不同含油量甘蓝型油菜种子和角果皮的动态比较转录组分析
发布时间：2024-11-22 16:28
植物油是人类饮食和工业应用可再生原料的重要组成部分。提高油料作物含油量是满足全球植物油供应需求的最可行、最环保、最可持续的途径。油菜(B.napus)是世界最重要的油料作物之一,占世界食用油供应的15%以上。深入了解油菜种子发育过程中油菜生物合成的基因网络是选育高油菜品种的前提。RNASeq被认为是一种检测低丰度转录本、鉴别生物关键亚型和识别遗传变异的先进技术。为了解油菜生物合成和油脂积累关键途径的动态调控,我们选用两个含油量差异13%的两个系对油菜种子和种皮组织发育进行了比较转录组学分析。我们共检测到62524个FPKM>1的基因在两个系的种子和种皮组织中表达。MapMan对这些基因分析表明,光合作用,碳水化合物代谢,脂质代谢和转运的差异基因大部分在高含油量材料中(HOCL)表现为上调,而降解、氨基酸代谢、蛋白质和次生代谢大部分在低含油量材料中(LOCL)表现为上调.结果表明,在种子和种皮发育的6个关键阶段,HOCL和LOCL之间共鉴定到差异表达基因(DEGs)3288个。基因富集分析表明,HOCL中与光合作用、代谢、碳水化合物、脂质、植物激素、转运体、三酰甘油和脂肪酸合成相关的...
【文章页数】：153 页
【学位级别】：博士
【文章目录】：
ABSTRACT
摘要
Abbreviations
1.REVIEW OF LITERATURE
1.1 General Introduction
1.2 The Economic Importance of Brassica napus Crop
1.3 Oil Yield Potential in B.napus
1.4 Central Metabolism in Developing Seed
1.5 Oil Biosynthesis
1.5.1 Fatty Acid Synthesis
1.5.2 Triacylglycerol Assembly
1.5.3 Triacylglycerol Storage
1.6 Role of Silique Wall in Oil Biosynthesis
1.7 Enhancement of Oil Production by Improving Photosynthesis
1.8 Acyl-Lipid Metabolism Genes and Their Expression Dynamics
1.9 Transcriptional Regulation in Lipid Accumulation
1.10 Negative Regulators of Oil Biosynthesis
1.11 FAs and TAG Degradation
1.12 Oil Associated Quantitative Trait Loci
1.13 Aims and Objectives
2.MATERIALS AND METHODS
2.1 Plant Material
2.2 Total RNA Extraction
2.3 c DNA Library Construction and Sequencing
2.4 Quality Control
2.5 Reads Mapping to Reference Genome
2.6 Differential Gene Expression Quantification
2.7 MapMan Analysis
2.8 Gene Ontology and Enrichment Analysis
2.9 KEGG and PANTHER Classification of DEGs
2.10 Oil Content Quantification
2.11 Carbohydrates Analysis
2.12 Hormones Quantification
2.13 Validation of RNA-Seq Data by qRT-PCR Assay
2.14 Mapping of DEGs to Oil QTLs
2.15 Acyl-lipid Metabolism Genes Expression Validation in Multiple NILs of Brassica napus by qRT-PCR
2.16 Statistical Analysis
3.RESULTS AND ANALYSIS
3.1 Dynamics of Oil Accumulation in HOC and LOC Lines
3.2 RNA-Sequencing and Gene Expression Quantification Analysis
3.2.1 RNA-Sequencing Data Statistics
3.2.2 Gene Expression Quantification
3.3 Expression Patterns of Genes Involved in Metabolic Pathways in High-and Low-Oil Content Lines
3.3.1 MapMan Classification of Expressed Genes in Seed
3.3.2 MapMan Classification of Expressed Genes in Silique Wall
3.4 Comparative Transcriptomic Dynamics During Oil Accumulation Between High-and Low-Oil Lines
3.4.1 Differentially Expressed Genes
3.4.2 Up-and Down-Regulation of DEGs
3.4.3 Protein Classes Enriched by DEGs
3.5 qRT-PCR Analysis of Selected DEGs to Validates the RNA-Seq Results
3.6 DEGs Co-Expression Clustering
3.7 Functional Classifications of DEGs
3.8 Identification of Up-and Down-Regulated Pathways in Seed and SW
3.9 Mapping of DEGs to Oil QTLs
3.9.1 Acyl-Lipid Metabolism DEGs
3.9.2 Transcription Factors DEGs
3.10 Verification of Putative Candidate ALM Genes in B.napus NILs with Contrasting Oil Contents
3.11 An Alternative Approach to Assess the Dynamics of Gene Expression Along the Development
3.11.1 Relative Differentially Expressed Genes Identification
3.11.2 Expression Dynamics of RDEGs
3.11.3 Functional Classification of RDEGs
3.12 Quantification of Carbohydrates Dynamics in Seed and Silique Wall Tissues of HOCL and LOCL
3.13 Quantification of Hormones Dynamics in Seed and Silique Wall Tissues of HOCL and LOCL
3.14 Functional Characterization of Candidate Genes by Arabidopsis Mutants Analysis
3.14.1 Plant Material
3.14.2 Arabidopsis Mutants Verification
3.14.3 Oil Content Quantification of Arabidopsis Mutant Seed
4.DISCUSSION
4.1 RNA-Sequencing Can Differentiate the Expression Variation of Homologous Genes in Brassica napus
4.2 Expression Dynamics of Genes Involved in Oil Biosynthesis
4.3 Co-expression of ALM and Stress-Related Genes
4.4 Carbohydrates Play Vital Role in Oil Biosynthesis
4.5 Regulatory Loop Between the Hormone Signalling and Oil Biosynthesis
4.6 This Study Validates the Previously Identified Oil QTLs
4.7 Future Prospects
5.SUMMARY
REFERENCES
APPENDIXES
Appendix A.Study Source and Supporting Projects
Appendix B.List of Primers Used in this Study
Appendix B-1.List of Primers Used for qRT-PCR Assays
Appendix B-2.List of Primers Used for Arabidopsis thaliana Mutant Verification
Appendix C.Significantly Enriched GO Categories by DEGs
Appendix C-1.List of Significantly Enriched GO Categories by Seed DEGs
Appendix C-2.List of Significantly Enriched GO Categories by SW DEGs
Appendix C-3.List of Enriched GO Categories by Seed and SW DEGs Corresponding to a Specific Stage
Appendix D.Lists of Putative Candidate Genes
Appendix D-1.A List of75 ALM Genes Found Differentially Expressed Among HOCL and LOCL
Appendix D-2.A List of42 Transcription factors(TFs)Found Differentially Expressed Among HOCL and LOCL
Appendix D-3.A List of JA,ABA,and Auxin Genes which are Differentially Expressed Among HOCL and LOCL
Appendix E.List of Publications
ACKNOWLEDGEMENTS
本文编号：4012482
【文章页数】：153 页
【学位级别】：博士
【文章目录】：
ABSTRACT
摘要
Abbreviations
1.REVIEW OF LITERATURE
1.1 General Introduction
1.2 The Economic Importance of Brassica napus Crop
1.3 Oil Yield Potential in B.napus
1.4 Central Metabolism in Developing Seed
1.5 Oil Biosynthesis
1.5.1 Fatty Acid Synthesis
1.5.2 Triacylglycerol Assembly
1.5.3 Triacylglycerol Storage
1.6 Role of Silique Wall in Oil Biosynthesis
1.7 Enhancement of Oil Production by Improving Photosynthesis
1.8 Acyl-Lipid Metabolism Genes and Their Expression Dynamics
1.9 Transcriptional Regulation in Lipid Accumulation
1.10 Negative Regulators of Oil Biosynthesis
1.11 FAs and TAG Degradation
1.12 Oil Associated Quantitative Trait Loci
1.13 Aims and Objectives
2.MATERIALS AND METHODS
2.1 Plant Material
2.2 Total RNA Extraction
2.3 c DNA Library Construction and Sequencing
2.4 Quality Control
2.5 Reads Mapping to Reference Genome
2.6 Differential Gene Expression Quantification
2.7 MapMan Analysis
2.8 Gene Ontology and Enrichment Analysis
2.9 KEGG and PANTHER Classification of DEGs
2.10 Oil Content Quantification
2.11 Carbohydrates Analysis
2.12 Hormones Quantification
2.13 Validation of RNA-Seq Data by qRT-PCR Assay
2.14 Mapping of DEGs to Oil QTLs
2.15 Acyl-lipid Metabolism Genes Expression Validation in Multiple NILs of Brassica napus by qRT-PCR
2.16 Statistical Analysis
3.RESULTS AND ANALYSIS
3.1 Dynamics of Oil Accumulation in HOC and LOC Lines
3.2 RNA-Sequencing and Gene Expression Quantification Analysis
3.2.1 RNA-Sequencing Data Statistics
3.2.2 Gene Expression Quantification
3.3 Expression Patterns of Genes Involved in Metabolic Pathways in High-and Low-Oil Content Lines
3.3.1 MapMan Classification of Expressed Genes in Seed
3.3.2 MapMan Classification of Expressed Genes in Silique Wall
3.4 Comparative Transcriptomic Dynamics During Oil Accumulation Between High-and Low-Oil Lines
3.4.1 Differentially Expressed Genes
3.4.2 Up-and Down-Regulation of DEGs
3.4.3 Protein Classes Enriched by DEGs
3.5 qRT-PCR Analysis of Selected DEGs to Validates the RNA-Seq Results
3.6 DEGs Co-Expression Clustering
3.7 Functional Classifications of DEGs
3.8 Identification of Up-and Down-Regulated Pathways in Seed and SW
3.9 Mapping of DEGs to Oil QTLs
3.9.1 Acyl-Lipid Metabolism DEGs
3.9.2 Transcription Factors DEGs
3.10 Verification of Putative Candidate ALM Genes in B.napus NILs with Contrasting Oil Contents
3.11 An Alternative Approach to Assess the Dynamics of Gene Expression Along the Development
3.11.1 Relative Differentially Expressed Genes Identification
3.11.2 Expression Dynamics of RDEGs
3.11.3 Functional Classification of RDEGs
3.12 Quantification of Carbohydrates Dynamics in Seed and Silique Wall Tissues of HOCL and LOCL
3.13 Quantification of Hormones Dynamics in Seed and Silique Wall Tissues of HOCL and LOCL
3.14 Functional Characterization of Candidate Genes by Arabidopsis Mutants Analysis
3.14.1 Plant Material
3.14.2 Arabidopsis Mutants Verification
3.14.3 Oil Content Quantification of Arabidopsis Mutant Seed
4.DISCUSSION
4.1 RNA-Sequencing Can Differentiate the Expression Variation of Homologous Genes in Brassica napus
4.2 Expression Dynamics of Genes Involved in Oil Biosynthesis
4.3 Co-expression of ALM and Stress-Related Genes
4.4 Carbohydrates Play Vital Role in Oil Biosynthesis
4.5 Regulatory Loop Between the Hormone Signalling and Oil Biosynthesis
4.6 This Study Validates the Previously Identified Oil QTLs
4.7 Future Prospects
5.SUMMARY
REFERENCES
APPENDIXES
Appendix A.Study Source and Supporting Projects
Appendix B.List of Primers Used in this Study
Appendix B-1.List of Primers Used for qRT-PCR Assays
Appendix B-2.List of Primers Used for Arabidopsis thaliana Mutant Verification
Appendix C.Significantly Enriched GO Categories by DEGs
Appendix C-1.List of Significantly Enriched GO Categories by Seed DEGs
Appendix C-2.List of Significantly Enriched GO Categories by SW DEGs
Appendix C-3.List of Enriched GO Categories by Seed and SW DEGs Corresponding to a Specific Stage
Appendix D.Lists of Putative Candidate Genes
Appendix D-1.A List of75 ALM Genes Found Differentially Expressed Among HOCL and LOCL
Appendix D-2.A List of42 Transcription factors(TFs)Found Differentially Expressed Among HOCL and LOCL
Appendix D-3.A List of JA,ABA,and Auxin Genes which are Differentially Expressed Among HOCL and LOCL
Appendix E.List of Publications
ACKNOWLEDGEMENTS
本文编号：4012482
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