声明
List of Abbreviations
Chapter 1INTRODUCTION
1.1History of cotton crop
1.2Evolution of different cotton species
1.3Cytogenetics of cotton
1.3.1Old world cotton (2n=26)
1.3.2New world cotton (2n=52)
1.4General botany of cotton
1.5Current situation of cotton production
1.6Utilization of wild cotton progenitors for commercially growing cotton species
1.7High throughput sequencing and molecular studies
1.8Weighted Co-expression network analysis
1.9Major objectives and justification of this research
Chapter 2MATERIALS AND METHODS
2.1Plant material
2.2RNA Extraction, Illumina sequencing and library construction
2.3Analysis of Differentially Expressed Genes
2.4Quantification, Gene Ontology and KEGG pathways analysis
2.5Weighted Gene Co-expression Network Analysis
2.6Gene expression level Analysis (qRT-PCR)to validate RNA-seq data
Chapter 3Results
3.1Experiment 1
3.1.1Summary of transcriptome data
3.1.2Principal component analysis (PCA)
3.1.3Transcriptome changes during imbibed seed (glandless) and seedling (glanded)
3.1.4Functional annotation of differentially expressed genes
3.1.5Gene co-expression correlation network analysis
3.1.6Quantitative Real-Time PCR Validation of RNA-Seq Data
3.2Results for Experiment 2
3.2.1Summary of RNA-seq data
3.2.2Correlation and Principal component analysis of RNA-seq data
3.2.3Analysis of differentially expressed genes during glandless seed, glanded leaf and stem
3.2.4Gene Ontology and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of differentially expressed genes
3.2.5DEGs involved in Metabolic pathways, biosynthesis of secondary metabolites and biosynthesis of antibiotics
3.2.6Co-expression Networks reveals a differentialregulatorynetwork of metabolic, biosynthesis of secondary metabolites and biosynthesis of antibioticsonly transcription factorsselected genes.
3.2.7Quantitative Real-Time PCRof selected differentially expressed genes to Validate the RNA-Seq Data
Chapter 4Discussion
4.1Transcriptomic sequencing of glandless imbibed seed, glanded seed, leaf and stem to the reference genome G. Arboreum
4.2Comparison of Expression profiles,Differentially expressed genes (DEGs) RNA sequences
4.3Gene ontology (GO) and Kyoto Encyclopedia Genes and Genomes (KEGG) Pathways enrichment analysis
4.4Hub genes identification using weighted gene co-expression network analysis
Chapter 5 Conclusions and Future perspectives
参考文献
Appendices
致谢
Curriculum Vitae
中国农业科学院;
