玉米响应盐胁迫的比较转录组学分析与植物耐盐机制研究
发布时间：2023-10-29 10:55
土壤盐渍化是严重影响全球农业的主要环境因素之一,提高作物的耐盐性已成为现代农业生产亟待解决的问题。深入理解植物耐盐的机制,鉴定和挖掘耐盐基因有助于培育耐盐植物新品种。盐胁迫条件下转录组水平的研究对于揭示植物耐盐机理具有十分重要的意义。天塔5是一代高产抗逆玉米杂交种。盐胁迫条件下,生理生化分析表明,天塔5极耐盐,其各项耐盐及生理指标均优于其亲本(母本HOO-108耐盐、父本825盐敏感)。为研究其杂种优势的耐盐表现机制,本研究利用高通量测序技术对天塔5及其父母本进行比较转录组学分析。结果表明,盐胁迫条件下共检测到26112个基因,其中5084个基因在天塔5及其父母本间差异表达。GO功能分析表明差异表达基因在细胞质囊泡、有机酸生物合成和代谢、离子结合与跨膜转运、氧化还原酶反应等过程显著富集。差异表达基因显著富集的代谢通路主要有苯丙素生物合成、类黄酮生物合成、亚麻酸代谢以及植物-病原互作等。鉴于转录因子对基因表达调控的重要作用,本研究进一步比较分析了耐盐性具有显著差异的两个玉米品系(天塔5号和825)中所有转录因子的表达情况。一系列转录因子家族在玉米响应盐胁迫过程中具有不同的表达模式,包括N...
【文章页数】：191 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
CHAPTER ONE: LITTERATURE REVIEW
1.1 Impact of salt stress in plants
1.1.1 Effects of salt stress on plant growth
1.1.2 Salinity and ionic toxicity
1.1.3 Effects of salt stress on plant photosynthesis
1.1.4 Salinity and oxidative stress
1.2 Plants response to stress
1.3 The regulation mechanism of plant response to stress
1.3.1 Sensory mechanisms of salt stress and signal transduction
1.3.2 Gene regulation of plants in response to salt stress
1.3.3 Gene expression profiles of plant response to salt stress
1.4 Biology of plant salt tolerance
1.4.1 Halophytes and the natural mechanisms for salt tolerance
1.4.2 Alters in plant hormone levels
1.4.3 Accumulation of compatible solutes
1.5 Heterosis and plant stress tolerance
1.5.1 Heterosis
1.5.2 Research progress of heterosis
1.5.3 Maize stress tolerance and heterosis
1.6 The research progress of L. Chinense
1.6.1 Advance of research in L. Chinense
1.6.2 L. Chinense and salt stress
1.6.3 Carotenoids biosynthesis in plants
1.7 Transcription factorsand regulation of genes expression
1.7.1 NAC TFs
1.7.2 bZIP TFs
1.7.3 WRKY TFs
1.7.4 MYB TFs
1.7.5 bHLH TFs
1.7.6 HSF TFs
1.8 Research objective and significance of this thesis
1.8.1 Comparative transcriptome analysis of maize Tianta5 and its parentsunder salt stress condition
1.8.2 De novo transcriptome analysis of L. chinense and identification andcharacterization of important functional genes
CHAPTER TWO: COMPARATIVE TRANSCRIPTOME ANALYSIS OFMAIZE RESPONSE TO SALT STRESS
2.1 Materials and methods
2.1.1 Maize materials
2.1.2 Evaluation of salt tolerance of the maize varieties
2.1.3 High throughput RNA sequencing
2.1.4 Data processing and analysis
2.1.5 Sequencing quality assessment
2.1.6 Gene expression annotation
2.1.7 Gene Ontology Functional Enrichment Analysis for DEGs
2.1.8 KEGG Pathway analysis
2.1.9 Quantitative real-time PCR Verification of the transcriptional data
2.2 Results
2.2.1 Evaluation of salt tolerance of Tianta5 and its inbred parents
2.2.2 Sequencing quality assessment
2.2.3 Transcriptome analysis of F1 hybrid and its parents
2.2.4 Identification and Characterization of the DEGs
2.2.5 Clustering analysis of the DEGs
2.2.6 Gene Ontology Functional Enrichment Analysis for DEGs
2.2.7 KEGG pathway analysis of DEGs
2.3 Discussion
2.3.1 Salt treatment
2.3.2 Salt stress related GO terms analysis of the DEGs
2.3.3 Salt stress related pathway analysis of these DEG
2.3.4 Heterosis related genes analysis
2.4 Summary
CHAPTER THREE: DE NOVO CHARACTERIZATION OF LYCIUMCHINENSE MILL. LEAF TRANSCRIPTOME
3.1 Materials and methods
3.1.1 Plant materials and RNA isolation
3.1.2 Illumina sequencing and de novo assembly
3.1.3 Sequence annotation
3.1.4 Gene expression levels analysis
3.1.5 Identification of TF genes in L.chinense
3.1.6 Identification of L. chinense unigenes related to carotenoidbiosynthesis
3.1.7 qRT-PCR analysis of L. chinense genes involved in carotenoidbiosynthesis
3.1.8 Carotenoid extraction and HPLC
3.2 Results
3.2.1 Illumina sequencing and de novo assembly
3.2.2 Annotation and classification of L. chinense unigenes
3.2.3 GO classification
3.2.4 COG classification
3.2.5 KEGG pathway mapping
3.2.6 Identification of TF genes in L. chinense
3.2.7 Gene expression levels analysis
3.2.8 Genes related to salt tolerance/stress
3.2.9 Analysis of genes involved in carotenoid biosynthesis pathway
3.2.10 Analysis of carotenoid contents in leaf and ripening fruit of L. chinense
3.3 Discussion
3.3.1 Plant samples selected for RNA sequencing
3.3.2 RNA-seq and de novo assembly
3.3.3 Analysis of TF genes in L. chinense
3.3.4 Salt tolerance related genes in L. chinense
3.4 Summary
CHAPTER FOUR: ANALYSIS OF TRANSCRIPTION FACTOR GENES INMAIZE UNDER SALT STRESS CONDITIONS
4.1 Materials and methods
4.1.1 Plant materials and salt stress treatments
4.1.2 Evaluation of salt tolerance in the maize varieties
4.1.3 Transcriptome analysis of TF genes and salt-responsive genes
4.1.4 Phylogenetic tree construction of HSFs and protein interactionnetworks analysis
4.1.5 RNA extraction and qRT-PCR analysis
4.2 Results
4.2.1 Evaluation of salt tolerance of the two maize varieties
4.2.2 Identification of TF genes and expression analysis
4.2.3 Expression profiles of the TF genes under salt stress conditions
4.2.4 Identification of salt-stress responsive genes and TFs
4.2.5 Phylogenetic analysis of HSF family and protein interaction networkanalysis
4.2.6 Expression analysis of HSF genes under salt stress conditions
4.3 Discussion
4.3.1 Characterization of expression profiles of TFs in response to saltstress
4.3.2 Salt-stress responsive genes and salt-tolerant genes
4.3.3 Critical TFs in plant response to salt stress
4.3.4 HSFs and their expression pattern in response to salt stress and theirpotential roles in maize salt tolerance
4.4 Summary
CHAPTER FIVE: CONCLUSION AND FUTURE PROSPECTS
5.1 Conclusion
5.2 Innovation
5.3 Future prospects and Concerns
REFERENCES
ADDITIONAL FILES
PAPER PUBLICATION AND SCIENTIFIC RESEARCH PROJECTS
ACKNOWLEDGEMENT
本文编号：3857938
【文章页数】：191 页
【学位级别】：博士
【文章目录】：
摘要
ABSTRACT
CHAPTER ONE: LITTERATURE REVIEW
1.1 Impact of salt stress in plants
1.1.1 Effects of salt stress on plant growth
1.1.2 Salinity and ionic toxicity
1.1.3 Effects of salt stress on plant photosynthesis
1.1.4 Salinity and oxidative stress
1.2 Plants response to stress
1.3 The regulation mechanism of plant response to stress
1.3.1 Sensory mechanisms of salt stress and signal transduction
1.3.2 Gene regulation of plants in response to salt stress
1.3.3 Gene expression profiles of plant response to salt stress
1.4 Biology of plant salt tolerance
1.4.1 Halophytes and the natural mechanisms for salt tolerance
1.4.2 Alters in plant hormone levels
1.4.3 Accumulation of compatible solutes
1.5 Heterosis and plant stress tolerance
1.5.1 Heterosis
1.5.2 Research progress of heterosis
1.5.3 Maize stress tolerance and heterosis
1.6 The research progress of L. Chinense
1.6.1 Advance of research in L. Chinense
1.6.2 L. Chinense and salt stress
1.6.3 Carotenoids biosynthesis in plants
1.7 Transcription factorsand regulation of genes expression
1.7.1 NAC TFs
1.7.2 bZIP TFs
1.7.3 WRKY TFs
1.7.4 MYB TFs
1.7.5 bHLH TFs
1.7.6 HSF TFs
1.8 Research objective and significance of this thesis
1.8.1 Comparative transcriptome analysis of maize Tianta5 and its parentsunder salt stress condition
1.8.2 De novo transcriptome analysis of L. chinense and identification andcharacterization of important functional genes
CHAPTER TWO: COMPARATIVE TRANSCRIPTOME ANALYSIS OFMAIZE RESPONSE TO SALT STRESS
2.1 Materials and methods
2.1.1 Maize materials
2.1.2 Evaluation of salt tolerance of the maize varieties
2.1.3 High throughput RNA sequencing
2.1.4 Data processing and analysis
2.1.5 Sequencing quality assessment
2.1.6 Gene expression annotation
2.1.7 Gene Ontology Functional Enrichment Analysis for DEGs
2.1.8 KEGG Pathway analysis
2.1.9 Quantitative real-time PCR Verification of the transcriptional data
2.2 Results
2.2.1 Evaluation of salt tolerance of Tianta5 and its inbred parents
2.2.2 Sequencing quality assessment
2.2.3 Transcriptome analysis of F1 hybrid and its parents
2.2.4 Identification and Characterization of the DEGs
2.2.5 Clustering analysis of the DEGs
2.2.6 Gene Ontology Functional Enrichment Analysis for DEGs
2.2.7 KEGG pathway analysis of DEGs
2.3 Discussion
2.3.1 Salt treatment
2.3.2 Salt stress related GO terms analysis of the DEGs
2.3.3 Salt stress related pathway analysis of these DEG
2.3.4 Heterosis related genes analysis
2.4 Summary
CHAPTER THREE: DE NOVO CHARACTERIZATION OF LYCIUMCHINENSE MILL. LEAF TRANSCRIPTOME
3.1 Materials and methods
3.1.1 Plant materials and RNA isolation
3.1.2 Illumina sequencing and de novo assembly
3.1.3 Sequence annotation
3.1.4 Gene expression levels analysis
3.1.5 Identification of TF genes in L.chinense
3.1.6 Identification of L. chinense unigenes related to carotenoidbiosynthesis
3.1.7 qRT-PCR analysis of L. chinense genes involved in carotenoidbiosynthesis
3.1.8 Carotenoid extraction and HPLC
3.2 Results
3.2.1 Illumina sequencing and de novo assembly
3.2.2 Annotation and classification of L. chinense unigenes
3.2.3 GO classification
3.2.4 COG classification
3.2.5 KEGG pathway mapping
3.2.6 Identification of TF genes in L. chinense
3.2.7 Gene expression levels analysis
3.2.8 Genes related to salt tolerance/stress
3.2.9 Analysis of genes involved in carotenoid biosynthesis pathway
3.2.10 Analysis of carotenoid contents in leaf and ripening fruit of L. chinense
3.3 Discussion
3.3.1 Plant samples selected for RNA sequencing
3.3.2 RNA-seq and de novo assembly
3.3.3 Analysis of TF genes in L. chinense
3.3.4 Salt tolerance related genes in L. chinense
3.4 Summary
CHAPTER FOUR: ANALYSIS OF TRANSCRIPTION FACTOR GENES INMAIZE UNDER SALT STRESS CONDITIONS
4.1 Materials and methods
4.1.1 Plant materials and salt stress treatments
4.1.2 Evaluation of salt tolerance in the maize varieties
4.1.3 Transcriptome analysis of TF genes and salt-responsive genes
4.1.4 Phylogenetic tree construction of HSFs and protein interactionnetworks analysis
4.1.5 RNA extraction and qRT-PCR analysis
4.2 Results
4.2.1 Evaluation of salt tolerance of the two maize varieties
4.2.2 Identification of TF genes and expression analysis
4.2.3 Expression profiles of the TF genes under salt stress conditions
4.2.4 Identification of salt-stress responsive genes and TFs
4.2.5 Phylogenetic analysis of HSF family and protein interaction networkanalysis
4.2.6 Expression analysis of HSF genes under salt stress conditions
4.3 Discussion
4.3.1 Characterization of expression profiles of TFs in response to saltstress
4.3.2 Salt-stress responsive genes and salt-tolerant genes
4.3.3 Critical TFs in plant response to salt stress
4.3.4 HSFs and their expression pattern in response to salt stress and theirpotential roles in maize salt tolerance
4.4 Summary
CHAPTER FIVE: CONCLUSION AND FUTURE PROSPECTS
5.1 Conclusion
5.2 Innovation
5.3 Future prospects and Concerns
REFERENCES
ADDITIONAL FILES
PAPER PUBLICATION AND SCIENTIFIC RESEARCH PROJECTS
ACKNOWLEDGEMENT
本文编号：3857938
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