The Handbook Of Plant Functional Genomics - Concepts And Protocols

This handbook spans over several aspects of current and emerging technologies in the field. The editors - two of the leading experts in research with a proven track record - combine their expertise to provide an invaluable reference on the topic. To make it more inclusive, this second volume in the Molecular Plant Biology Handbook Series is divided into four main parts:

• Transcriptome Analysis
• Gene Silencing, Mutation Analysis, and Functional Genomics
• Computational Analysis
• Functional Genomics and Emerging Technologies

Each chapter introduces the subject comprehensively, and provides state-of-the art experimental protocols. A handy glossary of relevant technical terms is included to facilitate reading for researchers, teachers and students.

• Plant genome analysis
• Transcriptome analyses in eukaryotic organisms
• Mutation detection.

Günter Kahl cooperates with a series of research institutions throughout Europe, in Japan, the USA, Israel, India, and Latin America. He served in expert missions for IAEA, FAO and UNESCO in many countries and presently is Editor-in-Chief of Plant genome and Systems Biology, and Chief Scientific Officer in GenXPro GmbH, an SME located at the Frankfurt Innovation Center Biotechnology.

Since 1996 Khalid Meksem is Associate Professor of Genome Biotechnology at Southern Illinois University, USA. He graduated from the University of Casablanca, Morocco, and joined the Plant Molecular and Cellular graduate program of the University Paris XI where he graduated with honors in 1990. Khalid Meksem gained his doctorate in Botany, Biochemistry and Genetics at the University of Cologne in collaboration with the Max-Planck-Institute Germany. His research interest covers both, structural and functional genomics, and his long time area of interest is the molecular dissection of plant disease resistance mechanisms to nematodes and fungi. Khalid Meksem is serving as Editor-in-Chief of Plant Genome and Systems Biology, as Associate Editor of the International Journal of Plant genomics, and as reviewer for a number of international scientific journals as well as for several granting agencies.

List of Contributors.

I: Transcriptome Analysis.

A. Whole Genome Expression Analysis.

1. Single Cell Expression Profiling: Transcript and Protein Analyses in Isolated Higher Plant Gametes and Zygotes (Stefan Scholten and Erhard Kranz).

2. AFLP-Based RNA Fingerprinting: Novel Variants and Applications (Christian W.B. Bachem, Wim H. Vriezen, Craita E. Bita, and Asun Fernandez del Carmen).

3. SuperSAGE: The Most Advanced Transcriptome Technology for Functional Genomics (Ryohei Terauchi, Hideo Matsumura, Detlev H. Kruger, and Günter Kahl).

4. From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis (Matthias Harbers, Thomas Werner, and Piero Carninci).

5. Gene Identification Signature-Paired End diTagging (GIS-PET): A Technology for Transcriptome Characterization (Patrick Ng, Yen-Ling Lee, Chia-Lin Wei, and Yijun Ruan).

6. High-Throughput Functional Screening of Genes In Planta (Thomas Berberich, Yoshihiro Takahashi, Hiromasa Saitoh, and Ryohei Terauchi).

7. Microarrays as Tools to Decipher Transcriptomes in Symbiotic Interactions (Helge Küster and Anke Becker).

B. Gene-by-Gene Analysis.

8. Genome-Wide Analysis of mRNA Expression by Fluorescent Differential Display (Suping Zhou, Jonathan D. Meade, Samuel Nahashon, Blake R. Shester, Jamie C. Walden, Zhen Guo, Julia Z, Liang, Joshua G. Liang, and Peng Liang).

9. Real-Time Quantitation of MicroRNAs by TaqMan MicroRNA Assays (Toni L. Ceccardi, Marianna M. Goldrick, Peifeng Ren, Rick C. Conrad, and Caifu Chen).

II: Gene Silencing, Mutation Analysis and Functional Genomics.

10. RNA Interference (Chris A. Brosnan, Emily J. McCallum, José R. Botella, and Bernard J. Carroll).

11. Extending Functional Genomics: VIGS for Model and Crop Plants (Steven Bernacki, John Richard Tuttle, Nooduan Muangsan, and Dominique Robertson).

12. TILLING: A Reverse Genetics and a Functional Genomics Tool in Soybean (Khalid Meksem, Shiming Liu, Xiao Hong Liu, Aziz Jamai, Melissa Goellner Mitchum, Abdelhafid Bendahmane, and Tarik El-Mellouki).

13. Transposon Tagging in Cereal Crops (Liza J. Conrad, Kazuhiro Kikuchi, and Thomas P. Brutnell).

14. Fast Neutron Mutagenesis for Functional Genomics (Christian Rogers and Giles Oldroyd).

III: Computational Analysis.

15. Bioinformatics Tools to Discover Co-Expressed Genes in Plants (Yoshiyuki Ogata, Nozomu Sakurai, Nicholas J. Provart, Dirk Steinhauser, and Leonard Krall).

16. AthaMap, a Database for the Identification and Analysis of Transcription Factor Binding Sites in the Arabidopsis thaliana Genome (Reinhard Hehl).

17. Structural Phylogenomic Inference of Plant Gene Function (Nandini Krishnamurthy, Jim Leebens-Mack, and Kimmen Sjölander).

18. Structural, Functional, and Comparative Annotation of Plant Genomes (Françoise Thibaud-Nissen, Jennifer Wortman, C. Robin Buell, and Wei Zhu).

19. Large-Scale Genomic Sequence Comparison and Gene Identification with ClustDB (Jürgen Kleffe).

IV: Functional Genomics and Emerging Technologies.

20. Nanotechnologies and Fluorescent Proteins for in planta Functional Genomics (C. Neal Stewart Jr.).

21. New Frontiers in Plant Functional Genomics Using Next Generation Sequencing Technologies (Robert C. Nutter).

22. 454 Sequencing: The Next Generation Tool for Functional Genomics (Lei Du, Jan Frederik Simons, Maithreyan Srinivasan, Thomas Jarvie, Bruce Taillon, and Michael Egholm).

Glossary.

Index.