Abstract: * 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, Francoise Daniel-Vedele, Helene 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 (Loic Lepiniec, Martine Devic, and Frederic 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 Flugge, 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 Soren 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 Jorg 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