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Plant Genomics

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Wolfgang Busch

    1. Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

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

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Genotypes

    1. Front Matter

      Pages 1-1
      Download chapter 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
      Download chapter 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
      Download chapter 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
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Keywords

About this book

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.


Editors and Affiliations

  • Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria

    Wolfgang Busch

Bibliographic Information

  • Book Title: Plant Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Wolfgang Busch

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7003-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7001-8Published: 25 April 2017

  • Softcover ISBN: 978-1-4939-8364-3Published: 20 July 2018

  • eBook ISBN: 978-1-4939-7003-2Published: 24 April 2017

  • 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

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