Plant Reverse Genetics

1. Front Matter

   Pages i-xi

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2. Analysis of High-Throughput Sequencing Data

   • Shrinivasrao P. Mane, Thero Modise, Bruno W. Sobral

   Pages 1-11

3. Identification of Plant microRNAs Using Expressed Sequence Tag Analysis

   • Taylor P. Frazier, Baohong Zhang

   Pages 13-25

4. Microarray Data Analysis

   • Saroj K. Mohapatra, Arjun Krishnan

   Pages 27-43

5. Setting Up Reverse Transcription Quantitative-PCR Experiments

   • Madana M. R. Ambavaram, Andy Pereira

   Pages 45-54

6. Virus-Induced Gene Silencing in Nicotiana benthamiana and Other Plant Species

   • Andrew Hayward, Meenu Padmanabhan, S. P. Dinesh-Kumar

   Pages 55-63

7. Agroinoculation and Agroinfiltration: Simple Tools for Complex Gene Function Analyses

   • Zarir Vaghchhipawala, Clemencia M. Rojas, Muthappa Senthil-Kumar, Kirankumar S. Mysore

   Pages 65-76

8. Full-Length cDNA Overexpressor Gene Hunting System (FOX Hunting System)

   • Mieko Higuchi, Youichi Kondou, Takanari Ichikawa, Minami Matsui

   Pages 77-89

9. Activation Tagging with En/Spm-I /dSpm Transposons in Arabidopsis

   • Nayelli Marsch-Martínez, Andy Pereira

   Pages 91-105

10. Activation Tagging and Insertional Mutagenesis in Barley

    • Michael A. Ayliffe, Anthony J. Pryor

    Pages 107-128

11. Methods for Rice Phenomics Studies

    • Chyr-Guan Chern, Ming-Jen Fan, Sheng-Chung Huang, Su-May Yu, Fu-Jin Wei, Cheng-Chieh Wu et al.

    Pages 129-138

12. Development of an Efficient Inverse PCR Method for Isolating Gene Tags from T-DNA Insertional Mutants in Rice

    • Sung-Ryul Kim, Jong-Seong Jeon, Gynheung An

    Pages 139-146

13. Transposon Insertional Mutagenesis in Rice

    • Narayana M. Upadhyaya, Qian-Hao Zhu, Ramesh S. Bhat

    Pages 147-177

14. Reverse Genetics in Medicago truncatula Using Tnt1 Insertion Mutants

    • Xiaofei Cheng, Jiangqi Wen, Million Tadege, Pascal Ratet, Kirankumar S. Mysore

    Pages 179-190

15. Screening Arabidopsis Genotypes for Drought Stress Resistance

    • Amal Harb, Andy Pereira

    Pages 191-198

16. Protein Tagging for Chromatin Immunoprecipitation from Arabidopsis

    • Stefan de Folter

    Pages 199-210

17. Yeast One-Hybrid Screens for Detection of Transcription Factor DNA Interactions

    • Pieter B. F. Ouwerkerk, Annemarie H. Meijer

    Pages 211-227

18. Plant Metabolomics by GC-MS and Differential Analysis

    • Joel L. Shuman, Diego F. Cortes, Jenny M. Armenta, Revonda M. Pokrzywa, Pedro Mendes, Vladimir Shulaev

    Pages 229-246

19. Gramene Database: A Hub for Comparative Plant Genomics

    • Pankaj Jaiswal

    Pages 247-275

20. Back Matter

    Pages 277-282

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After the generation of genome sequence data from a wide variety of plants, databases are filled with sequence information of genes with no known biological function, and while bioinformatics tools can help analyze genome sequences and predict gene structures, experimental approaches to discover gene functions need to be widely implemented. In Plant Reverse Genetics: Methods and Protocols, leading researchers in the field describe cutting-edge methods, both high-throughput and genome-wide, involving the models Arabidopsis and rice as well as several other plants to provide comparative functional genomics information. With chapters on the analysis of high-throughput genome sequence data, the identification of non-coding RNA from sequence information, the comprehensive analysis of gene expression by microarrays, and metabolomic analysis, the thorough methods of the book are fully supported by scripts to aid their computational use. Written in the highly successful Methods in Molecular Biology™ series format, the chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and essential, Plant Reverse Genetics: Methods and Protocols is an ideal guide for researchers seeking an understanding of how the complex web of plant genes work together in a systems biology view.

• Arabidopsis and rice
• Developmental mutant phenotypes
• Functional genomics
• Genome sequencing
• Metabolomic analysis
• Microarrays
• Non-coding RNA
• Systems biology

From the reviews:

“This book includes a compendium of methods and protocols derived from functional genomics that have been developed during the last decade … . The book is organized in chapters written by leading researchers from different groups … . Large scale phenotyping is also described with protocols suitable for application in different lab conditions. … Gramene database is presented as an example of integrated information … derived from different species, providing details of the information gathered in it as well as available tools for sequence comparisons.” (Ruth Heinz and Norma Paniego, Boletin de Bibleoteca del IMYZA-INTA, Issue 26, June, 2011)

• , Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, USA

  Andy Pereira

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