Main description:

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 (TM) 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.

Contents:

1. Analysis of High-Throughput Sequencing Data

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

2. Identification of Plant MicroRNAs Using Expressed Sequence Tag Analysis

Taylor P. Frazier and Baohong Zhang

3. Microarray Data Analysis

Saroj K. Mohapatra and Arjun Krishnan

4. Setting Up Reverse Transcription Quantitative-PCR Experiments

Madana M.R. Ambavaram and Andy Pereira

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

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

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

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

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

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

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

Nayelli Marsch-Martinez and Andy Pereira

9. Activation Tagging and Insertional Mutagenesis in Barley

Michael A. Ayliffe and Anthony J. Pryor

10. Methods for Rice Phenomics Studies

Chyr-Guan Chern, Ming-Jen Fan, Sheng-Chung Huang, Su-May Yu, Fu-Jin Wei,

Cheng-Chieh Wu, Arunee Trisiriroj, Ming-Hsing Lai, Shu Chen, and Yue-Ie C. Hsing

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

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

12. Transposon Insertional Mutagenesis in Rice

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

13. Reverse Genetics in Medicago truncatula Using Tnt1 Insertion Mutants

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

14. Screening Arabidopsis Genotypes for Drought Stress Resistance

Amal Harb and Andy Pereira

15. Protein Tagging for Chromatin Immunoprecipitation (ChIP) from Arabidopsis

Stefan de Folter

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

Pieter B.F. Ouwerkerk and Annemarie H. Meijer

17. Plant Metabolomics by GC-MS and Differential Analysis

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

18. Gramene Database: A Hub for Comparative Plant Genomics

Pankaj Jaiswal