比较转录组分析鉴定比克氏棉色素腺体延缓发生相关基因
发布时间：2022-08-23 10:58
棉花属于锦葵科棉属植物,植物学上称为陆地棉。棉花是主要的工业作物之一,可以提供天然纤维和工业用油。棉花常被称为“白金”,因为作为主要的国际商品之一,棉花产量的多少与全球的纺织品消费相匹配。澳洲野生棉具有种子无腺体性状,而种子萌发后幼苗、茎和叶都转变为有腺体。比克氏棉属于澳洲野生棉,它的种子是无腺体,但是植株的其它部分有腺体。本研究旨在探索比克氏棉种子色素腺体延缓发生的机制。总共构建了21个RNA-seq文库,分别来源于两部分实验的12个样品和9个样品。第一部分实验我们比对了比克氏棉无腺体种子和亚洲棉有腺体种子,以及比克氏棉和亚洲棉的有腺体子苗。第二部分实验包括比克氏棉无腺体的胚珠和有腺体茎和叶。高通量测序技术用以分析和鉴定这些棉花材料种子和子苗里腺体相关基因的表达模式。所有21个样品包含3个生物学重复,两部分实验分别获得了131.33Gb和63.93Gb原始数据。从上述数据中总共获得了7176和2153个差异表达基因。第一部分实验筛选到7196个差异表达基因（DEGs）包含3716个上调表达基因和3480个下调表达基因,第二部分2153个差异表达基因（DEGs）包含1176个上调表达基...
【文章页数】：86 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[1]权重基因共表达网络分析在生物医学中的应用[J]. 刘伟,李立,叶桦,屠伟. 生物工程学报. 2017(11)
[2]Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis[J]. Kai Shi,Zhi-Tong Bing,Gui-Qun Cao,Ling Guo,Ya-Na Cao,Hai-Ou Jiang,Mei-Xia Zhang. International Journal of Ophthalmology. 2015(02)
[3]我国棉花产业形势分析与发展策略[J]. 杨红旗,崔卫国. 作物杂志. 2010(05)
[4]种子低酚、植株有酚的棉花新品种[J]. 张雪林,金林,张天真. 中国农业科学. 2001(05)
[5]Inheritance of the delayed gland morphogenesis trait in Australian wild species of Gossypium[J]. ZHU Shuijin ＆ Jl DaofanCollege of Agriculture and Biotechnology, Zhejiang University, Hang-zhou 310029, China (e-mail: shjzhu@zju. edu.cn). Chinese Science Bulletin. 2001(14)
[6]棉花亲本遗传距离与杂种优势间的相关性研究[J]. 王学德,潘家驹. 作物学报. 1990(01)
[7]亚洲棉与比克氏棉杂交的研究[J]. 李炳林,张伯静,张新润,牛永章. 遗传学报. 1987(02)
本文编号：3677641
【文章页数】：86 页
【学位级别】：博士
【文章目录】：
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
【参考文献】：
期刊论文
[1]权重基因共表达网络分析在生物医学中的应用[J]. 刘伟,李立,叶桦,屠伟. 生物工程学报. 2017(11)
[2]Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis[J]. Kai Shi,Zhi-Tong Bing,Gui-Qun Cao,Ling Guo,Ya-Na Cao,Hai-Ou Jiang,Mei-Xia Zhang. International Journal of Ophthalmology. 2015(02)
[3]我国棉花产业形势分析与发展策略[J]. 杨红旗,崔卫国. 作物杂志. 2010(05)
[4]种子低酚、植株有酚的棉花新品种[J]. 张雪林,金林,张天真. 中国农业科学. 2001(05)
[5]Inheritance of the delayed gland morphogenesis trait in Australian wild species of Gossypium[J]. ZHU Shuijin ＆ Jl DaofanCollege of Agriculture and Biotechnology, Zhejiang University, Hang-zhou 310029, China (e-mail: shjzhu@zju. edu.cn). Chinese Science Bulletin. 2001(14)
[6]棉花亲本遗传距离与杂种优势间的相关性研究[J]. 王学德,潘家驹. 作物学报. 1990(01)
[7]亚洲棉与比克氏棉杂交的研究[J]. 李炳林,张伯静,张新润,牛永章. 遗传学报. 1987(02)
本文编号：3677641
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