Description
Book SynopsisAfter 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.
Trade ReviewFrom 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)
Table of Contents1. 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-Martínez 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
