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Table of contents
Chapter 1 Introduction
1.Plant stress response to combined stress
1.1 Consequence of stress response to combined stress
1.2 Convergent physiological alterations of the combined stress response.
1.3 Signalling mechanisms of combine stress
2. Nitrogen and water as major limiting factors for plant growth
2. Water and nitrogen stress acclimation
2.1 Physiological and Metabolism coordination
2.1.1 Nitrogen supply can affect stomatal regulation in drought stress
2.1.2 Nitrogen regulates root water uptake through aquaporin under drought stress
2.1.3 N metabolism under drought
2.1.4 N assimilation and remobilisation is affected by drought stress
2.2 Signal sensing networks during drought and N deficiency
2.2.1 Specific stress sensor for drought and N deficiency
2.2.2 Common secondary messenger: Ca 2+
2.2.3 Crosstalk of ABA – Nitrate in regulating root growth
3. Systems Biology, an indispensable approach for investigating abiotic stress responses in plants
3.1 multi-omics integration strategy used in plants research
3.2 Multivariate analysis
4. Systems genetics, exploiting natural variation as a source of phenotypic diversity
4.1 Natural variation in stress response: GXE
4.2 GWAS: as a tool to study natural variation
4.2.1 GWAS, a robust mapping method.
4.2.2 Metabolite GWAS use molecular trait as a quantitative trait
4.2.3 Recent approaches to aid GWAS detection.
4.3 Arabidopsis thaliana as a model to study natural variation
4.3.1 From phenotypic variation to genotypic diversity
4.3.2 The complexity of traits’ genetic architecture
4.3.3 Available resource
5 Objective of my thesis
5.1 Identify specific stress response features/pathways in combined stress
5.2 Describe the genetic of their interaction with the environment (G x E)
5.3 Decompose quantitative variation at different levels of complexity (growth, metabolite)
Chapter 2 WxN project
2.1 Phenotypic plasticity among five accessions subjected to N deficiency, mild drought and their combination
2.1.1 N deficiency as well as water deficit affects plant biomass accumulation
2.1.2 Morphological rosette parameters and colour parameters
2.1.3 Physiological parameters are less affected under combined stress than under N deficiency alone.
2.2 Transcriptome changes in plants subjected to N deficiency, mild drought and combined stress
2.2.1 General features in Col-0
2.2.2 Specificities of other accessions
2.2.3 Conserved responses between accessions
2.2.4 General transcriptomic responses to single and combined stress
2.3 Metabolic disruptions caused by stress induced growth limitation among five accessions
2.4 Integrative analyses
2.4.1 Multi-Omics Factor Analysis (MOFA) based on metabolome/transcriptome profiling
2.4.2 Correlation network analysis (WGCNA) failed to identify the most consensual module among accessions
2.4.3 Coexpression networks by Mixomics
2.5 Discussion
Supplementary file
Chapter 3 GWAS project
3.1 Species-wide natural variation in metabolism and growth parameters
3.2 Genome-Wide Association analysis of growth traits and primary metabolism
Test Case: Flowering Time analysis confirms that the DOG1 locus modulates time to flowering
GWAS failed to identify associations with most of the growth traits
GWAS revealed specific metabolic biosynthesis pathways: examples
Colocalized QTL indicates pleiotropic hub controlling central metabolism
GWAS with metabolite ratio identifies genes controlling metabolic architecture
GWAS on principal component traits failed to identify genes comprehensively controlling metabolic architecture and growth
Unknown candidate genes revealed by GWAS
Analysis of KO and HIF Lines for selected candidate genes
3.3 Discussion
Supplementary file
Chapter 4 Methods and material
Plant Materials, Growth Conditions, and Harvest
Relative water content
Total N, Total C
Nitrate analysis
Metabolites Measurements
RNA Extraction and Complementary DNA Synthesis
qPCR
Statistical Analysis
Genome-wide association mapping
Chapter 5 General Conclusion
Reference
