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Plant Functional Genomics

Methods and Protocols, Volume 1

  • Book
  • © 2024

Overview

Editors:
  1. Fatemeh Maghuly

    1. Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2787)

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About this book

This detailed book gathers hands-on techniques to characterize, identify, localize, profile, and determine genome functions in plants. Volume 1 opens with a section exploring protocols to advance our understanding of plant genetics and ecology via phenomics, and it continues with chapters on plant genetics, transcriptomics, and proteomics to unravel plant protein structures and functions, bridging proteomics and phosphoproteomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and comprehensive, Plant Functional Genomics: Methods and Protocols serves as an ideal guide to the immense promise of functional genomics, spanning from fundamental evolutionary studies to practical advancements in crop improvement.

Keywords

Table of contents (23 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Phenomics

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management

      • Wanneng Yang, Hui Feng, Xiao Hu, Jingyan Song, Jing Guo, Bingjie Lu
      Pages 3-38

    3. A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel

      • Sofia A. Bengoa Luoni, Francesco Garassino, Mark G. M. Aarts
      Pages 39-53

    4. Methods for Functional Physiological Phenotyping and High-Order Data Quantification

      • Ting Sun, Rujia Jiang, Yunxiu Liu, Pei Xu
      Pages 55-68

    5. Physiotyping of Plants and Modeling the Soil Plant Atmospheric Continuum (SPAC)

      • Gert Bachmann, Franz Hadacek
      Pages 69-80

    6. Root Hair Imaging Using Confocal Microscopy

      • Krishna Vasant Mutanwad, Monika Debreczeny, Doris Lucyshyn
      Pages 81-94

    7. Cytogenetic Bioindication in Root Meristems for Vitality Assessment of Trees

      • Anna Gasperl, Maria Müller
      Pages 95-103

  3. Genomics

    1. Front Matter

      Pages 105-105
      Download chapter PDF

    2. Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data

      • José P. Jiménez-Madrigal, Bradley J. Till, Andrés Gatica-Arias
      Pages 107-122

    3. Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data

      • Bradley J. Till, José P. Jiménez-Madrigal, Andrés Gatica-Arias
      Pages 123-139

    4. Identification of Induced Copy Number Variation from Low Coverage Sequence Data

      • Bradley J. Till
      Pages 141-152

    5. Genetic Map Construction Using F2 and RIL/DH Mapping Population

      • Beata MyÅ›ków, PaweÅ‚ Milczarski, Stefan StojaÅ‚owski
      Pages 153-168

    6. QTL Mapping Using RIL Population

      • PaweÅ‚ Milczarski, Stefan StojaÅ‚owski, Beata MyÅ›ków
      Pages 169-181

    7. Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine

      • Hymavathi Salava, Tamás Deák, Carmen Czepe, Fatemeh Maghuly
      Pages 183-197

  4. Transcriptomics

    1. Front Matter

      Pages 199-199
      Download chapter PDF

    2. RNA Isolation Method in Marginal Crops with High Agronomic Potential

      • Kena Casarrubias-Castillo, John Paul Délano-Frier, Paola Andrea Palmeros-Suárez
      Pages 201-207

    3. A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection

      • Andrés Gatica-Arias, Carolina Muñoz-Flores, Alejandro Bolívar-González
      Pages 209-223

    4. Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example

      • Thiely Patricia Fabian Dos Santos, Elodia Sánchez-Barrantes, Luiz Filipe Pereira, Andrés Gatica-Arias
      Pages 225-243

    5. Quantitative Estimation of Promoter Activity in Cannabis sativa Using Agroinfiltration-Based Transient Gene Expression

      • Jan Fousek, Jakub DuÅ¡ek, Hana Hoffmeisterová, Noemi ÄŒeÅ™ovská, Jiban Kumar Kundu, Tomáš Moravec
      Pages 245-253
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Editors and Affiliations

  • Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria

    Fatemeh Maghuly

Bibliographic Information

  • Book Title: Plant Functional Genomics

  • Book Subtitle: Methods and Protocols, Volume 1

  • Editors: Fatemeh Maghuly

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3778-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3777-7Published: 25 April 2024

  • Softcover ISBN: 978-1-0716-3780-7Due: 09 May 2025

  • eBook ISBN: 978-1-0716-3778-4Published: 24 April 2024

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 357

  • Number of Illustrations: 14 b/w illustrations, 87 illustrations in colour

  • Topics: Plant Genetics and Genomics

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