Plant gene silencing : mechanisms and applications

225 Pages·2017·7.421 MB·English

by  Tamas Dalmay

Plant Gene Silencing:
Mechanisms and Applications
CABI Biotechnology SerieS
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Animal Nutrition with Transgenic Plants
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Bt Resistance: Characterization and Strategies for GM Crops Producing Bacillus thuringiensis
Toxins
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Plant Gene Silencing: Mechanisms and Applications
Edited by T. Dalmay
Plant Gene Silencing:
Mechanisms and Applications
Edited by
Tamas Dalmay
School of Biological Sciences, University
of East Anglia, Norwich, UK
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British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library, London, UK.
Library of Congress Cataloging-in-publication data
Names: Dalmay, Tamas, editor.
Title: Plant gene silencing : mechanisms and applications / edited by Tamas Dalmay.
Other titles: Plant gene silencing (Dalmay) | CABI biotechnology series ; 5.
Description: Wallingford, Oxfordshire, UK ; Boston, MA : CABI, [2017] |
Series: CABI biotechnology series ; 5 | Includes bibliographical references.
Identifiers: LCCN 2016057958 (print) | LCCN 2017009210 (ebook) | ISBN
9781780647678 (hbk : alk. paper) | ISBN 9781780647685 (ePDF) | ISBN
9781780647692 (ePub)
Subjects: LCSH: Plant gene silencing. | MESH: Gene Silencing | Gene
Expression Regulation, Plant
Classification: LCC QK981.4 .P5794 2017 (print) | LCC QK981.4 (ebook) | NLM
QK 981.4 | DDC 572.8/652--dc23
LC record available at https://lccn.loc.gov/2016057958
ISBN: 978 1 78064 767 8 (hardback)
978 1 78064 768 5 (e-book)
978 1 78064 769 2 (e-pub)
Commissioning editor: David Hemming
Editorial assistant: Emma McCann
Production editors: Alan Worth/Lauren Povey
Typeset by SPi, Pondicherry, India.
Printed and bound in the UK by CPI Group (UK) Ltd, Croydon, CR0 4YY.
Contents
Contributors vii
Preface ix
1 Diversity of RNA Silencing Pathways in Plants 1
Emilie Elvira-Matelot, Ángel Emilio Martínez de Alba and Hervé Vaucheret
2 Induction and Suppression of Silencing by Plant Viruses 32
Ares Mingot, Adrian Valli, Juan José López-Moya and Juan Antonio García
3 Artificial Induction and Maintenance of Epigenetic Variations in Plants 59
Soumita Das, Rahul Raj Singh and P.V. Shivaprasad
4 Gene Silencing in Archaeplastida Algae 75
Xinrong Ma, Eun-Jeong Kim and Heriberto Cerutti
5 Gene Silencing in Fungi: A Diversity of Pathways and Functions 94
Santiago Torres-Martínez and Rosa M. Ruiz-Vázquez
6 Artificial Small RNA-based Strategies for Effective and Specific
Gene Silencing in Plants 110
Alberto Carbonell
7 Application of RNA Silencing in Improving Plant Traits
for Industrial Use 128
Sumit Ghosh, Mohammad Irfan and Asis Datta
8 Increasing Nutritional Value by RNA Silencing 147
Elsa Pons and Leandro Peña
9 RNA-based Control of Plant Diseases: A Case Study with
Fusarium graminearum 166
Aline Koch and Karl-Heinz Kogel
v
vi Contents
10 Targeting Nematode Genes by RNA Silencing 176
John Fosu-Nyarko, Sadia Iqbal and Michael G.K. Jones
11 Gene Silencing Provides Efficient Protection against Plant Viruses 193
Mario Tavazza, Alessandra Lucioli and Vincenza Ilardi
Index 209
Contributors
Alberto Carbonell, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV),
Campus UPV, Valencia, Spain. E-mail: [email protected]
Heriberto Cerutti, School of Biological Sciences and Center for Plant Science Innovation,
University of Nebraska-Lincoln, Lincoln, USA. E-mail: [email protected]
Tamas Dalmay, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ,
UK. E-mail: [email protected]
Soumita Das, National Centre for Biological Sciences, Bellary Road, Bangalore 560065,
India. E-mail: [email protected]
Asis Datta, National Institute of Plant Genome Research, New Delhi 110067, India. E-mail:
[email protected]
Emilie Elvira-Matelot, Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS,
Université Paris-Saclay, RD10, 78000 Versailles, France. E-mail: emilie.elvira-matelot@
inserm.fr
John Fosu-Nyarko, Plant Biotechnology Research Group, Western Australian State
Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch
University, Perth, Western Australia. E-mail: [email protected]
Juan Antonio García, National Centre for Biotechnology CNB, CSIC, Cantoblanco, Madrid,
Spain. E-mail: [email protected]
Sumit Ghosh, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015,
India. E-mail: [email protected]
Vincenza Ilardi, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria –
Centro di Ricerca per la Patologia Vegetale (CREA-PAV), Rome, Italy. E-mail: vincenza.
[email protected]
Sadia Iqbal, Plant Biotechnology Research Group, Western Australian State Agricultural
Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth,
Western Australia. E-mail: [email protected]
Mohammad Irfan, National Institute of Plant Genome Research, New Delhi 110067, India.
E-mail: [email protected]
vii
viii Contributors
Michael G.K. Jones, Plant Biotechnology Research Group, Western Australian State
Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch
University, Perth, Western Australia. E-mail: [email protected]
Eun-Jeong Kim, School of Biological Sciences and Center for Plant Science Innovation,
University of Nebraska-Lincoln, Lincoln, USA. E-mail: [email protected]
Aline Koch, Institute for Phytopathology, Centre for BioSystems, Land Use and Nutrition,
Justus Liebig University, Giessen, Germany. E-mail: [email protected]
Karl-Heinz Kogel, Institute for Phytopathology, Centre for BioSystems, Land Use and
Nutrition, Justus Liebig University, Giessen, Germany. E-mail: karl-heinz.kogel@agrar.
uni-giessen.de
Juan José López-Moya, Centre for Research in Agricultural Genomics CRAG, CSIC-IRTA-
UAB-UB, Campus Bellaterra, Barcelona, Spain. E-mail: [email protected]
Alessandra Lucioli, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo
Economico Sostenibile (ENEA), C.R. Casaccia, Rome, Italy. E-mail: alessandra.lucioli@
enea.it
Xinrong Ma, School of Biological Sciences and Center for Plant Science Innovation,
University of Nebraska-Lincoln, Lincoln, USA. E-mail: [email protected]
Ángel Emilio Martínez de Alba, Institut Jean-Pierre Bourgin, INRA, AgroParisTech,
CNRS, Université Paris-Saclay, RD10, 78000 Versailles, France. E-mail: aemartidealba@
gmail.com
Ares Mingot, Centre for Research in Agricultural Genomics CRAG, CSIC-IRTA-UAB-UB,
Campus Bellaterra, Barcelona, Spain. E-mail: [email protected]
Leandro Peña, Laboratorio de Biotecnología de Cítricos, Instituto de Biología Molecular y
Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas/Universidad
Politécnica de Valencia, Valencia, Spain; Laboratorio de Biotecnologia Vegetal, Pesquisa &
Desenvolvimento, Fundo de Defensa da Citricultura (Fundecitrus), Araraquara, Sao
Paulo, Brazil. E-mail: [email protected]
Elsa Pons, Laboratorio de Biotecnología de Cítricos, Instituto de Biología Molecular y
Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas/Universidad
Politécnica de Valencia, Valencia, Spain; Laboratorio de Biotecnologia Vegetal, Pesquisa &
Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, Sao Paulo,
Brazil. E-mail: [email protected]
Rosa M. Ruiz-Vázquez, University of Murcia, Murcia, Spain. E-mail: [email protected]
P.V. Shivaprasad, National Centre for Biological Sciences, Bellary Road, Bangalore 560065,
India. E-mail: [email protected]
Rahul Raj Singh, National Centre for Biological Sciences, Bellary Road, Bangalore 560065,
India. E-mail: [email protected]
Mario Tavazza, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo
Economico Sostenibile (ENEA), C.R. Casaccia, Rome, Italy. E-mail: [email protected]
Santiago Torres-Martínez, University of Murcia, Murcia, Spain. E-mail: [email protected]
Adrian Valli, National Centre for Biotechnology CNB, CSIC, Cantoblanco, Madrid, Spain.
E-mail: [email protected]
Hervé Vaucheret, Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université
Paris-Saclay, RD10, 78000 Versailles, France. E-mail: [email protected]
Preface
It is more than 25 years ago that gene silencing was described for the first time, although at
that stage the mechanism was not understood (Napoli et al., 1990; van der Krol et al., 1990).
The progress during the last 25 years or so has been simply remarkable: we now do not just
understand how gene silencing happens down to a very detailed molecular level, but many
strategies have been developed to harness this phenomenon. This book describes both the
theory of gene silencing and also the application.
The first five chapters discuss different aspects of the gene silencing mechanism. Since
the silencing pathways are particularly diverse in plants, a whole chapter is dedicated to de-
scribe these (Chapter 1). It is a generally accepted view that gene silencing has evolved in
plants as a defence mechanism against viruses, therefore Chapter 2 discusses the ‘arms race’
between plants and viruses, how viruses trigger silencing and also evolved proteins that can
suppress it. Another aspect of gene silencing is the epigenetic changes caused by silencing.
This, and how we can direct epigenetic changes, is described in Chapter 3. Finally, the the-
oretical part is closed by two chapters on how gene silencing works in algae (Chapter 4) and
fungi (Chapter 5), two groups of organisms related to plants.
The second part of the book is dedicated to application of gene silencing. Small
non-coding RNAs are key molecules in the mechanism and Chapter 6 discusses various
strategies to produce small artificial RNAs. The following chapters describe the application
of gene silencing to influence specific, agronomically important traits in plants, including
traits for industrial use (Chapter 7) and nutritional value (Chapter 8). The last three chap-
ters review the use of gene silencing to provide resistance against different types of patho-
gens including fungi (Chapter 9), nematodes (Chapter 10) and viruses (Chapter 11).
ix