Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield (eBook)

PREFACE.- Dedication.- PART I: INTRODUCTION.- 1. Seed development: A comparative overview on biology of morphology, physiology, and biochemistry between monocot and dicot plants.- Introduction.- Seed development: key events.- Comparative morphology of seed development.- Comparative physiology: phytohormones, signaling, and metabolism.- Comparative biochemistry.- Dormancy and desiccation tolerance.- Concluding remarks.- 2. Proteomics reveals a potential role of the perisperm in starch remobilization during sugarbeet seed germination.- Introduction.- Experimental strategies.- Results and discussion.- Concluding remarks.- 3. Omics platforms: Importance of 21st century genome-enabled technologies in seed developmental research for improved seed quality and crop yield.- Introduction.- Biotechnologies role in improving seed quality and development.- Concluding remarks.- PART II: TRANSCRIPTOMICS.- 4. Rice seed development: A cornerstone for cereal crops.- Introduction.- Rice seed morphology, development, and germination.- Seed transcriptomics.- Comparative transcriptome evidence for monocot embryo organ homologies.- Concluding remarks.- 5. A transcriptional roadmap for seed development in maize.- Introduction.- A portrait of maize seed development.- Transcriptional regulation of maize seed development.- Concluding remarks.- 6. Using transcriptomics to reveal gene networks of seed development in Arabidopsis.- Introduction.- Analyzing the Arabidopsis seed transcriptome data.- Identifying gene networks.- Interactome.- Further analysis of candidate genes.- Advantages of using next-generation sequencing for transcriptome analysis.- Concluding remarks.- 7. The Medicago truncatula gene expression atlas (MtGEA): A tool for legume seed biology and biotechnology.- Introduction.- The Medicago truncatula gene expression atlas (MtGEA).- The MtGEA and seed development.- Concluding remarks.- 8. Transcriptomics of legume seed: Soybean a model grain legume.- Soybean seed development: an overview.- Transcriptomics of soybean seed: recent developments.- Soybean: a model grain legume for legume transcriptomics.- Concluding remarks.- 9. Peanut seed development: Molecular mechanisms of storage reserve mobilization and effect of water deficit stress on seed metabolism.- Introduction,- Stages of seed development.- Signaling networks and seed development.- Storage protein synthesis.- Fatty acid metabolism.- Starch metabolism Flavonoids in developing seeds.- Effects of water deficit stress on seed metabolism at molecular level.- Concluding remarks.- 10. Probing the genes expressed in developing seed of oilseed plants: Brassica napus (L.) as a case example.- Introduction.- Differential expression of genes during seed development.- Genes involved in lipid metabolism.- Biology of starch and sugar metabolism.- Storage protein accumulation in rapeseeds.- Carotenoid accumulation and gene expression Phenolics accumulation.- Regulatory and signalling genes related to seed development.- Concluding remarks.- 11. Networks of seed storage protein regulation networks in cereals and legumes at the dawn of the omics era.- Introduction.- Seed storage proteins.- Transcriptional regulation of SSPs.- Environmental regulation.- Future directions.- Concluding remarks.- PART III: PROTEOMICS.- 12. Organelle proteomics of developing seeds: Comparison with other plant tissue organelles.- Introduction.- Mitochondria: strategic roles in development and upon abiotic stresses.- Peroxisomes are key players in carbon metabolism (breakdown of storage lipids) during germination of oilseeds and seedling growth.- Plastids: photosynthetic carbon fixation, synthesis of amino- and fatty- acids, starch and secondary metabolites.- Endoplasmic reticulum: an inticulum endomembrane system for SSP processing, trafficking, and lipid biosynthesis.- Oil bodies: a reservoir of lipids as carbon and energy source.- Nuclei: site of gene expression and regulatory processes for seed development.- Concluding remarks.- 13. Proteomics in identifying new regulatory mechanisms involved in seed development and ultimately seed quality.- Introduction.- Functional view of maize endosperm development from proteomic analysis and complementary transcriptomic measurements.- Interpretation of protein expression associated to metabolism in relation with evolution of endosperm physiology during development.- Epistatic relationship between CyPPDK1 and O2 genes in relation with starch/protein balance and lysine content.- Concluding remarks.- 14. Digging deeper into the seed proteome: Pre-fractionation of total proteins.- Background.- Strategies for addressing the dynamic range problem inherent to seed biology.- Concluding remarks.- 15. The central role of phosphoenolpyruvate metabolism in developing oilseeds.- Introduction.- PK and PEPC exert a major influence on the metabolic control of oilseed glycolysis and respiration.- Cytosolic versus plastidic PEP metabolism of developing oilseeds.- PEPC supports oilseed storage protein and fatty acid biosynthesis.- Molecular and biochemical properties of cytosolic and plastidic PK isozymes of developing oilseeds.- The incredible complexity of oilseed PEPC.- Castor bean class-1 PEPC is controlled by allosteric effectors, reversible phosphorylation, and regulatory monoubiquitination.- Castor bean class-1 PEPC may interact with a cytosolic-targeted PDC.- The class-2 PEPC complex of developing castor beans exhibits remarkable structural and kinetic/regulatory properties.- Class-2 PEPC of developing castor beans appears to associate with the mitochondrial outer envelope.- Concluding remarks.- PART IV: METABOLOMICS.- 16. Search for low-molecular-weight biomarkers in plant tissues and seeds using metabolomics: tools, strategies, and applications.- Introduction.- Metabolomic approaches and strategies.- Metabolomic study of the maize response to herbivory as an example.- Multiple facets of LC-MS in plant metabolomics.- Data mining and localization of biomarkers.- Strategies for the de novo identifications of unknown biomarkers.- Application of plant metabolomics.- Concluding remarks.- PART V: TOWARDS SYSTEMS BIOLOGY: ORGANIZATION, INTEGRATION AND MODELIZATION OF DATA.- 17. Plant metabolic pathways: Database and pipeline for stoichiometric analysis.- Introduction.- Plant metabolic pathway database: organization and integration of plant metabolic information.- Resources for the constraint-based analysis of plant metabolic models: modelization of plant metabolism.- Pipeline for the integrated constraint-based model reconstruction, analysis, and visualization.- Application example.- Concluding remarks.- 18. Coupled transcript-metabolite profiling: Towards systems biology approaches to unravel regulation of seed secondary metabolism.- Introduction.- Different ways of integrating transcript and metabolite data to unravel seed secondary metabolism.- Atlas of gene expression and secondary metabolism in Arabidopsis seeds.- Using natural genetic diversity as a source of variation to identify quantitative trait transcripts – the example of carotenoid metabolism in the starchy maize endosperm.- Use of growth environment as a source of variation to build metabolic networks – the metabolism of chlorogenic acids in coffee seeds as a case study.- Concluding remarks.- Perspectives.- 19. Using systems approaches to analyze metabolic networks involved in storage reserves synthesis in developing seeds.- Introduction.- Stoichiometric modelling.- Metabolic flux analysis.- Dynamic behaviour in enzymatic reaction networks: kinetic modelling.- Concluding remarks.- 20. Metabolic specialization of maternal and filial tissues.- Introduction.- Development and main functions of seed tissues.- Examples of large-scale omics studies of seed tissues: a focus on starch metabolism.- Partitioning of metabolic activities between seed tissues.- Regulation of seed-tissue metabolic specialization.- Concluding remarks.- PART VI: DISCOVERY-DRIVEN SEED AND YIELD IMPROVEMENT.- 21. Marker-aided breeding revolutionizes 21st century crop improvement.- Introduction.- DNA markers in plant breeding.- Genetic maps, association genetics, and QTL.- Marker-aided breeding.- Progress of marker-aided breeding in maize and rice.- Concluding remarks.- 22. Metabolomics-assisted crop breeding towards improvement in seed quality and yield.- Introduction.- State of the art metabolomics-assisted breeding technologies – an overview.- Correlation (network) analysis – a tool to identify functional groups of metabolites.- From seed development to seed germination: the metabolic basis of seed quality traits.- Limitations and future perspectives.- 23. A role for "omics" technologies in exploration of the seed nutritional quality.- Introduction.- From Arabidopsis to rice to understand crop species.- Contribution of omics technologies to decipher biology and improve nutritional value of seeds.- Proof-of-concept: Physiological conditions influence nutritional rice quality as highlighted by omics experiments.- Concluding remarks.- 24. Using genome-enabled technologies to address allergens in seeds of crop plants: Legumes as a case study.- Introduction.- Identification of allergens.- Genome-enabled technologies to create low allergen seeds.- Concluding remarks.- 25. Improving quality and content of oils in seeds: Strategies, approaches, and application towards engineering new oilseed crop plants.- Introduction.- Seed lipid composition and metabolic pathways.- Manipulation of oil seed composition using omics.- Discovery-driven seed and yield improvement.- Concluding remarks.- 26. Integrating “omics” in food quality and safety assessment.- Introduction.- Linking omics to the improvement of seed quality and nutritional value.- Omics and food safety assessment.- Omics and biomarkers.- Concluding remarks.- PART VII: APPENDIX.- References.- Abbreviations.- Editors’ acknowledgment to contributors.- Editors’ biographies.- Index.