Discover cutting-edge knowledge for engineering a more productive and environment-friendly agriculture!In Plant Functional Genomics, youll find a cross-section of state-of-the-art research on the biological function of plant genes and how they work together in health and disease. World-leading scientists in the field present breakthrough techniques, discuss the results of projects aimed at dissecting particular plant functions, and provide an overview on the state of functional genomics for several plant and plant-related species. With figures, tables, and illustrations, this book will help scientists, researchers, and advanced students in botany find new ways of creating novel plant forms to better serve the needs of a rapidly expanding human population. Plant Functional Genomics will increase your understanding of gene networks and systems rules, as well as gene expression during specific conditions or development or treatments. This important resource contains a wealth of data generated by various plant genome sequencing projects, including the newest results from experiments with Arabidopsis thaliana?the first plant to be completely sequenced. This book also contains innovative research on: T-DNA mutagenesis transcriptomics and metabolic profiling in plants large-scale yeast two-hybrid analyses the exceptional model system of Chlamydomonas genomics functional genomics in rice, maize, and Physcomitrella prospects for functional genomics in a new model grass chloroplast and plant mitochondrial proteomics plant transporters so much morePlant Functional Genomics will help speed up the identification and isolation of genes that might be of interest with respect to diverse biological questions. This valuable contribution to the field clarifies the challenges yet to be faced and the opportunities that could some day expand the frontiers of plant sciences.
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About the Editor Contributors Preface. Definition and Origin of Plant Functional Genomics Abbreviations SECTION I: BREAKTHROUGH TECHNIQUES Chapter 1. Full-Length cDNAs for the Discovery and Annotation of Genes in Arabidopsis thaliana (Motoaki Seki, Mari Narusaka, Masakazu Satou, Miki Fujita, Tetsuya Sakurai, Youko Oono, Kenji Akiyama, Kazuko Yamaguchi-Shinozaki, Kei Iida, Piero Carninci, Junko Ishida, Jun Kawai, Maiko Nakajima, Yoshihide Hayashizaki, Akiko Enju, and Kazuo Shinozaki) Introduction Collection of Arabidopsis Full-Length cDNAs Application of Full-Length cDNAs to Genome Annotation Application of Full-Length cDNAs to Functional Analysis Conclusions and Perspectives Chapter 2. T-DNA Mutagenesis: From Tagging to Insertion Sequence Databases (Allen Sessions) Crown Galls, Neoplasia, and Agrobacterium Agrobacteria As Friend Not Foe Development of Transformation Protocols for the Efficient Generation of T-DNA Insertion Mutants Even Faster and More Efficient Transformation From a Population of T-DNA Insertion Mutants to a File of T-DNA Flanking Sequence Tags Amplification of T-DNA Borders and the Distribution of Predicted Insertions Chapter 3. Novel Reverse Genetics Tools in Plant Functional Genomics (Xin Li and Yuelin Zhang) Introduction Deleteagene TILLING Combinatorial Gene Slicing Chapter 4. Transcriptomics in Plants: From Expression to Gene Function (Laurent Zimmerli and Shauna Somerville) Introduction The Technologies Experimental Design Analysis Data Verification and Quality Checks Limitations Perspective Chapter 5. Metabolite Profiling in Plants (Richard N. Trethewey) Introduction Background and Fundamentals of Metabolite Profiling Metabolite-Profiling Technologies Applications of Metabolite Profiling to Plants Outlook for Metabolite Profiling Chapter 6. Large-Scale Yeast Two-Hybrid Analysis (Barry Causier, John Graham, and Brendan Davies) Introduction The Basis of the Yeast Two-Hybrid System Large-Scale Yeast Two-Hybrid Studies: A Brief History High-Throughput Yeast Two-Hybrid Methodologies Applications of Large-Scale Yeast Two-Hybrid Screening The Caveat SECTION II: SPECIES EXAMPLES Chapter 7. Functional Genomics of a Cyanobacterium, Synechocystis sp. PCC 6803 (Takakazu Kaneko, Shusei Sato, and Satoshi Tabata) Introduction A Large-Scale Gene Disruption Transcriptome Analysis Proteome Analysis Analysis of Protein Interactions with the Yeast Two-Hybrid System Genome Databases Conclusions and Future Perspectives Chapter 8. Chlamydomonas Genomics: New Approaches for a Classical Model System (Heidi K. Ledford, Rachel M. Dent, and Krishna K. Niyogi) Introduction The Chloroplast Genome The Mitochondrial Genome The Nuclear Genome Functional Genomics Transcriptomics Proteomics and Metabolomics Tying It All Together: Databases for the Chlamydomonas Community Closing Thoughts and Future Directions Chapter 9. Functional Genomics in Physcomitrella (Wolfgang Frank, Hauke Holtorf, and Ralf Reski) Introduction Mass Production of Standardized Moss Material Production of a Physcomitrella EST Collection In Vivo Transposon Mutagenesis of cDNA Libraries Fast-Forward Production of Single Knockout Constructs High-Throughput Transformation Protocol Mutant Quality Control Screening for Mutant Phenotypes Molecular Analysis of Mutants Conclusion Chapter 10. Arabidopsis Functional Genomics Tools: An Overview (Koen Dekker) Introduction Curriculum Vitae of a Model Functional Genomics Tools Tools for Reverse Genetics Tools for Forward Screening Tools for Studying Mechanisms Weaknesses Threats to Continued Impact Opportunities Chapter 11. Rice Functional Genomics: From Nucleotide Sequence to Gene Function (Takuji Sasaki) Introduction Functional Genomics Based on Forward Genetics Functional Genomics Based on Reverse Genetics Functional Genomics Based on Activation Tagging Conclusion Chapter 12. Maize Genomics (Joachim Messing) Maize As a Crop Genome Size Genome Expansion Clone Maps Genetic Maps Gene Tagging Gene-Enrichment Procedures ESTs Microarrays Genomic Sequences Rice/Maize Clone Maps Chapter 13. Prospects for Functional Genomics in a New Model Grass (Glyn Jenkins, Luis A. J. Mur, Pauline Bablak, Robert Hasterok, and John Draper) Why a New Model Grass? Understanding the Plant Understanding the Genome Toward Functional Genomics of Pathogenic Interactions SECTION III: ORGANELLES Chapter 14. Chloroplast Proteomics (Klaas J. van Wijk) The Dynamic Nature of the Plastid and Its Proteome The Scope of This Chapter Prediction of the Plastid Proteome Prediction of Proteomes of Nonphotosynthetic Plastids Systematic Experimental Identification and Characterization of the Plastid Proteome Posttranslational Modifications of the Chloroplast Proteome Plastid-Localized Protein Complexes and Protein-Protein Interactions Conclusions and Future Perspectives Chapter 15. Plant Mitochondrial Proteomics (A. Harvey Millar and Joshua L. Heazlewood) Defining the Plant Mitochondrial Proteome Technology Issues Science Issues Future Directions SECTION IV: PATHWAYS AND PROCESSES Chapter 16. Functional Characterization of the Photosynthetic Apparatus in Arabidopsis thaliana (Henrik Vibe Scheller, Christina Lunde, Anna Haldrup, and Poul Erik Jensen) Introduction Overview of Electron Transport Photosystem II The Cytochrome b/f Complex Photosystem I Accessory Electron Transport Systems Elements Involved in Nonphotochemical Quenching The ATP Synthase Conclusion Chapter 17. Functional Genomics of Plant Nitrogen Metabolism (Mathilde Orsel, Anne Krapp, Karine Boivin, Françoise Daniel-Vedele, Hélène Roussel, Christian Meyer, and Christelle Thibault) Introduction Functional Genomics of Nitrate Transport in Arabidopsis Transcriptome Analysis in Relation to Variations in Nitrogen Supply Conclusion Chapter 18. Functional Genomics of Plant Salinity (Hans J. Bohnert) Salinity Tolerance in Context Problems Plants Face in High Salinity The Genomics Tool Kit Applied to Salinity Stress Research Mutants and Mutant Phenotypes in Salinity Stress Tolerance ESTs and cDNAs from Salt-Stressed Plants Salinity-Induced Changes of the Transcriptome Salinity-Dependent Signal Transduction Salinity Stress Engineering Future Developments Chapter 19. Functional Genomics Applied to Plant Fatty Acid Biosynthesis (Sari A. Ruuska and John B. Ohlrogge) Introduction Directed Gene Discovery: Approach Large-Scale DNA Sequencing and Gene-Expression Analysis Summary and Future Prospects Chapter 20. Genetic and Molecular Control of Seed Development in Arabidopsis (Loïc Lepiniec, Martine Devic, and Frédéric Berger) Introduction From Genetic to Molecular Bases of Seed Development Ovule Development Endosperm Development Embryogenesis Limitations of the Genetic Approach and New Prospects SECTION V: PROTEIN FAMILIES Chapter 21. Plant Transporters (Marcelo Desimone, Reinhard Kunze, Ulf-Ingo Flügge, and Wolf B. Frommer) Introduction Identification of Novel Transporters by Heterologous Expression Gene Expression Subcellular Localization Protein Interactions Analysis of Loss-of-Fuction (?Knockout?) Mutants and ?Knockdown? Mutants The ARAMEMNON Database: A Novel Bioinformatics Tool for Sequence Interpretation and Data Mining on Transporters and Membrane Proteins Connecting Arabidopsis Functional Genomics Resources with Crop Plant Research Chapter 22. Functional Genomics of the Cytochrome P450 Gene Superfamily in Arabidopsis thaliana (David W. Galbraith and Søren Bak) What are Cytochrome P450s? Comparative Genome Analysis A Small Proportion of the Arabidopsis P450s Have Been Assigned a Specific Cellular Function A Variety of New Methods Are Becoming Increasingly Available to Assign Function to P450 Family Members Conclusions and Perspectives Chapter 23. Functional Genomics of Protein Phosphorylation in Arabidopsis thaliana (Claudia Hass, Stefan Weinl, Klaus Harter, and Jörg Kudla) Introduction Protein Kinases and Phosphatases Encoded in the Arabidopsis Genome Histidine Kinases and Two-Component Signaling System Early Steps in Plant Histidine Kinase Signaling Conclusion Index Reference Notes Included
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