caister.com/transgenic Genes, Genetics and Transgenics for Virus Resistance in Plants https://doi.org/10.21775/9781910190814 Edited by Basavaprabhu L. Patil ICAR-National Research Centre on Plant Biotechnology (NRCPB) LBS centre, IARI, Pusa campus New Delhi, India Caister Academic Press caister.com/transgenic Copyright © 2018 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-910190-81-4 (paperback) ISBN: 978-1-910190-82-1 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from images provided by Basavaprabhu L. Patil. Ebooks Ebooks supplied to individuals are single-user only and must not be reproduced, copied, stored in a retrieval system, or distributed by any means, electronic, mechanical, photocopying, email, internet or otherwise. Ebooks supplied to academic libraries, corporations, government organizations, public libraries, and school libraries are subject to the terms and conditions specified by the supplier. caister.com/transgenic Contents Foreword Preface 1 Mechanisms of Virus Resistance in Plants v vii 1 M. E. Chrissie Rey and Vincent N. Fondong 2 Role of Host Transcription Factors in Modulating Defense Response During Plant–Virus Interaction 25 Saurabh Pandey, Pranav P. Sahu, Ritika Kulshreshtha and Manoj Prasad 3 Surfacing the Role of Epigenetics in Host–Virus Interaction 55 Namisha Sharma, Pranav P. Sahu, Ritika Kulshreshtha and Manoj Prasad 4 Molecular Markers as Tools for Identification and Introgression of Virus-Resistant Genes 87 Mamta Sharma, Avijit Tarafdar, U. S. Sharath Chandran, Devashish R. Chobe and Raju Ghosh 5 Genetic Engineering for Virus Resistance in Plants: Principles and Methods 103 Basavaprabhu L. Patil 6 Tools and Techniques for Production of Double-stranded RNA and its Application for Management of Plant Viral Diseases 119 Andreas E. Voloudakis, Maria C. Holeva, Athanasios Kaldis and Dongho Kim 7 Transgenic Virus-Resistant Papaya: Current Status and Future Trends 141 Gustavo Fermin, Paula Tennant and Sudeshna Mazumdar-Leighton 8 Development and Delivery of Transgenic Virus-resistant Cassava in East Africa 159 Henry Wagaba, Andrew Kiggundu and Nigel Taylor 9 Viruses Infecting Rice and their Transgenic Control 177 Gaurav Kumar, Shweta Sharma and Indranil Dasgupta 10 Whitefly-transmitted Begomoviruses and Advances in the Control of their Vectors Surapathrudu Kanakala and Murad Ghanim 201 iv | Contents 11 caister.com/transgenic Virus-resistant Transgenic Tomato: Current Status and Future Prospects 221 S.V. Ramesh and Shelly Praveen 12 Management of Geminiviruses Focusing on Small RNAs in Tomato 235 Archana Singh and Sunil Kumar Mukherjee 13 Viruses Infecting Banana and their Transgenic Management 255 Ramasamy Selvarajan, Chelliah Anuradha, Velusamy Balasubramanian, Sivalingam Elayabalan and Kanicheluam Prasanya Selvam 14 Virus-induced Gene Silencing (VIGS) and its Applications 277 Deep Ratan Kumar, Tejbhan Saini and Radhamani Anandalakshmi 15 Possible Strategies for Establishment of VIGS Protocol in Chickpea 329 Ranjita Sinha and Muthappa Senthil-Kumar Index 345 caister.com/transgenic Foreword In 1986, the first report on the use of genetic engineering to control Tobacco mosaic virus in tobacco plants was published and it opened the gate to a flood of publications for the possible control of many viruses in many hosts. At that time, this concept of engineering virus resistance was a breakthrough. Controlling plant viruses has always been a big challenge to breeders, and suddenly it was possible to control almost any virus in any crop through genetic engineering! Evidently, over the years many natural sources of resistance for numerous plant viruses had been identified; however, combining these resistance sources with other traits was always a challenge to breeders. Therefore, genetic engineering appeared as the solution to control plant viruses! But three decades later, we have to acknowledge that we have not seen the expected revolution in farmers’ fields. On the contrary, we have seen the emergence and outbreak of many new and known plant viral diseases, threatening food security. Even though some plants have been engineered with multiple virus resistance, they have never been commercialized. The engineered papaya with immunity to Papaya ringspot virus remains the most successful example of commercialization of virus-resistant transgenics. The failure to commercialize virus-resistant transgenics is the result not of technical or scientific problems or any sort of biological barrier, but mostly of political pressures from so-called ecological groups. In the meantime, improved technologies were developed and transferred to new crops and novel viruses, and in some instances made real scientific breakthroughs. However, the vested interests of these groups of fanatics, with a false claim of saving the earth’s ecology, raised biosafety standards to the point where only large multinationals could afford them, which de facto prevented the application of these technologies to many important food crops in the world. In the beginning of the twenty-first century, the genomic revolution brought new hopes to control plant viruses by harnessing natural genes of resistance. Whole-genome sequencing of many plants, along with scores of novel DNA technologies, facilitated the use of modern tools in gene discovery for virus resistance. However, the introgression of these resistant loci was restricted due to their multigenic or recessive nature, making it difficult to transfer them to a suitable genetic background without using genetic engineering technologies. Recently, the discovery and use of gene-editing technologies such as CRISPR/Cas9 and TALENs may now allow plant virologists, genomics experts and breeders to work together for a breakthrough in controlling plant viruses. This can be a reality only if these technologies are not considered to be GM- technologies by policy makers. This book, Genes, Genetics and Transgenics for Virus Resistance in Plants, provides a very nice update on the status of current knowledge on the use of genetic engineering and other biotechnological strategies for the control of plant viruses. It is hoped that this information will be used in conjunction with the latest gene technologies to achieve the urgently needed scientific breakthroughs for the successful control of plant viruses, ultimately for the benefit of humankind. Claude M. Fauquet Director, Global Cassava Partnership for the 21st Century (GCP-21) International Center for Tropical Agriculture (CIAT), Cali, Colombia caister.com/transgenic Current Books of Interest Lactobacillus Genomics and Metabolic Engineering Cyanobacteria: Signaling and Regulation Systems Viruses of Microorganisms Protozoan Parasitism: From Omics to Prevention and Control DNA Tumour Viruses: Virology, Pathogenesis and Vaccines Pathogenic Escherichia coli: Evolution, Omics, Detection and Control Postgraduate Handbook: A Comprehensive Guide for PhD and Master’s Students and their Supervisors Enteroviruses: Omics, Molecular Biology, and Control Molecular Biology of Kinetoplastid Parasites Bacterial Evasion of the Host Immune System Illustrated Dictionary of Parasitology in the Post-genomic Era Next-generation Sequencing and Bioinformatics for Plant Science The CRISPR/Cas System: Emerging Technology and Application Brewing Microbiology: Current Research, Omics and Microbial Ecology Metagenomics: Current Advances and Emerging Concepts Bacillus: Cellular and Molecular Biology (Third Edition) Cyanobacteria: Omics and Manipulation Foot-and-Mouth Disease Virus: Current Research and Emerging Trends Brain-eating Amoebae: Biology and Pathogenesis of Naegleria fowleri Staphylococcus: Genetics and Physiology Chloroplasts: Current Research and Future Trends Microbial Biodegradation: From Omics to Function and Application Influenza: Current Research MALDI-TOF Mass Spectrometry in Microbiology Aspergillus and Penicillium in the Post-genomic Era The Bacteriocins: Current Knowledge and Future Prospects Omics in Plant Disease Resistance Acidophiles: Life in Extremely Acidic Environments Climate Change and Microbial Ecology: Current Research and Future Trends Biofilms in Bioremediation: Current Research and Emerging Technologies Microalgae: Current Research and Applications Gas Plasma Sterilization in Microbiology: Theory, Applications, Pitfalls and New Perspectives Virus Evolution: Current Research and Future Directions Arboviruses: Molecular Biology, Evolution and Control Full details at www.caister.com 2019 2018 2018 2018 2018 2018 2018 2018 2018 2017 2017 2017 2017 2017 2017 2017 2017 2017 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 2016 caister.com/transgenic Preface Viral diseases of crop plants cause significant yield losses, which is a major threat to global food security. Unlike other pests and pathogens, the only remedy available for control of plant viral diseases is through introgression of resistance trait, either through conventional breeding or through genetic engineering. Availability of few natural sources of virus resistance has hampered development of virus-resistant crop plants through conventional crop improvement methods. Thus genetic engineering for virus resistance is the sole option available for effective management of viral diseases. Since the first report on transgenic virus resistance in tobacco in 1986, huge progress has been made in our understanding of the molecular basis of virus resistance, complimented by the significant improvement in the tools and techniques used for genetic engineering. Despite major advancements in plant genomics and transgenics, there has been no commercialization of virus-resistant transgenic crops, except transgenic papaya. Thus, to provide an up-to-date reference book on genes, genetics and transgenics for virus resistance in plants for students, faculties and researchers, here we have compiled 15 diverse chapters. In the first chapter the current knowledge on mechanisms of virus resistance in plants is discussed, followed by a chapter on the role of host transcription factors in modulating defence response during plant-virus interaction, and a chapter on the role of epigenetics in host-virus interactions. There is a chapter on how molecular markers could be employed as tools for identification and introgression of virus-resistant genes. This book also thoroughly discusses the principles and methods involved in the genetic engineering for virus resistance in plants. The book also elaborates on topical application of double-stranded RNA for control of plant viral diseases, without having to develop transgenic plants. Further, the book deals with individual crops such as papaya, cassava, rice, tomato, and banana, for which virus resistance has been accomplished by employing different transgenic technologies. The management of whitefly-transmitted begomoviruses and advances in the control of their vectors is also covered as an independent chapter. Virus-induced gene silencing (VIGS), another frontier area of research in which virus-derived silencing vectors are extensively used in gene function studies and functional genomics, is also discussed elaborately.