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Brachypodium Genomics

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Gaurav Sablok

    1. Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

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  2. Hikmet Budak

    1. Sabanci University, Istanbul, Turkey

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    You can also search for this editor in PubMed   Google Scholar

  3. Peter J. Ralph

    1. Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia

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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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1667)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Methods for Cytogenetic Chromosome Barcoding and Chromosome Painting in Brachypodium distachyon and Its Relative Species

    • Dominika Idziak-Helmcke, Alexander Betekhtin
    Pages 1-19

  3. Transcriptional and Posttranscriptional Regulation of Drought Stress Treatments in Brachypodium Leaves

    • Edoardo Bertolini, Mario Enrico Pè, Erica Mica
    Pages 21-29

  4. Brachypodium distachyon Long Noncoding RNAs: Genome-Wide Identification and Expression Analysis

    • Concetta De Quattro, Erica Mica, Mario Enrico Pè, Edoardo Bertolini
    Pages 31-42

  5. A Highly Efficient and Reproducible Fusarium spp. Inoculation Method for Brachypodium distachyon

    • Anuj Rana, Aneesh Karunakaran, Timothy L. Fitzgerald, Rosalie Sabburg, Elizabeth A. B. Aitken, Robert J. Henry et al.
    Pages 43-55

  6. Tissue Culture (Somatic Embryogenesis)-Induced Tnt1 Retrotransposon-Based Mutagenesis in Brachypodium distachyon

    • Upinder S. Gill, Juan C. Serrani-Yarce, Hee-Kyung Lee, Kirankumar S. Mysore
    Pages 57-63

  7. Methods for Xyloglucan Structure Analysis in Brachypodium distachyon

    • Lifeng Liu
    Pages 65-71

  8. Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon

    • Sonia Irigoyen, Renesh H. Bedre, Karen-Beth G. Scholthof, Kranthi K. Mandadi
    Pages 73-85

  9. Information Resources for Functional Genomics Studies in Brachypodium distachyon

    • Keiichi Mochida, Kazuo Shinozaki
    Pages 87-99

  10. Methods for Functional Transgenics: Development of Highly Efficient Transformation Protocol in Brachypodium and Its Suitability for Advancing Brachypodium Transgenics

    • Ron Vunsh
    Pages 101-117

  11. Molecular Markers in Whole Genome Evolution of Brachypodium

    • Xin-Chun Mo, De-Quan Zhang, Can Kou, Ling-Juan Yin
    Pages 119-137

  12. Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)

    • Zhenguo Zhang, Gaurav Sablok
    Pages 139-148

  13. Identification of Pseudogenes in Brachypodium distachyon Chromosomes

    • Salvatore Camiolo, Andrea Porceddu
    Pages 149-171

  14. TILLING in Brachypodium distachyon

    • Louise de Bang, Anna Maria Torp, Søren K. Rasmussen
    Pages 173-186

  15. Method for the Large-Scale Identification of phasiRNAs in Brachypodium distachyon

    • Kun Yang, Xiaopeng Wen, Gaurav Sablok
    Pages 187-194

  16. Evaluation of Genome-Wide Markers and Orthologous Markers in Brachypodium distachyon

    • Gaurav Sablok, Suresh B. Mudunuri, Korneliya Gudys, Kranthi Chennamsetti, G. P. Saradhi Varma, Miroslaw Kwasniewski
    Pages 195-201

  17. Protocol for Coexpression Network Construction and Stress-Responsive Expression Analysis in Brachypodium

    • Sanchari Sircar, Nita Parekh, Gaurav Sablok
    Pages 203-221

  18. Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq)

    • I-Hsuan Lin
    Pages 223-287

  19. Application of Tissue Culture and Transformation Techniques in Model Species Brachypodium distachyon

    • Bahar Sogutmaz Ozdemir, Hikmet Budak
    Pages 289-310

  20. Erratum to: Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq)

    • I-Hsuan Lin
    Pages E1-E1
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Keywords

About this book

This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. 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.

Cutting-edge and comprehensive, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.

Editors and Affiliations

  • Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach IASMA, Trentino, Italy

    Gaurav Sablok

  • Sabanci University, Istanbul, Turkey

    Hikmet Budak

  • Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia

    Peter J. Ralph

Bibliographic Information

  • Book Title: Brachypodium Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Gaurav Sablok, Hikmet Budak, Peter J. Ralph

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7278-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7276-0Published: 20 October 2017

  • Softcover ISBN: 978-1-4939-8439-8Published: 18 May 2018

  • eBook ISBN: 978-1-4939-7278-4Published: 16 October 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 312

  • Number of Illustrations: 17 b/w illustrations, 52 illustrations in colour

  • Topics: Plant Sciences

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