Joanna Jankowicz-Cieslak · Thomas H. Tai Jochen Kumlehn · Bradley J. Till Editors Biotechnologies for Plant Mutation Breeding Protocols Biotechnologies for Plant Mutation Breeding Joanna Jankowicz-Cieslak • Thomas H. Tai • Jochen Kumlehn • Bradley J. Till Editors Biotechnologies for Plant Mutation Breeding Protocols Editors Joanna Jankowicz-Cieslak Thomas H. Tai Plant Breeding and Genetics Laboratory Crops Pathology and Genetics Research Unit Joint FAO/IAEA Division of Nuclear USDA-ARS Techniques in Food and Agriculture Davis Vienna, Austria California, USA Jochen Kumlehn Bradley J. Till Plant Reproductive Biology Plant Breeding and Genetics Laboratory Leibniz Institute of Plant Genetics and Joint FAO/IAEA Division of Nuclear Crop Plant Research (IPK) Techniques in Food and Agriculture Gatersleben, Germany Vienna, Austria ISBN 978-3-319-45019-3 ISBN 978-3-319-45021-6 (eBook) DOI 10.1007/978-3-319-45021-6 Library of Congress Control Number: 2016959193 © International Atomic Energy Agency 2017. The book is published open access at SpringerLink.com. Open Access This book is distributed under the terms of the Creative Commons Attribution- Noncommercial 2.5 License (http://creativecommons.org/licenses/by-nc/2.5/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. 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The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland In memory of Dr Pierre J.L. Lagoda (1961–2016) for his tireless efforts and endless enthusiasm for plant mutation breeding. Preface Sustainable global food security remains a serious challenge. The compounding factors of a growing population, a changing climate and finite and dwindling natural resources mean that food production needs to increase dramatically in the coming decades. Genetic improvement of crops has historically led to vast gains in yields and subsequently has reduced famine. Variation is the source of all breeding, and inducing mutations is an important and successful approach for generating novel variation and developing new crop varieties that are climate smart and nutritious and increase farmer’s incomes. The use of induced mutations dates back to the 1920s, and today there are over 3200 mutant crop varieties registered in a database curated by the FAO/IAEA. The process can be improved through the development, adaptation and transfer of technologies for optimizing the density of induced mutations and increasing the efficiency of phenotypic and genotypic screening of large mutant plant populations. Towards this end, the Joint FAO/IAEA Programme of Nuclear Techniques for Food and Agriculture initiated a collaborative Coordinated Research Project (CRP) titled “Enhancing the Efficiency of Induced Mutagenesis through an Integrated Biotechnology Pipeline“. The project brought together researchers from developing and developed countries with the aim to develop protocols and guidelines to improve the efficiency of the different steps of the plant mutation breeding process. This book provides protocols resulting from this CRP. A range of methods are provided suitable for those new to the field The views expressed in this text do not necessarily reflect those of the IAEA or FAO or governments of their Member States. The mention of names of specific companies or products does not imply an intention to infringe on proprietary rights, nor should it be construed as an endorsement or recommendation on the part of IAEA or FAO. vii viii Preface as well as to those seeking more advanced phenotypic and genotypic screening techniques. To guarantee high scientific quality, all chapters of this book have been peer reviewed. We are thankful to the participants of the CRP, authors of the chapters and also to all the reviewers (for list, see overleaf) who donated their time to improve the chapters. Vienna, Austria Bradley J. Till Acknowledgements We thank the participants of the IAEA Coordinated Research Project (CRP) D24012 for the valuable input into the project which stimulated this book. We also thank many PBG and PBGL staff past and present who supported activities and initiated new thinking about novel biotechnology approaches for increasing effi- ciencies in mutation induction and detection. Specifically, we would like to thank Dr Chikelu Mba for the preparation of the Coordinated Research Programme proposal. Funding for this work was provided by the Food and Agriculture Orga- nization of the United Nations and the International Atomic Energy Agency through their Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture. ix Contents Part I Introduction 1 Mutagenesis for Crop Breeding and Functional Genomics ....... 3 Joanna Jankowicz-Cieslak, Chikelu Mba, and Bradley J. Till Part II Mutation Induction and Chimera Dissociation 2 Chemical and Physical Mutagenesis in Jatropha curcas ......... 21 Fatemeh Maghuly, Souleymane Bado, Joanna Jankowicz-Cieslak, and Margit Laimer 3 Chemical Mutagenesis and Chimera Dissolution in Vegetatively Propagated Banana ..................................... 39 Joanna Jankowicz-Cieslak and Bradley J. Till 4 Mutation Induction Using Gamma Irradiation and Embryogenic Cell Suspensions in Plantain (Musa spp.) .................... 55 Jorge Lo´pez, Ayme´ Rayas, Arletys Santos, Vı´ctor Medero, Yoel Beovides, and Milagros Basail 5 Optimisation of Somatic Embryogenesis in Cassava ............ 73 Kenneth E. Danso and Wilfred Elegba 6 Creation of a TILLING Population in Barley After Chemical Mutagenesis with Sodium Azide and MNU ................... 91 Iwona Szarejko, Miriam Szurman-Zubrzycka, Malgorzata Nawrot, Marek Marzec, Damian Gruszka, Marzena Kurowska, Beata Chmielewska, Justyna Zbieszczyk, Janusz Jelonek, and Miroslaw Maluszynski 7 Site-Directed Mutagenesis in Barley by Expression of TALE Nuclease in Embryogenic Pollen ........................... 113 Maia Gurushidze, Stefan Hiekel, Ingrid Otto, Gotz€ Hensel, and Jochen Kumlehn xi xii Contents 8 Doubled Haploidy as a Tool for Chimaera Dissolution of TALEN-Induced Mutations in Barley ..................... 129 Maia Gurushidze, Hannes Trautwein, Petra Hoffmeister, Ingrid Otto, Andrea Muller,€ and Jochen Kumlehn Part III Phenotypic Screening 9 Field Evaluation of Mutagenized Rice Material ............... 145 Sydney D. Johnson, Dennis R. Taylor, Thomas H. Tai, Joanna Jankowicz-Cieslak, Bradley J. Till, and Alpha B. Jalloh 10 Root Phenotyping Pipeline for Cereal Plants ................. 157 Michal Slota, Miroslaw Maluszynski, and Iwona Szarejko 11 Breeding New Aromatic Rice with High Iron Using Gamma Radiation and Hybridization .............................. 173 Phuong Tan Tran and Cua Quang Ho 12 Utilising NIRS for Qualitative and Non-destructive Identification of Seed Mutants in Large Populations ...................... 193 Johann Vollmann and Joanna Jankowicz-Cieslak 13 Proteome Analyses of Jatropha curcas ...................... 203 Fatemeh Maghuly, Gorji Marzban, Ebrahim Razzazi-Fazeli, and Margit Laimer Part IV Genotypic Screening 14 Low-Cost Methods for DNA Extraction and Quantification ...... 227 Owen A. Huynh, Joanna Jankowicz-Cieslak, Banumaty Saraye, Bernhard Hofinger, and Bradley J. Till 15 A Protocol for Benchtop Extraction of Single-Strand-Specific Nucleases for Mutation Discovery .......................... 241 Bernhard J. Hofinger, Owen A. Huynh, Joanna Jankowicz-Cieslak, and Bradley J. Till 16 A Protocol for Validation of Doubled Haploid Plants by Enzymatic Mismatch Cleavage ..................................... 253 Bradley J. Till, Bernhard J. Hofinger, Ays¸e S¸en, Owen A. Huynh, Joanna Jankowicz-Cieslak, Likyelesh Gugsa, and Jochen Kumlehn 17 Bioinformatics-Based Assessment of the Relevance of Candidate Genes for Mutation Discovery ............................ 263 Michal Slota, Miroslaw Maluszynski, and Iwona Szarejko 18 Mutation Detection by Analysis of DNA Heteroduplexes in TILLING Populations of Diploid Species .................. 281 Miriam Szurman-Zubrzycka,