The evaluation of Differentially Expressed Genes (DEGs)

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Table of contents

Chapter I – General introduction 
1. Grapevine rootstocks
1.1 Influence of rootstocks on grapevine abiotic stresses tolerance
1.2 Rootstocks widely used in viticulture and characterization of new genotypes with OMICS techniques
2. Study of genes expression by using a transcriptomic approach
3. Grapevine and its genome
4. References (Chapter I)
Chapter II – Transcriptomes comparison of a susceptible and a putative tolerant grapevine rootstocks to drought give insight into the mechanisms of water stress tolerance 
1. Introduction
2. Materials and methods
2.1 Experimental design and plant material
2.2 Whole transcriptome analysis
2.3 Multifactorial and pairwise statistical analysis
2.4 Ontology and Differential Clustering Analyses (DCA)
3. Results
3.1 Physiological traits analyses
3.2 mRNA-seq sequencing and mapping of reads to the grapevine genome
3.3 Multi-factor design and discovering of differentially expressed genes
3.4 Differential cluster analysis (DCA)
4. Discussion
5. Acknowledgements
6. References (Chapter II)
Chapter III – Grapevine rootstocks differentially affected ripening inception and auxin-related genes of Cabernet sauvignon berries 
1. Introduction
2. Materials and methods
2.1 Plant Material and experimental design
2.2 RNA-seq and qPCR analyses
2.3 Statistical and bioinformatics analyses on mRNA-seq and microRNA-seq data
2.4 Phylogenetic analyses of ARF and AUX/IAA auxin-related gene families
3. Results
3.1 Physical and biochemical analyses
3.2 Differentially expressed (DE) genes, DEmiRNA and time course clustering analyses
3.3 Characterization and phylogenetic analyses of grape AUX/IAA and ARF auxin-related families
3.4 CS/1103P and CS/M4 berries highlights differential regulation of auxin-related genes
3.5 Effect of rootstock on miRNA expression and their control of auxin metabolisms
4. Discussion
5. Acknowledgements
6. References (Chapter III)
Chapter IV – Grape berry ripening delay induced by a prevéraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene related genes 
1. Introduction
2. Materials and methods
2.1 Plant Material and treatment
2.2 RNA extraction, microarray analysis and quantitative real time PCR
2.3 Microarray annotation and enrichment analysis
2.4 HORMONOMETER analyses
3. Results
3.1 Biochemical analyses
3.2 Differentially expressed genes and enrichment analysis
3.3 MapMan analysis
3.4 HORMONOMETER analysis
3.5 Expression of auxin-, ethylene-, and abscisic acid related genes
4. Discussion
5. Conclusions
6. Acknowledgements
7. References (Chapter IV)
Chapter V – General conclusions 
References (Chapter V)