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Seed Development: OMICS Technologies Toward Improvement of Seed Quality and Crop Yield is about the seed development in the model and crop plants. Seed development is a key step of the plant life cycle that determines the nutrient value of seeds - the life for human civilization, growth, and development. The nutrient value of seeds is mainly due to storage reserve products such as carbohydrates, lipids (triacylglycerols), and proteins.
Seed Development primarily focuses on application of the 21st century high-throughput technologies transcriptomics, proteomics, metabolomics, and systems biology in near complete understanding of the various processes involved in seed development in different crop plants. Seed Development: OMICS Technologies Toward Improvement of Seed Quality and Crop Yield reveals how such technologies have revolutionized our understanding of the multilayer processes and regulations involved therein by generating large-scale datasets. Accumulated datasets provide basic knowledge to develop integrated strategies to eventually improve the nutritional value of plant seed and crop yield, a critical goal in food security issues around the globe.
- 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
