drought Effect and Adaptive Response by Cotton Plants | 第22-23页 |
| 1.5.Strategies to Induce Abiotic Stress Tolerance in Cotton | 第23-30页 |
| 1.5.1.Marker‐Assisted Selection(MAS)Based on Drought‐Related QTLs/Transcription Factors | 第23页 |
| 1.5.2.Genotyping by Sequencing and QTL Mapping of Drought Tolerant Traits | 第23-24页 |
| 1.5.3.Mapping of the BC_2F_2 Progenies and Mining of Drought Stress Responsive Genes | 第24-25页 |
| 1.5.4.The NODULE-INCEPTION-like proteins(NLPs)role in cotton | 第25-26页 |
| 1.5.5.Characterization of the Late Embryogenesis Abundant(LEA)Proteins Family in Cotton | 第26-27页 |
| 1.5.6.Functional Characterization of Cyclin Dependent Kinase Gene Family in Cotton | 第27-28页 |
| 1.5.7.Trihelix Transcription Factors and Overexpression of Gh_A05G2067(GT-2)in Cotton | 第28-29页 |
| 1.5.8.Identification and Functional Characterization of the CYP450 Genes in Cotton | 第29页 |
| 1.5.9.The Alba Genes and their Putative Role in Cotton under Abiotic Stress Conditions | 第29-30页 |
| 1.6.The Objective of this Research | 第30-32页 |
| CHAPTER TWO MATERIALS AND METHODS | 第32-52页 |
| 2.1 Plant Materials and Treatments | 第32-34页 |
| 2.1.1 Mapping Population and Drought Treatment | 第32页 |
| 2.1.2.Materials for Stomata Examination and RT-qPCR Analysis of the Five Genes under Drought and/or Salt Treatments | 第32-33页 |
| 2.1.3.Materials Used For RNA Extraction for Examining Expression Patterns of NLP Genes under Nitrogen Deficiency Treatments | 第33-34页 |
| 2.1.4.Materials Used For Transformation or VIGS Researches of Six Functional Gene Families | 第34页 |
| 2.2 Data Collection of Various Traits on the BC_2F_2 Populations under Drought stress Condition | 第34-36页 |
| 2.2.1 Soil Moisture,Soil Temperature,and Soil Electrical Conductivity | 第34页 |
| 2.2.2.Determination of the Morphological Characteristics of Plants | 第34-35页 |
| 2.2.3 Cell Membrane Stability(CMS) | 第35页 |
| 2.2.4 Relative Leaf Water Content(RLWC) | 第35页 |
| 2.2.5 Excised Leaf Water Loss(ELWL) | 第35-36页 |
| 2.3.Sample Collection,GBS library Preparation,Sequencing,and SNP Genotyping | 第36-38页 |
| 2.3.1.Extraction,Quantification and Quality Determination of DNA | 第36页 |
| 2.3.2.The GBS Library Preparation,Sequencing and SNP Genotyping | 第36-37页 |
| 2.3.3.Genotyping by Sequencing(GBS)Protocol | 第37-38页 |
| 2.4.Data Analysis,Linkage Map Construction,QTL Mapping,and Gene Mining | 第38-42页 |
| 2.4.1.Data Analysis | 第38-39页 |
| 2.4.2.Linkage Map Construction and QTL Mapping | 第39-40页 |
| 2.4.3.Gene Mining,Functional Annotation,Phylogenetic tree,and Gene Structure Analysis | 第40页 |
| 2.4.4.RNA Sequence Analysis of the Mined Genes | 第40页 |
| 2.4.5.The miRNA Target and Promoter Analysis | 第40-41页 |
| 2.4.6.RT-qPCR Validation of the Key Functional Genes | 第41-42页 |
| 2.5.Functional Characterization of Six Stress Responsive Gene Families in Cotton | 第42-47页 |
| 2.5.1.Identification of Stress Responsive Gene Families in Cotton | 第42-43页 |
| 2.5.2.Chromosomal Locations and Syntenic Analysis of Abiotic Stress-Responsive Gene Families | 第43页 |
| 2.5.3.Phylogenetic and Gene Structure Analysis of the Abiotic Stress Responsive Genes | 第43页 |
| 2.5.4.Prediction of miRNA’s Targeting the Various Stress Responsive Genes in Cotton | 第43-44页 |
| 2.5.5.Cis-regulatory Element Analysis and Gene Ontology(GO)Annotation | 第44页 |
| 2.5.6.RNA Isolation and RT-qPCR Verification | 第44-47页 |
| 2.6.Functional Analysis of the Stress Responsive Gene Families in Cotton | 第47-52页 |
| 2.6.1.Transformation of the Novel Genes,LEA2,CDK and TH in A.thaliana | 第47-48页 |
| 2.6.2.Profiling of Abiotic stress Responsive Genes in Transformed Arabidopsis plants | 第48页 |
| 2.6.3.Biochemical Assays in Transgenic and WT Arabidopsis Lines Under Abiotic Stress | 第48-49页 |
| 2.6.4.Stress Conditions and Physiological Measurements on the Overexpressed and the Wild Types | 第49页 |
| 2.6.5.Determination of the Subcellular Location of Gh_D12G2017(CDKF4)Protein | 第49页 |
| 2.6.6.Virus Induced Gene Silencing of TH,CYP450,Alba and NLP Genes in Cotton | 第49-50页 |
| 2.6.7.Profiling of Stress-Responsive Genes on the VIGS and WT Cotton Plants | 第50-51页 |
| 2.6.8.Physiological and Biochemical Evaluations of the VIGS Plants and WT Cotton Plants | 第51页 |
| 2.6.9 Root Evaluation of the VIGS and WT Cotton Plants | 第51-52页 |
| CHAPTER THREE RESULTS | 第52-240页 |
| 3.1.QTL Mapping and Functional Characterization of Key Genes | 第52-101页 |
| 3.1.1.Phenotype Variation between Parental Lines and their BC2F1 Generation | 第52-54页 |
| 3.1.2 Correlation Analysis | 第54页 |
| 3.1.3.Microscopic Examination of the Parents and Their BC2F1 Generation | 第54-56页 |
| 3.1.4.SNP detection,InDel Detection,Annotation,Genetic Markers,and Marker Coding | 第56-57页 |
| 3.1.5.Genetic Map Construction | 第57-59页 |
| 3.1.6.High-density Genetic Linkage Map Construction | 第59-62页 |
| 3.1.7.Evaluation of Reorganization Relationship and Collinearity of Genetic Maps and Genomes | 第62页 |
| 3.1.8.Gene Mining Within the GBS Marker Regions of the Mapping Population | 第62-65页 |
| 3.1.9.Chromosome Mapping of the Genes Mined for the Dominant Domain,Pkinase | 第65-67页 |
| 3.1.10.RNA Sequence Data of the Genes of the Pkinase Domain | 第67页 |
| 3.1.11.The miRNA Target Analysis of the271 Dominant Genes | 第67-68页 |
| 3.1.12.Cis-regulatory Element Analysis | 第68-70页 |
| 3.1.13.Gene Ontology(GO)Analysis of the Mined Genes | 第70-72页 |
| 3.1.14.RT-qPCR Validation of the Candidate Genes | 第72-73页 |
| 3.1.15.Identification of Consistent and Clustering QTLs for Physio-Morphological Traits | 第73-79页 |
| 3.1.16.Gene Mining within the3 Major QTLs Clusters Regions | 第79-84页 |
| 3.1.17.Bioinformatics Analysis of the Mined Genes within the Major QTL Clusters | 第84-88页 |
| 3.1.17.1 Physiochemical-Subcellular Localization of the Proteins Encoded by the Mind Genes | 第84-87页 |
| 3.1.17.2 Gene Ontological Annotation of the Mind Genes | 第87-88页 |
| 3.1.18.Phylogenetic Tree Analysis of the Protein Encoded by the Mined Genes | 第88-94页 |
| 3.1.19.The miRNA Target and Cis-regulatory Element Analysis of the Mined Genes | 第94-98页 |
| 3.1.19.1 Determination of the various miRNA targeting the Mined Genes | 第94-97页 |
| 3.1.19.2 Determination of the Various Cis-regulatory Element Associated with the Mined Genes | 第97-98页 |
| 3.1.20.RNA Seq.Expression Analysis of the Mined Genes | 第98页 |
| 3.1.21.RT-qPCR Validation of the Key Genes | 第98-101页 |
| 3.2 A Novel NLP Genes Identified within the QTL Region Enhances N deficiency Tolerance | 第101-124页 |
| 3.2.1 Identification and Sequence Analysis of the Cotton NLP Proteins | 第101页 |
| 3.2.2 Phylogenetic Tree Analysis | 第101-110页 |
| 3.2.3 Physiochemical Properties of the Cotton Proteins Encoded by the NLP Genes | 第110-112页 |
| 3.2.4 Gene Structure Analysis and Motif Identification of the Cotton NLP Proteins | 第112页 |
| 3.2.5 Cis-regulatory Element Analysis of the Cotton NLP Genes | 第112-117页 |
| 3.2.6 The miRNA Target Prediction of the Cotton NLP Genes | 第117-120页 |
| 3.2.7 RT-qPCR Validation of the Selected GhNLP Genes | 第120-121页 |
| 3.2.8 Silencing of Gh_A05G3286(NLP5)and Evaluation of VIGS and WT plants | 第121-123页 |
| 3.2.9 Stress Responsive Genes profiling and biochemical analysis on NLP knocked plants | 第123-124页 |
| 3.3.Genomewide Analysis and Functional Characterization of LEA Gene Family | 第124-151页 |
| 3.3.1.Identification of the LEA Genes in Cotton | 第124-126页 |
| 3.3.2.Phylogenetic Analyses,Gene Structure and Protein Motifs of LEA Genes in Upland Cotton | 第126-133页 |
| 3.3.3.Phylogenetic Analyses of the LEA Proteins in Cotton with Other Plants | 第133-134页 |
| 3.3.4.Chromosomal Distribution of Cotton LEA Genes | 第134-138页 |
| 3.3.5.Gene Duplication and Syntenic Analysis | 第138-142页 |
| 3.3.6.Prediction of LEA Genes(mRNA)Targeted by miRNAs in Upland Cotton | 第142-143页 |
| 3.3.7.Gene Ontology(GO)Annotation | 第143-148页 |
| 3.3.8.Cis-regulatory Element Analysis | 第148-149页 |
| 3.3.9.Upland Cotton LEA Genes Expression Analysis under Drought Stress | 第149-151页 |
| 3.4.Comprehensive Analysis of Cotton LEA2 Genes | 第151-182页 |
| 3.4.1.LEA2 Proteins Identification in Cotton and Other Plants | 第151-153页 |
| 3.4.2.Phylogenetic Analyses of LEA2 Proteins in G.hirsutum,G.arboreum,and G.raimondii | 第153-154页 |
| 3.4.3.Physiochemical Analysis and Subcellular Localization of LEA2 Genes in Upland Cotton | 第154-160页 |
| 3.4.4.Genomic Organization and Motif Detection of the LEA2 Proteins in Cotton | 第160-161页 |
| 3.4.5.Chromosomal Location and Duplication events of the LEA2 Genes in Cotton | 第161-165页 |
| 3.4.6.Cis-regulatory Element Prediction in LEA2 Proteins | 第165-166页 |
| 3.4.7.Gene Ontology(GO)Annotation | 第166-168页 |
| 3.4.8.Prediction of LEA2 Genes Targeted by miRNAs | 第168-171页 |
| 3.4.9.Analysis of Tertiary Protein Structure of Upland Cotton LEA2s | 第171-173页 |
| 3.4.10.LEA2 Gene Interactional Dynamics under Drought Stress | 第173页 |
| 3.4.11.RNA Seq.Expression Patterns of LEA2 Genes in Different Tissues of Upland Cotton | 第173-175页 |
| 3.4.12.Expression Profiles of LEA2 Genes in Leaf,Stem,and Roots of Upland Cotton | 第175-176页 |
| 3.4.13.Expression Profiles of LEA2 Genes under Drought Stress | 第176-178页 |
| 3.4.14.RT-qPCR Analysis of the Transformed Gene in Upland Cotton Tissues | 第178-179页 |
| 3.4.15.CotAD_24498 Overexpressed Plants have Increased Root Growth and improved Tolerance to Drought Stress | 第179-180页 |
| 3.4.16.Transcripts Investigation of Drought Stress-Responsive Genes | 第180-181页 |
| 3.4.17.Oxidants and Antioxidant Enzyme Determination in the Transgenic Lines | 第181-182页 |
| 3.5.Functional Characterization of the CDK Genes under Drought and Salt Stress Condition | 第182-198页 |
| 3.5.1.Identification and Sequence Analysis of CDK Proteins in Cotton Genome | 第182-183页 |
| 3.5.2.Gene Structure and Amino Acid Motif Analysis of the CDK Genes in Cotton | 第183-184页 |
| 3.5.3.Phylogenetic Analyses and Protein Alignments of the CDKs Proteins | 第184-185页 |
| 3.5.4.Chromosomal Distribution of Cotton CDK Genes | 第185-188页 |
| 3.5.5.Gene Duplication,Orthologs,Paralogs and Selection Type of the CDK Genes | 第188页 |
| 3.5.6.Promoter(Cis-regulatory Element)Analysis | 第188-189页 |
| 3.5.7.RNA Seq.Analysis of the CDK Genes under Drought and Salt Stress Condition | 第189-190页 |
| 3.5.8.RT-qPCR Analysis of the Cotton CDK Genes under Drought and Salt Stress | 第190-192页 |
| 3.5.9.RT-qPCR Validation of the Highly Upregulated CDK Genes | 第192页 |
| 3.5.10.Determination of the Subcellular Localization of Gh_D12G2017(CDKF4)Protein | 第192-193页 |
| 3.5.11.RT-qPCR Analysis of Gh_D12G2017(CDKF4)Gene in Upland Cotton Tissues | 第193-194页 |
| 3.5.12.The Response of the Overexpressed and WT Plants under Drought and salt Stress Conditions.. | 第194-197页 |
| 3.5.13.Evaluation of Stress Responsive Genes on the Tissues of Transgenic and WT Plants | 第197-198页 |
| 3.6.Genomewide Identification and Functional Analysis of Gh_A05G2067(GT‐2) | 第198-210页 |
| 3.6.1.Identification of Trihelix Proteins in Cotton | 第198页 |
| 3.6.2.Phylogenetic Analysis of Cotton Trihelix Proteins with Other Plants | 第198-199页 |
| 3.6.3.Genomic Organization and Chromosomal Distribution of the Cotton Trihelix Genes | 第199-200页 |
| 3.6.4.RNA Sequence Analysis Profiled under Abiotic Stress Conditions | 第200-201页 |
| 3.6.5.RT-qPCR Validation of the Selected Genes | 第201-203页 |
| 3.6.6.RT-qPCR and subcellular determination of the Transformed Gene,Gh_A05G2067(GT-2) | 第203-204页 |
| 3.6.7.Oxidant and Antioxidant Enzymes Assays in Gh_A05G2067(GT-2) -Overexpressed plants | 第204-205页 |
| 3.6.8.Physiological Traits Evaluation under Drought and Salt Stress Conditions | 第205-206页 |
| 3.6.9.Profiling of Abiotic Stress Responsive Genes in GT-2-Overexpressed Lines and WT | 第206-207页 |
| 3.6.10.Physiological Traits Evaluation in Gh_A05G2067(GT-2) -Silenced Plants | 第207-208页 |
| 3.6.11.Biochemical and RT-qPCR Analysis of the Abiotic Stress-Responsive Genes | 第208-210页 |
| 3.7.Reverse Genetics Reveals the Putative Role of CYP450 Gene Family in Cotton | 第210-218页 |
| 3.7.1.Identification of the Cotton Cytochrome P450(CYPs)Genes | 第210页 |
| 3.7.2.Subcellular Localization Analysis of the Cotton Cytochrome P | 第210-211页 |
| 3.7.3.Cis-regulatory Element Analysis of the Cotton Cytochrome P | 第211页 |
| 3.7.4.Chromosomal Mapping of the Upland G.hirsutum Cytochrome CYP450 Genes | 第211-212页 |
| 3.7.5.RNA Seq.Analysis and RT-qPCR Validation of the Upland Cotton CYP450 Genes | 第212-214页 |
| 3.7.6.Expression Analysis of Gh_D07G1197 and Gh_A13G2057 in VIGS and WT Plants | 第214-216页 |
| 3.7.7.Evaluation of Performance of the VIGS Plants and WT plants | 第216-218页 |
| 3.7.8.Stress-Responsive Gene Profiling on the Tissues of VIGS Plants and WT Plants | 第218页 |
| 3.8.Functional Characterization of Aba Genes via RNAi Method in Cotton | 第218-240页 |
| 3.8.1 Identification of the Alba Proteins in Cotton Species | 第218-221页 |
| 3.8.2 Phylogenetic Tree Analysis of the Cotton Alba Proteins | 第221-223页 |
| 3.8.3 Physiochemical Properties of the Cotton Alba Proteins | 第223-225页 |
| 3.8.4 Gene Structure and Motif Identification | 第225-227页 |
| 3.8.5 The miRNA Target on the Varies Alba Genes in Cotton | 第227-231页 |
| 3.8.6 Cis-regulatory Elements Analysis of the Cotton Alba Genes | 第231页 |
| 3.8.7 RNA Seq.Analysis and RT-qPCR Validation of the Various Alba Genes | 第231-233页 |
| 3.8.8 The Efficiency of Knockdown of the Two Alba Genes in Cotton | 第233-234页 |
| 3.8.9 Physiological and Root Assays of the VIGS Plants and the WT Plants | 第234-237页 |
| 3.8.10 Biochemical and Abiotic Stress Responsive Profiling on the VIGS and WT plants | 第237-240页 |
| CHAPTER FOUR DISCUSSION | 第240-265页 |
| 4.1.QTL Mapping and Functional Characterization of Key Genes | 第240-244页 |
| 4.2.GBS Mapping and Analysis of Conserved Genes that Respond to Drought Stress tolerance | 第244-248页 |
| 4.3.A Novel NLP Genes Identified Within the QTL Enhancing Nitrogen Deficiency Tolerance in Cotton | 第248-251页 |
| 4.4.Characterization of the LEA Proteins Family in Cotton under Drought Stress Condition | 第251-254页 |
| 4.5.Functional Characterization of the CDK Gene Family in Cotton | 第254-257页 |
| 4.6.Genomewide Identification and Functional Analysis of the Trihelix Transcription Factors | 第257-260页 |
| 4.7.Reverse Genetics Reveals the Putative Role of CYP450 Gene Family in Cotton | 第260-262页 |
| 4.8 Functional Analysis of the Alba Genes in Cotton | 第262-265页 |
| CONCLUSION | 第265-267页 |
| 5.1.QTL Mapping and Functional Characterization of Key Genes within the QTL regions | 第265页 |
| 5.2 Genomewide Identification of the Six Gene Families in Cotton | 第265-266页 |
| 5.3 RNA and RT-qPCR Validation of Protein Encoded by the Various Gene Families | 第266页 |
| 5.4 Functional Characterization of the Five Gene Families Under Drought and/or Salt Stress | 第266-267页 |
| REFERENCES | 第267-296页 |
| ACKNOWLEDGEMENT | 第296-298页 |
| CURRICULUM VITAE | 第298-302页 |
