Plant Functional Genomics: 1st Edition (Paperback) book cover

Plant Functional Genomics

1st Edition

Edited by Dario Leister

CRC Press

692 pages

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Paperback: 9781560229995
pub: 2004-12-28
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Description

Discover cutting-edge knowledge for engineering a more productive and environment-friendly agriculture!

In Plant Functional Genomics, you’ll 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 more
Plant 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.

Table of Contents

  • 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

Subject Categories

BISAC Subject Codes/Headings:
SCI011000
SCIENCE / Life Sciences / Botany
SCI029000
SCIENCE / Life Sciences / Genetics & Genomics
SCI086000
SCIENCE / Life Sciences / General