声明
List of Abbreviations
Chapter 1INTRODUCTION
1.1 History of cotton crop
1.2 Crop domestication and selection
1.3 History upland cotton in China
1.4 Genetic diversity
1.5 Gossypium hirsutum purpurascens
1.6 Genome wide association studies (GWAS)
1.7 Justifications and objectives of this research
Chapter 2MATERIALS AND METHODS
2.1 Revisiting Gossypium hirsutum purpurascens
2.1.1 Plant material and field experiments
2.1.2 Yield and yield component evaluation
2.1.3 DNA extraction, sequencing, alignment, and SNP detection
2.1.4 Sequence quality checking and filtering
2.1.5 Sequence alignment
2.1.6 Annotation of genetic variants
2.1.7 Population stratification
2.1.8 Population genomics analyses
2.1.9 GWAS Analysis
2.1.10 Statistical analyses
2.1.11 Quantitative real-time PCR (qRT-PCR) analysis
2.2 Domestication and selection history of Chinese Upland cotton
2.2.1 Plant Material
2.2.2 DNA Extraction, Sequencing, Alignment and SNP Detection
2.2.3 Population Genetic Analyses
2.2.4 Identification of Selection/Improvement Signals
2.2.5 GWAS Analysis
Chapter 3Results
3.1 Revisiting Gossypium hirsutum purpurascens
3.1.1 Population stratification of Gossypium hirsutum purpurascens
3.1.2 Genetic differentiation between G. purpurascens and cultivated genotypes
3.1.3 Genetic differentiation between G. purpurascens and G. hirsutum landraces (Central American)
3.2 Domestication and selection history of upland cotton in China
3.2.1 Population classification and structure variations
3.2.2 Differentiation and Selection signals between MCl and OCl group
3.2.3 Differentiation and domestication between G. hirsutum landraces and cultivar groups
3.3 Genome Wide Association Studies (GWAS)
3.3.1 GWAS for flowering time and fiber quality
3.3.2 GWAS for fiber quality
3.3.3 GWAS for anther color
Chapter 4Discussion
4.1 G. purpurascens, a primitive landrace
4.2 Genetic differentiation and selection history in upland cotton
Chapter 5 Conclusions and Future perspectives
参考文献
Appendices
致谢
Curriculum Vitae
中国农业科学院;
