Plant reverse genetics : methods and protocols / edited by Andy Pereira.

Contributor(s): Pereira, Andy
Material type: TextTextSeries: Springer protocols (Series): ; Methods in molecular biology (Clifton, N.J.): v. 678.Publisher: [New York, N.Y.] : Humana Press : Springer [distributor], ©2011Description: 1 online resource (xi, 282 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781607616825; 1607616823Subject(s): Plant genomes -- Research | Genes | Databases, Genetic | Publication Formats | Genetic Techniques | Biology | Genome | Eukaryota | Biological Science Disciplines | Databases, Factual | Genome Components | Investigative Techniques | Genetic Structures | Organisms | Publication Characteristics | Genes, Plant | Laboratory Manuals | Sequence Analysis | Genome, Plant | Plants | Databases, Nucleic Acid | Databases as Topic | Genetic Phenomena | Natural Science Disciplines | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Disciplines and Occupations | Phenomena and Processes | Information Storage and Retrieval | Information Systems | Medical Informatics Applications | Information Science | Medical Informatics | Genetics | Botany | Life sciences | Medical genetics | Plant breeding | planten | plants | moleculaire genetica | molecular genetics | genexpressieanalyse | genomics | plantengenetica | plant genetics | functionele genomica | functional genomics | arabidopsis thaliana | oryza sativa | laboratoriummethoden | laboratory methods | protocollen | protocols | Genome informatics | Plant Molecular Biology | Biological Techniques | Genoominformatica | Moleculaire plantenbiologie | Biologische techniekenGenre/Form: Laboratory Manual. | Electronic books. Additional physical formats: Print version:: Plant reverse genetics.DDC classification: 572.862 LOC classification: QK981Online resources: Click here to access online
Contents:
Analysis of high-throughput sequencing data / S.P. Mane, T. Modise and B.W. Sobral -- Identification of plant microRNAs using expressed sequence tag analysis / T.P. Frazier and B. Zhang -- Microarray data analysis / S.K. Mohapatra and A. Krishnan -- Setting up reverse transcription quantitative-PCR experiments / M.M. Ambavaram and A. Pereira -- Virus-induced gene silencing in Nicotiana benthamiana and other plant species / A. Hayward, M. Padmanabhan and S.P. Dinesh-Kumar -- Agroinoculation and agroinfiltration: Simple tools for complex gene function analyses / Z. Vaghchhipawala [and others] -- Full-length cDNA overexpressor gene hunting system (FOX hunting system) / M. Higuchi [and others] -- Activation tagging with En/Spm-i /dSpm transposons in Arabidopsis / N. Marsch-Martinez and A. Pereira -- Activation tagging and insertional mutagenesis in barley / M.A. Ayliffe and A.J. Pryor -- Methods for rice phenomics studies / C.G. Chern [and others] -- Development of an efficient inverse PCR method for isolating gene tags from T-DNA insertional mutants in rice / S.R. Kim, J.S. Jeon and G. An -- Transposon insertional mutagenesis in rice / N.M. Upadhyaya, Q.H. Zhu and R.S. Bhat -- Reverse genetics in Medicago truncatula using Tnt1 insertion mutants / X. Cheng [and others] -- Screening Arabidopsis genotypes for drought stress resistance / A. Harb and A. Pereira -- Protein tagging for chromatin immunoprecipitation from Arabidopsis / S. de Folter -- Yeast one-hybrid screens for detection of transcription factor DNA interactions / P.B. Ouwerkerk and A.H. Meijer -- Plant metabolomics by GC-MS and differential analysis / J.L. Shuman [and others] -- Gramene database: A hub for comparative plant genomics / P. Jaiswal.
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.
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Includes bibliographical references and index.

Analysis of high-throughput sequencing data / S.P. Mane, T. Modise and B.W. Sobral -- Identification of plant microRNAs using expressed sequence tag analysis / T.P. Frazier and B. Zhang -- Microarray data analysis / S.K. Mohapatra and A. Krishnan -- Setting up reverse transcription quantitative-PCR experiments / M.M. Ambavaram and A. Pereira -- Virus-induced gene silencing in Nicotiana benthamiana and other plant species / A. Hayward, M. Padmanabhan and S.P. Dinesh-Kumar -- Agroinoculation and agroinfiltration: Simple tools for complex gene function analyses / Z. Vaghchhipawala [and others] -- Full-length cDNA overexpressor gene hunting system (FOX hunting system) / M. Higuchi [and others] -- Activation tagging with En/Spm-i /dSpm transposons in Arabidopsis / N. Marsch-Martinez and A. Pereira -- Activation tagging and insertional mutagenesis in barley / M.A. Ayliffe and A.J. Pryor -- Methods for rice phenomics studies / C.G. Chern [and others] -- Development of an efficient inverse PCR method for isolating gene tags from T-DNA insertional mutants in rice / S.R. Kim, J.S. Jeon and G. An -- Transposon insertional mutagenesis in rice / N.M. Upadhyaya, Q.H. Zhu and R.S. Bhat -- Reverse genetics in Medicago truncatula using Tnt1 insertion mutants / X. Cheng [and others] -- Screening Arabidopsis genotypes for drought stress resistance / A. Harb and A. Pereira -- Protein tagging for chromatin immunoprecipitation from Arabidopsis / S. de Folter -- Yeast one-hybrid screens for detection of transcription factor DNA interactions / P.B. Ouwerkerk and A.H. Meijer -- Plant metabolomics by GC-MS and differential analysis / J.L. Shuman [and others] -- Gramene database: A hub for comparative plant genomics / P. Jaiswal.

Print version record.

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.

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