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© 2017

Plant Genomics

Methods and Protocols

  • Wolfgang Busch
Book

Part of the Methods in Molecular Biology book series (MIMB, volume 1610)

Table of contents

  1. Front Matter
    Pages i-xi
    PDF

  2. Genotypes

    1. Front Matter
      Pages 1-1
      PDF
    2. CRISPR/Cas-Mediated In Planta Gene Targeting
      Simon Schiml, Friedrich Fauser, Holger Puchta
      Pages 3-11
    3. User Guide for the LORE1 Insertion Mutant Resource
      Terry Mun, Anna Małolepszy, Niels Sandal, Jens Stougaard, Stig U. Andersen
      Pages 13-23
    4. Enabling Reverse Genetics in Medicago truncatula Using High-Throughput Sequencing for Tnt1 Flanking Sequence Recovery
      Xiaofei Cheng, Nick Krom, Shulan Zhang, Kirankumar S. Mysore, Michael Udvardi, Jiangqi Wen
      Pages 25-37
    5. The Generation of Doubled Haploid Lines for QTL Mapping
      Daniele L. Filiault, Danelle K. Seymour, Ravi Maruthachalam, Julin N. Maloof
      Pages 39-57

  3. Phenotypes

    1. Front Matter
      Pages 59-59
      PDF
    2. Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing
      Jörg Hagmann, Claude Becker
      Pages 61-72
    3. Circular Chromosome Conformation Capture in Plants
      Stefan Grob
      Pages 73-92
    4. Genome-Wide Profiling of Histone Modifications and Histone Variants in Arabidopsis thaliana and Marchantia polymorpha
      Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima
      Pages 93-106
    5. Tissue-Specific Transcriptome Profiling in Arabidopsis Roots
      Erin E. Sparks, Philip N. Benfey
      Pages 107-122
    6. Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues
      Gaoyuan Song, Maxwell R. McReynolds, Justin W. Walley
      Pages 123-133
    7. Automated High-Throughput Root Phenotyping of Arabidopsis thaliana Under Nutrient Deficiency Conditions
      Santosh B. Satbhai, Christian Göschl, Wolfgang Busch
      Pages 135-153
    8. Large-Scale Phenotyping of Root Traits in the Model Legume Lotus japonicus
      Marco Giovannetti, Anna Małolepszy, Christian Göschl, Wolfgang Busch
      Pages 155-167
    9. Long-Term Confocal Imaging of Arabidopsis thaliana Roots for Simultaneous Quantification of Root Growth and Fluorescent Signals
      Delyana Stoeva, Christian Göschl, Bruce Corliss, Wolfgang Busch
      Pages 169-183

  4. Molecular Bases of Phenotypes

    1. Front Matter
      Pages 185-185
      PDF
    2. Identification of Protein–DNA Interactions Using Enhanced Yeast One-Hybrid Assays and a Semiautomated Approach
      Allison Gaudinier, Michelle Tang, Anne-Maarit Bågman, Siobhan M. Brady
      Pages 187-215
    3. Mapping Protein-Protein Interaction Using High-Throughput Yeast 2-Hybrid
      Jessica Lopez, M. Shahid Mukhtar
      Pages 217-230
    4. Mapping Protein–Protein Interactions Using Affinity Purification and Mass Spectrometry
      Chin-Mei Lee, Christopher Adamchek, Ann Feke, Dmitri A. Nusinow, Joshua M. Gendron
      Pages 231-249
    5. Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS)
      Natalie M. Clark, Rosangela Sozzani
      Pages 251-266
    6. Studying Protein–Protein Interactions In Planta Using Advanced Fluorescence Microscopy
      Marc Somssich, Rüdiger Simon
      Pages 267-285
    7. Chemiluminescence-Based Detection of Peptide Activity and Peptide-Receptor Binding in Plants
      Mari Wildhagen, Markus Albert, Melinka A. Butenko
      Pages 287-295
    8. Application of Chemical Genomics to Plant–Bacteria Communication: A High-Throughput System to Identify Novel Molecules Modulating the Induction of Bacterial Virulence Genes by Plant Signals
      Elodie Vandelle, Maria Rita Puttilli, Andrea Chini, Giulia Devescovi, Vittorio Venturi, Annalisa Polverari
      Pages 297-314
  5. Back Matter
    Pages 315-317
    PDF

About this book

Introduction

This volume provides protocols that revolve around three pillars of progress in the plant genomics field: genotypes, phenotypes, and the molecular processes in between. Chapters in Plant Genomics: Methods and Protocols are not restricted to the predominant model species Arabidopsis thaliana, hoping to encourage and facilitate other researchers to expand their research to other species. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Plant Genomics: Methods and Protocols aims to serve as an inspiration for further studies in plant genomics.

Keywords

genomics genotypes phenotypes plant genomics transcriptomes proteins metabolites

Editors and affiliations

  • Wolfgang Busch
    • 1
  1. 1.Gregor Mendel Institute (GMI)Austrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria

Bibliographic information

  • Book Title Plant Genomics
  • Book Subtitle Methods and Protocols
  • Editors Wolfgang Busch
  • Series Title Methods in Molecular Biology
  • Series Abbreviated Title Methods Molecular Biology
  • DOI https://doi.org/10.1007/978-1-4939-7003-2
  • Copyright Information Springer Science+Business Media LLC 2017
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-1-4939-7001-8
  • Softcover ISBN 978-1-4939-8364-3
  • eBook ISBN 978-1-4939-7003-2
  • Series ISSN 1064-3745
  • Series E-ISSN 1940-6029
  • Edition Number 1
  • Number of Pages XI, 317
  • Number of Illustrations 14 b/w illustrations, 60 illustrations in colour
  • Topics Plant Sciences
  • Buy this book on publisher's site