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Methods and ProtocolsExplores various issues and methodologies in plant genomics, specifically addressing areas of gene discovery and the functional analysis of genes with a focus on the primary tools and sub-disciplines of genetic mapping, mRNA, protein and metabolite profiling.Plant genomics is a growing and constantly evolving field of study, one which has gained much ground in past years through the development of advanced research and data management tools. In "Plant Genomics: Methods and Protocols", expert researchers explore the current issues and methodologies of this expanding field, specifically addressing areas of gene discovery and the functional analysis of genes with a focus on the primary tools and sub-disciplines of genetic mapping, mRNA, protein and metabolite profiling. Chapters employ exciting new methods to investigate molecular plant breeding technology and gene functional analysis via transformation, mutation, protein function, and gene expression. Composed in the highly successful "Methods in Molecular Biology" series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Comprehensive and innovative, "Plant Genomics: Methods and Protocols" is an essential guide for all plant scientists who are interested in further studies in the area of genomics research.Plant Genomics: Methods and Protocols Daryl J. Somers, Peter Langridge, and J. P. Gustafson, eds. Table of Contents Preface Contributors 1. Role of Model Plant Species Richard Flavell 2. New Technologies for Ultra-High Throughput Genotyping in Plants Nikki Appleby; David Edwards; Jacqueline Batley 3. Genetic Maps and the Use of Synteny Chris Duran; David Edwards; Jacqueline Batley 4. A Simple TAE-based Method to Generate Large Insert BAC Libraries from Plant Species Bu-Jun Shi; J. Perry Gustafson; Peter Langridge 5. Transcript Profiling and Expression Level Mapping Elena Potokina; Arnis Druka; Michael J. Kearsey 6. Methods for Functional Proteomic Analyses Christof Rampitsch; Natalia V. Bykova 7. Stable Transformation of Plants Huw D. Jones; Caroline A. Sparks 8. Transient Transformation of Plants Huw D. Jones; Angela Doherty; Caroline A. Sparks 9. Bridging the Gene-to-Function Knowledge Gap Through Functional Genomics Stephen J. Robinson; Isobel A. P. Parkin 10. Heterologous and Cell Free Protein Expression Systems Naser Farrokhi; Maria Hrmova; Rachel A. Burton; Geoffrey B. Fincher 11. Functional Genomics and Structural Biology in the Definition of Gene Function Maria Hrmova; Geoffrey B. Fincher 12. In situ Analysis of Gene Expression in Plants Sinead Drea; Paul Derbyshire; Rachil Koumproglou; Liam Dolan; John H. Doonan; Peter Shaw 13. Plant and Crop Databases David E. Matthews; Gerard R. Lazo; Olin D. Anderson 14. Plant Genome Annotation Methods Shu Ouyang; Francoise Thibaud-Nissen; Kevin L. Childs; Wei Zhu; C. Robin Buell 15. Molecular Plant Breeding: Methodology and Achievements Rajeev K. Varshney; Dave A. Hoisington; Spurthi N. Nayak; Andreas Graner 16. Practical Delivery of Genes to the Marketplace David A. Fischhoff; Molly N. Cline 17. Ecological Genomics of Natural Plant Populations: The Israeli Perspective Eviatar Nevo 18. Genome Sequencing Approaches and Successes Michael Imelfort; Jacqueline Batley; Sean Grimmond; David Edwards