| Abstract | 第8-10页 |
| 摘要 | 第11-13页 |
| List of abbreviations | 第13-14页 |
| Chapter 01 Introduction | 第14-26页 |
| 1.1 Cotton taxonomy and economic importance | 第14页 |
| 1.2 Era of cotton genomics | 第14-15页 |
| 1.3 Genetic linkage mapping | 第15-16页 |
| 1.4 Bulk segregation analysis(BSA) | 第16页 |
| 1.5 Mapping populations | 第16-17页 |
| 1.6 Molecular markers and QTL mapping | 第17-18页 |
| 1.7 Mapping QTLs for complex yield traits | 第18-19页 |
| 1.8 Fine mapping strategies | 第19-20页 |
| 1.9 Fine mapping complex trait in crops | 第20-21页 |
| 1.10 Fine mapping and map-based cloning in cotton | 第21-22页 |
| 1.11 Boll development phases in cotton | 第22-23页 |
| 1.12 Microsatellites motif imperfection | 第23页 |
| 1.13 Mechanism of motif imperfection in SSRs | 第23-24页 |
| 1.14 Intrinsic DNA features relate imperfection in microsatellites | 第24-25页 |
| 1.15 Motif imperfection and evolution of polyploidy in crops | 第25页 |
| 1.16 Study objectives and significance | 第25-26页 |
| Chapter 02 Map-based cloning qSCW-cl2 | 第26-70页 |
| 2.1 Introduction | 第26-29页 |
| 2.2 Materials and methods | 第29-38页 |
| 2.2.1 Plant materials and mapping populations | 第29-30页 |
| 2.2.2 Phenotype evaluation and analysis | 第30-31页 |
| 2.2.3 Designing markers from genomic sequences | 第31页 |
| 2.2.4 PCR, PAGE and SSR genotyping | 第31-32页 |
| 2.2.5 Genetic map construction and QTL mapping | 第32页 |
| 2.2.6 Regional association mapping | 第32页 |
| 2.2.7 Scanning electron microscopy (SEM) | 第32页 |
| 2.2.8 Ovule culture assay | 第32-33页 |
| 2.2.9 Measurement of total fiber units (TFU) | 第33-34页 |
| 2.2.10 Gene annotations prediction | 第34页 |
| 2.2.11 Digital expression analysis in Li_1 transcriptome | 第34-35页 |
| 2.2.12 RNA extraction and real-time PCR | 第35-36页 |
| 2.2.13 Cloning for structural variations in GhBRH1_A12 | 第36-37页 |
| 2.2.14 Shoot elongation and BL sensitivity assay | 第37页 |
| 2.2.15 Histological analysis | 第37-38页 |
| 2.3 Results | 第38-64页 |
| 2.3.1 Boll size variations between Emian22 and BS41 | 第38-40页 |
| 2.3.2 Phenotypic analysis of boll weight traits | 第40-41页 |
| 2.3.3 Detecting yield trait QTLs on chr12 | 第41-43页 |
| 2.3.4 qSCW-c12 identification, validation in different populations | 第43-46页 |
| 2.3.7 Fine mapping qSCW-c12 | 第46-48页 |
| 2.3.8 Refine mapping qSCW-c12 | 第48-49页 |
| 2.3.9 Homology mapping and candidate gene prediction | 第49-51页 |
| 2.3.10 Map-based cloning qSCW-c12 | 第51-53页 |
| 2.3.11 Candidate gene prediction based on their expression | 第53-54页 |
| 2.3.12 GhBRH1_A12 was differentially expressed in ODPA ovules | 第54-56页 |
| 2.3.13 GhBRH1_A12 involved in modulating BR homeostasis | 第56-58页 |
| 2.3.14 BS41 exhibited BR-deficient mutant like phenotype | 第58-59页 |
| 2.3.15 BS41, a novel BR-insensitive mutant | 第59-61页 |
| 2.3.16 BR insensitivity attenuated cell expansion in BS41 | 第61-62页 |
| 2.3.17 BS41 features quality fiber production | 第62-64页 |
| 2.4 Discussion | 第64-69页 |
| 2.4.1 BILs are valuable resource for fine mapping QTLs | 第64页 |
| 2.4.2 Boll size regulating QTLs on chr12 | 第64-65页 |
| 2.4.3 qSCW-c12 interval consistent with previously mapped QTLs | 第65-66页 |
| 2.4.4 GhBRH_A12, a new player in regulating Fiber initiation | 第66页 |
| 2.4.5 QTL qSCW-c12 is a pleiotropic locus | 第66-67页 |
| 2.4.6 GhBRH1_A12 involved in modulating BR homeostasis | 第67-68页 |
| 2.4.7 BS41, a novel boll size mutant producing quality fiber | 第68-69页 |
| 2.5 Conclusion | 第69-70页 |
| Chapter 03 Functional analysis of BRH1 gene family in cotton | 第70-90页 |
| 3.1 Introduction | 第70-72页 |
| 3.2 Material and methods | 第72-79页 |
| 3.2.1 Sequence retrieval, gene structure, and phylogenetic analysis | 第72页 |
| 3.2.2 Protein domain, motif, annotation, and GO analysis | 第72页 |
| 3.2.3 Prediction of transmembrane topology | 第72-73页 |
| 3.2.4 Expression profiling | 第73页 |
| 3.2.5 Digital expression analysis in Li_1 transcriptome | 第73页 |
| 3.2.6 Cloning for structural variations in GhBRH1_A12 | 第73-74页 |
| 3.2.7 Constructing overexpression vectors | 第74-75页 |
| 3.2.8 RNAi vector construction | 第75-76页 |
| 3.2.9 Genetic transformation and cotton tissue culture | 第76-77页 |
| 3.2.10 RNA extraction and qRT-PCR | 第77-78页 |
| 3.2.11 Phenotype evaluation and analysis | 第78-79页 |
| 3.3 Results | 第79-89页 |
| 3.3.1 Structure of BRH1 peptide | 第79页 |
| 3.3.2 Identification of putative BRH1 genes in four cotton genomes | 第79-81页 |
| 3.3.3 Phylogenetic analysis of cotton BRH1 genes | 第81-82页 |
| 3.3.4 Genetic diversity and evolution of GhBRH1 gene family | 第82页 |
| 3.3.5 Characteristics of GhBRH1 gene family | 第82-83页 |
| 3.3.6 Expression profiling of GhBRH1 genes in cultivated cotton | 第83-84页 |
| 3.3.7 GhBRH1 differentially expressed during fiber development | 第84-85页 |
| 3.3.8 Gene regulatory elements of GhBRH1_A12 in BS41 | 第85-86页 |
| 3.3.9 Genetic transformation of a GhBRH1_A12 in cotton | 第86-87页 |
| 3.3.10 GhBRH1_A12 expression in transgenic (T_0) plants | 第87-89页 |
| 3.4 Discussion | 第89-90页 |
| Chapter 04 Evolutionary dynamics of motif imperfection in cotton | 第90-114页 |
| 4.1 Introduction | 第90-92页 |
| 4.2 Material and methods | 第92-96页 |
| 4.2.1 Genome assemblies of 13 plant species | 第92页 |
| 4.2.2 Imperfect microsatellites identification | 第92-93页 |
| 4.2.3 Motif Imperfection and repeat length analyses | 第93-94页 |
| 4.2.4 Transposable elements (TEs)distribution | 第94页 |
| 4.2.5 Motif imperfection in coding region of Gossypium species | 第94页 |
| 4.2.6 Microsatellites conservation analysis | 第94-95页 |
| 4.2.7 Microsatellite loss during paleopolyploidization event | 第95-96页 |
| 4.3 Results | 第96-110页 |
| 4.3.1 Frequency and distribution of microsatellites | 第96-98页 |
| 4.3.2 Motif imperfection and repeat length relationship | 第98-101页 |
| 4.3.3 Motif imperfection in Gossypium genomes | 第101-103页 |
| 4.3.4 Motif interruptions in coding sequence | 第103-105页 |
| 4.3.5 Large motif repeats well conserved in Gossypium species | 第105-106页 |
| 4.3.6 Microsatellite decay estimation | 第106-108页 |
| 4.3.7 Biased distribution of 2nt repeats in Gossypium species | 第108-110页 |
| 4.4 Discussion | 第110-113页 |
| 4.5 Conclusion | 第113-114页 |
| References | 第114-133页 |
| Supplementary information | 第133-148页 |
| Publications | 第148-149页 |
| Acknowledgement | 第149-150页 |
| 附件 | 第150页 |
