棉花屬于錦葵科棉屬植物,植物學上稱為陸地棉。棉花是主要的工業(yè)作物之一,可以提供天然纖維和工業(yè)用油。棉花常被稱為“白金”,因為作為主要的國際商品之一,棉花產量的多少與全球的紡織品消費相匹配。澳洲野生棉具有種子無腺體性狀,而種子萌發(fā)后幼苗、莖和葉都轉變?yōu)橛邢袤w。比克氏棉屬于澳洲野生棉,它的種子是無腺體,但是植株的其它部分有腺體。本研究旨在探索比克氏棉種子色素腺體延緩發(fā)生的機制。總共構建了21個RNA-seq文庫,分別來源于兩部分實驗的12個樣品和9個樣品。第一部分實驗我們比對了比克氏棉無腺體種子和亞洲棉有腺體種子,以及比克氏棉和亞洲棉的有腺體子苗。第二部分實驗包括比克氏棉無腺體的胚珠和有腺體莖和葉。高通量測序技術用以分析和鑒定這些棉花材料種子和子苗里腺體相關基因的表達模式。所有21個樣品包含3個生物學重復,兩部分實驗分別獲得了131.33Gb和63.93Gb原始數(shù)據(jù)。從上述數(shù)據(jù)中總共獲得了7176和2153個差異表達基因。第一部分實驗篩選到7196個差異表達基因（DEGs）包含3716個上調表達基因和3480個下調表達基因,第二部分2153個差異表達基因（DEGs）包含1176個上調表達基... 

【文章頁數(shù)】：86 頁

【學位級別】：博士

【文章目錄】：
摘要
Abstract
List of Abbreviations
Chapter1 INTRODUCTION
    1.1 History of cotton crop
    1.2 Evolution of different cotton species
    1.3 Cytogenetics of cotton
        1.3.1 Old world cotton(2n=26)
        1.3.2 New world cotton(2n=52)
    1.4 General botany of cotton
    1.5 Current situation of cotton production
    1.6 Utilization of wild cotton progenitors for commercially growing cotton species
    1.7 High throughput sequencing and molecular studies
    1.8 Weighted Co-expression network analysis
    1.9 Major objectives and justification of this research
Chapter2 MATERIALS AND METHODS
    2.1 Plant material
    2.2 RNA Extraction,Illumina sequencing and library construction
    2.3 Analysis of Differentially Expressed Genes
    2.4 Quantification,Gene Ontology and KEGG pathways analysis
    2.5 Weighted Gene Co-expression Network Analysis
    2.6 Gene expression level Analysis(q RT-PCR)to validate RNA-seq data
Chapter3 Results
    3.1 Experiment 1
        3.1.1 Summary of transcriptome data
        3.1.2 Principal component analysis(PCA)
        3.1.3 Transcriptome changes during imbibed seed(glandless)and seedling(glanded)
        3.1.4 Functional annotation of differentially expressed genes
        3.1.5 Gene co-expression correlation network analysis
        3.1.6 Quantitative Real-Time PCR Validation of RNA-Seq Data
    3.2 Results for Experiment 2
        3.2.1 Summary of RNA-seq data
        3.2.2 Correlation and Principal component analysis of RNA-seq data
        3.2.3 Analysis of differentially expressed genes during glandless seed,glanded leaf and stem
        3.2.4 Gene Ontology and Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis of differentially expressed genes
        3.2.5 DEGs involved in Metabolic pathways,biosynthesis of secondary metabolites and biosynthesis of antibiotics
        3.2.6 Co-expression Networks reveals a differential regulatory network of metabolic,biosynthesis of secondary metabolites and biosynthesis of antibiotics only transcription factors selected genes
        3.2.7 Quantitative Real-Time PCR of selected differentially expressed genes to Validate the RNA-Seq Data
Chapter4 Discussion
    4.1 Transcriptomic sequencing of glandless imbibed seed,glanded seed,leaf and stem to the reference genome G.Arboreum
    4.2 Comparison of Expression profiles,Differentially expressed genes(DEGs)RNA sequences
    4.3 Gene ontology(GO)and Kyoto Encyclopedia Genes and Genomes(KEGG)Pathways enrichment analysis
    4.4 Hub genes identification using weighted gene co-expression network analysis
Chapter5 Conclusions and Future perspectives
References
Appendices
Acknowledgements
Curriculum Vitae


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