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Plant Reverse Genetics

Methods and Protocols

  • Book
  • © 2011

Overview

Editors:
  1. Andy Pereira

    1. , Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, USA

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  • Presents an experimental framework to ascribe functions to plant genes in model and crop plants
  • Describes methods for generating mutants in model and specific target plants
  • Includes detailed protocols for the analysis of transcriptome, metabolome, and ultra high-throughput sequencing data
  • Examines high-throughput analysis supported by simple computer scripts to automate the process
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 678)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  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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Keywords

About this book

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.

Reviews

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)

Editors and Affiliations

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

    Andy Pereira

Bibliographic Information

  • Book Title: Plant Reverse Genetics

  • Book Subtitle: Methods and Protocols

  • Editors: Andy Pereira

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60761-682-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-60761-681-8Published: 11 October 2010

  • Softcover ISBN: 978-1-4939-6127-6Published: 23 August 2016

  • eBook ISBN: 978-1-60761-682-5Published: 08 October 2010

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 282

  • Topics: Plant Sciences, Plant Genetics and Genomics, Gene Function

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