| Acknowledgements | 第8-9页 |
| Contents | 第9-12页 |
| List of abbreviations | 第12-13页 |
| Abstract | 第13-15页 |
| 摘要 | 第16-18页 |
| 1 General introduction | 第18-26页 |
| 1.1 Origin of cotton cultivation | 第18-19页 |
| 1.2 Cotton growth cycle | 第19-20页 |
| 1.3 Types of commercially cultivated cotton | 第20-21页 |
| 1.4 World production of cptton | 第21-22页 |
| 1.5 Uses of cotton | 第22页 |
| 1.6 Cottonseed germplasm resources and variation | 第22-23页 |
| 1.7 Progress in cottonseed breeding | 第23-24页 |
| 1.8 The application of nir spectroscopy to plant breeding | 第24-25页 |
| 1.9 Objectives of the present study | 第25-26页 |
| 2 Literature review | 第26-64页 |
| 2.1 Characteristics of seed quality traits | 第26页 |
| 2.2 Seed quality traits and inheritance in oilseed plants | 第26-27页 |
| 2.3 Oil quality | 第27页 |
| 2.4 Fatty acids | 第27-34页 |
| 2.4.1 Classification of fatty acids | 第28-29页 |
| 2.4.1.1 Unsaturated fatty acids | 第28-29页 |
| 2.4.1.2 Saturated fatty acids | 第29页 |
| 2.4.2 Fatty acids in cottonseed | 第29-31页 |
| 2.4.2.1 Palmitic acid (c16:0) | 第29-30页 |
| 2.4.2.2 Oleic acid (c18:1) | 第30页 |
| 2.4.2.3 Linoleic acid (c18:2) | 第30页 |
| 2.4.2.4 Linolenic acid (c18:3) | 第30-31页 |
| 2.4.2.5 Eicosenoic acid (c20:1) | 第31页 |
| 2.4.3 The fatty acid biosynthetic pathway | 第31-32页 |
| 2.4.4 The pathway to oil accumulation in seed | 第32-33页 |
| 2.4.5 Nutritional and health implications of fatty acids | 第33-34页 |
| 2.5 Chemical analysis of oil and fatty acid contents | 第34-35页 |
| 2.6 Near infrared reflectance spectroscopy (NIRS) and its application | 第35-53页 |
| 2.6.1 The origin and characteristics of nirs | 第36页 |
| 2.6.2 The theoretical basis of nirs quantitative analysis | 第36-42页 |
| 2.6.2.1 The classical mechanical model for a diatomic molecule | 第38-39页 |
| 2.6.2.2 Limitations of the harmonic model | 第39-40页 |
| 2.6.2.3 The anharmonic model | 第40-41页 |
| 2.6.2.4 Dipole moment | 第41-42页 |
| 2.6.3 Using NIRS for measurement | 第42-43页 |
| 2.6.4 NIRS instrumentation:spectrophotometers | 第43-44页 |
| 2.6.4.1 Sample compartment | 第43页 |
| 2.6.4.2 Light sources | 第43页 |
| 2.6.4.3 Wavelength selection | 第43-44页 |
| 2.6.4.4 Detectors | 第44页 |
| 2.6.5 Data analysis and calibration development | 第44-48页 |
| 2.6.5.1 The pre-treatment of NIR spectral data | 第45-46页 |
| 2.6.5.2 Multiplicative scatter correction | 第46页 |
| 2.6.5.3 Standard normal variance and detrending | 第46页 |
| 2.6.5.4 Derivatives | 第46-48页 |
| 2.6.5.5 Measurement of calibration model performance | 第48页 |
| 2.6.5.6 Over-fitting | 第48页 |
| 2.6.6 Population definition | 第48-49页 |
| 2.6.6.1 Variability of sample-population | 第48-49页 |
| 2.6.6.2 Compensation of temperature | 第49页 |
| 2.6.6.3 Robustness of a calibration model | 第49页 |
| 2.6.7 Qualitative analysis | 第49-50页 |
| 2.6.8 Development of a calibration model | 第50页 |
| 2.6.9 Model validation | 第50-51页 |
| 2.6.10 Establishment of the workflow of NIR spectroscopy measurement and calibration | 第51页 |
| 2.6.11 Advantages and limitations of NIR spectroscopy | 第51-52页 |
| 2.6.11.1 Advantages of NIR spectroscopy | 第51-52页 |
| 2.6.11.2 Limitations of NIR spectroscopy | 第52页 |
| 2.6.12 Features of NIRS application to agricultural products | 第52-53页 |
| 2.7 Genetics of cottonseed quality traits | 第53-64页 |
| 2.7.1 Gene expression for quality traits in cottonseed | 第53页 |
| 2.7.2 Genetic variability in cottonseed | 第53-54页 |
| 2.7.3 Cotton fatty acid content and nutrition quality | 第54-55页 |
| 2.7.4 Construction of genetic map | 第55-64页 |
| 2.7.4.1 Molecular markers | 第56页 |
| 2.7.4.2 Types of molecular markers | 第56-58页 |
| 2.7.4.2.1 Restriction fragments length polymorphism (RFLP) | 第57页 |
| 2.7.4.2.2 Microsatellites (simple sequence repeats or SSR) | 第57页 |
| 2.7.4.2.3 Amplified frangment length polymorphisms (AFLP) | 第57-58页 |
| 2.7.4.3 Application of molecular markers to cotton research | 第58页 |
| 2.7.4.4 Progress in mapping the cotton genome | 第58-59页 |
| 2.7.4.5 QTL mapping for seed quality traits | 第59-60页 |
| 2.7.4.6 The principle and method of QTL location | 第60页 |
| 2.7.4.7 Statistical methods for QTL mapping | 第60-62页 |
| 2.7.4.7.1 Single marker approach | 第61页 |
| 2.7.4.7.2 Simple interval mapping | 第61页 |
| 2.7.4.7.3 Composite interval mapping method (CIM) | 第61-62页 |
| 2.7.4.7.4 Multiple interval mapping (MIM) | 第62页 |
| 2.7.4.7.5 Mixed linear model based composite interval mapping | 第62页 |
| 2.7.4.8 Applications of QTL information | 第62-64页 |
| 3 Materials and methods | 第64-82页 |
| 3.1 Experiment materials | 第64页 |
| 3.2 Field experiments | 第64页 |
| 3.3 Analysis of oil and fatty acid contents of samples | 第64-72页 |
| 3.3.1 Sample preparation | 第65页 |
| 3.3.2 Reference methods | 第65-66页 |
| 3.3.2.1 Oil extraction and fatty acid determination | 第65页 |
| 3.3.2.2 Gas liquid chromatography | 第65-66页 |
| 3.3.3 NIRS determination of oil and fatty acid contents in cottonseed kernel | 第66-72页 |
| 3.3.3.1 WinISI Ⅱ calibration software | 第66页 |
| 3.3.3.2 Spectral data collection | 第66-67页 |
| 3.3.3.3 Definition of calibration and validation sets | 第67页 |
| 3.3.3.4 Principal component analysis | 第67-68页 |
| 3.3.3.5 Spectral signal pre-treatment and calibration | 第68-69页 |
| 3.3.3.6 Measurement of calibration model performance | 第69-72页 |
| 3.4 Linkage map for QTL mapping | 第72页 |
| 3.5 Data analysis and QTL mapping software | 第72-78页 |
| 3.6 Characteristics of upland cotton interspecific RIL linkage map | 第78页 |
| 3.7 Likelihood analysis | 第78-79页 |
| 3.8 Hypothesis tests/permutation tests | 第79页 |
| 3.9 Parameter setting | 第79页 |
| 3.10 QTL mapping data | 第79-80页 |
| 3.11 QTL mapping | 第80-82页 |
| 3.11.1 Mixed linear model-based composite interval mapping | 第80-82页 |
| 4 Results | 第82-98页 |
| 4.1 NIRS analysis of oil and fatty acid content in cottonseed | 第82-91页 |
| 4.1.1 Variability for oil content and fatty acid composition | 第82-83页 |
| 4.1.2 Selection of spectral pre-treatment method | 第83-85页 |
| 4.1.3 Calibration | 第85-86页 |
| 4.1.4 External validation | 第86-91页 |
| 4.2 Analysis of QTL related to oil and fatty acid content in cottonseed kernel | 第91-98页 |
| 4.2.1 Phenotypic analysis of oil content in the parents and IF_2 populations | 第91-94页 |
| 4.2.2 QTL analysis for oil and fatty acid contents | 第94页 |
| 4.2.3 Genetic effects on QTL controlling cottonseed oil content | 第94-95页 |
| 4.2.4 Genetic systems controlling fatty acids in cotton seed kernel | 第95-98页 |
| 5 Discussions | 第98-101页 |
| 5.1 Variability for oil content and fatty acid composition | 第98页 |
| 5.2 NIRS analysis of samples | 第98页 |
| 5.3 Analysis of QTL related to oil and fatty acid content in cottonseed kernel | 第98-101页 |
| 5.3.1 Effects of genetic systems controlling oil and fatty acid contents in cottonseed | 第99-101页 |
| 6 Conclusion and future recommendtions | 第101-102页 |
| 7 References | 第102-120页 |
| 8 List of publications | 第120页 |
