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Plant Functional Genomics

Methods and Protocols

  • Jose M. Alonso
  • Anna N. Stepanova

Part of the Methods in Molecular Biology book series (MIMB, volume 1284)

Table of contents

  1. Front Matter
    Pages i-xv
  2. Epigenetics

  3. Transcriptional, Translational, and Metabolic Analysis

    1. Front Matter
      Pages 91-91
    2. Hilda van Mourik, Jose M. Muiño, Alice Pajoro, Gerco C. Angenent, Kerstin Kaufmann
      Pages 93-121
    3. Nobutoshi Yamaguchi, Cara M. Winter, Frank Wellmer, Doris Wagner
      Pages 123-138
    4. Piyada Juntawong, Maureen Hummel, Jeremie Bazin, Julia Bailey-Serres
      Pages 139-173
    5. Pui-Leng Ip, Kenneth D. Birnbaum
      Pages 175-183
    6. Mauricio A. Reynoso, Piyada Juntawong, Marcos Lancia, Flavio A. Blanco, Julia Bailey-Serres, María Eugenia Zanetti
      Pages 185-207
    7. Reed Sorenson, Julia Bailey-Serres
      Pages 209-219
    8. José L. Rambla, M. P. López-Gresa, J. M. Bellés, Antonio Granell
      Pages 221-235
  4. Forward and Reverse Genetics

    1. Front Matter
      Pages 237-237
    2. Jian-Feng Li, Dandan Zhang, Jen Sheen
      Pages 239-255
    3. Tiffany M. Jamann, Peter J. Balint-Kurti, James B. Holland
      Pages 257-285
    4. Miguel A. Flores, Maria I. Reyes, Dominique (Niki) Robertson, Susanne Kjemtrup
      Pages 305-322
    5. Ronan C. O’Malley, Cesar C. Barragan, Joseph R. Ecker
      Pages 323-342
    6. Radka Slovak, Christian Göschl, Ümit Seren, Wolfgang Busch
      Pages 343-357
    7. Helen Tsai, Kathie Ngo, Meric Lieberman, Victor Missirian, Luca Comai
      Pages 359-380
  5. Tools to Accelerate Gene Functional Analysis and Plant Synthetic Biology

    1. Front Matter
      Pages 397-397
    2. Marta Vazquez-Vilar, Alejandro Sarrion-Perdigones, Peio Ziarsolo, Jose Blanca, Antonio Granell, Diego Orzaez
      Pages 399-420
    3. Jos R. Wendrich, Che-Yang Liao, Willy A. M. van den Berg, Bert De Rybel, Dolf Weijers
      Pages 421-431
    4. Ha-il Jung, Jiapei Yan, Zhiyang Zhai, Olena K. Vatamaniuk
      Pages 433-452
  6. Computational Approaches to Functional Genomics

    1. Front Matter
      Pages 453-453
    2. J. Davila-Velderrain, J. C. Martinez-Garcia, E. R. Alvarez-Buylla
      Pages 455-479
    3. Ann E. Loraine, Ivory Clabaugh Blakley, Sridharan Jagadeesan, Jeff Harper, Gad Miller, Nurit Firon
      Pages 481-501
    4. Tomás C. Moyano, Elena A. Vidal, Orlando Contreras-López, Rodrigo A. Gutiérrez
      Pages 503-526
  7. Back Matter
    Pages 527-532

About this book

Introduction

This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utilized by a wide array of plant biologists to address specific questions in their favorite model systems. This book is organized into five parts. Part I examines the tools and methods required for identifying epigenetic and conformational changes at the whole-genome level. Part II presents approaches used to determine key aspects of a gene’s function, such as techniques used to identify and characterize gene regulatory networks. This is followed by a discussion of tools used to analyze the levels of mRNA, mRNA translation rates, and metabolites. Part III features a compilation of forward and reverse genetic approaches that include recent implementation of high-throughput sequencing in classical methodologies such as QTL mapping. The final two parts explore strategies to facilitate and accelerate the generation and testing of functional DNA elements, and basic computational tools used to facilitate the use of systems biology approached by a broad spectrum of plant researchers. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls.

Practical and timely, Plant Functional Genomics: Methods and Protocols, Second Edition highlights the latest developments in DNA sequencing technologies that are likely to continue shaping the future of functional genomics.

Keywords

DNA sequencing RNA secondary structure conformational changes epigemetic changes genome genomics techniques mRNA translatiin rates

Editors and affiliations

  • Jose M. Alonso
    • 1
  • Anna N. Stepanova
    • 2
  1. 1.Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighUSA
  2. 2.Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-4939-2444-8
  • Copyright Information Springer Science+Business Media New York 2015
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-2443-1
  • Online ISBN 978-1-4939-2444-8
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site