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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(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.
List of contents
Analysis of High-Throughput Sequencing Data.- Identification of Plant MicroRNAs Using Expressed Sequence Tag Analysis.- Microarray Data Analysis.- Setting Up Reverse Transcription Quantitative-PCR Experiments.- Virus-Induced Gene Silencing in Nicotiana benthamiana and Other Plant Species.- Agroinoculation and Agroinfiltration: Simple Tools for Complex Gene Function Analyses.- Full-Length cDNA Overexpressor Gene Hunting System (FOX Hunting System).- Activation Tagging with En/Spm-I/dSpm Transposons in Arabidopsis.- Activation Tagging and Insertional Mutagenesis in Barley.- Methods for Rice Phenomics Studies.- Development of an Efficient Inverse PCR Method for Isolating Gene Tags from T-DNA Insertional Mutants in Rice.- Transposon Insertional Mutagenesis in Rice.- Reverse Genetics in Medicago truncatula Using Tnt1 Insertion Mutants.- Screening Arabidopsis Genotypes for Drought Stress Resistance.- Protein Tagging for Chromatin Immunoprecipitation (ChIP) from Arabidopsis.- Yeast One-Hybrid Screens for Detection of Transcription Factor DNA Interactions.- Plant Metabolomics by GC-MS and Differential Analysis.- Gramene Database: A Hub for Comparative Plant Genomics.
Summary
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.
Additional text
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)
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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)
