Methods in Molecular Biology 1815 Victor M. Loyola-Vargas Neftalí Ochoa-Alejo Editors Plant Cell Culture Protocols Fourth Edition M ETHODS IN M OLECULAR B IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Plant Cell Culture Protocols Fourth Edition Edited by Víctor M. Loyola-Vargas Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico Neftalí Ochoa-Alejo Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico Editors Víctor M. Loyola-Vargas Neftalí Ochoa-Alejo Unidad de Bioquímica y Biología Departamento de Ingeniería Genética Molecular de Plantas Unidad Irapuato Centro de Investigación Científica de Yucatán Centro de Investigación y de Estudios Avanzados Mérida, Yucatán, Mexico del Instituto Politécnico Nacional Irapuato, Guanajuato, Mexico ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-8593-7 ISBN 978-1-4939-8594-4 (eBook) https://doi.org/10.1007/978-1-4939-8594-4 Library of Congress Control Number: 2018945533 © Springer Science+Business Media, LLC, part of Springer Nature 2018 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. 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. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC part of Springer Nature. The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface Plant cell, tissue, and organ culture techniques have been utilized for a long time and surely will continue to be important biological systems for a series of basic studies and also as biotechnological tools for clonal propagation of plants, for crop improvement programs, and for genetic manipulation of important crop species through genetic engineering or by genomic editing approaches. New avenues and possibilities for plant cell, tissue, and organ culture have been incorporated to enrich this fourth edition of Plant Cell Culture Protocols composed of 34 chapters dealing with a series of basic auxiliary protocols for tissue culture (confocal microscopy for immunolocalization of auxins, histological techniques and photographic analysis to follow morphogenetic events, and cytometry applied to the analysis of regenerated plants). A micropropagation chapter in the twenty-first century describing its importance, limitations, challenges, and possible solutions provides the reader with new horizons and perspectives, and also a collection of protocols for the micropropagation and embryo rescue of Agave spp., the conditions for the clonal propagation of Yucca spp., and the somatic embryogenesis- mediated plant regeneration systems for Cocos nucifera, Phaseolus vulgaris, Musa spp., Theobroma cacao, Quercus, and Jatropha curcas form part of the content of this volume. One of the most frequently faced problems in tissue culture is microbial contamination, and for many years it was thought that only those microorganisms present in the surface of the explants were important; however, endophytic bacteria very often can affect the establishment and the responses of cell, tissue, or organ cultures; because of the importance of endophytes, a description and identification of some commonly found endophytic bacteria as well as some of the effects caused by them and how to control this problem is provided in the current edition. Somaclonal variation is still an interesting issue and a protocol for the selection of molecular markers to estimate somaclonal variation in cell and tissue cultures is now presented here. Elimination of plant viruses through meristem isolation and subsequent culture or the use of thermotherapy combined with meristem culture are the regular methods to get virus-free plant materials of high phytosanitary quality; however, a protocol using cryotherapy represents a new alternative for this purpose and is integrated here. The production of haploid and doubled haploid plant production of carrot using induced parthenogenesis and ovule excision can be used for both basic and applied crop improvement programs. Conservation of germplasm of important crops has been always an issue of primary interest due to the potential utilization of genetic variation for crop improvement programs; therefore, protocols for the cryopreservation of pollen grains from pineapple and other bromeliads were considered as a part of the strategies for the preservation of germplasm of these plant species. v vi Preface Plant cell, tissue, and organ culture are used as systems to study the potential of different plant species to produce secondary metabolites; this is the case of the chili pepper (Capsicum chinense) protocol for the establishment of cell suspensions and immobilized placenta tissues, which are used as models to investigate the production of capsaicinoids, compounds responsible for the hot taste. Moreover, genetic transformation is certainly another tool of great value for the genetic manipulation of agricultural crops, but also when the aim is to carry out metabolic engineering of secondary metabolite pathways, such as the protocol for the Agrobacterium tumefaciens-genetic transformation of the Mayan medicinal species Pentalinon andrieuxii, which produces pentacyclic triterpenes with potential application in the pharmaceutical industry. In this fourth edition, a special focus was paid to the inclusion of protocols regarding the omics (transcriptomics, proteomics, and metabolomics) applied to different aspects of plant cell, tissue, and organ cultures. For example, protocols for the analysis of secondary metabolites (terpenes, carotenoids, phytosterols) through NMR-based metabolomics of Catharanthus roseus or hairy root cultures from several medicinal plants. Of relevance in this volume are the protocols for the application of proteomics and transcriptomics to study somatic embryogenesis and morphogenesis processes. Moreover, the participation of microRNAs and transcription factors as important actors in somatic embryogenesis is also described. Epigenetic changes involving histone modifications and changes in chromatin organization during biological processes can be analyzed using the chromatin immunoprecipitation assay (Chip) protocol presented in the current edition. Perhaps the most spectacular current tool for genomic editing is undoubtedly the CRISPR/ Cas9 technology, and a review on its use in plant tissue culture is reported. Among the miscellaneous applications of cell culture, the readers can consult and follow a protocol for the use of cell suspensions to test heavy metal toxicity and accumulation for a possible phytoremediation alternative. As in the previous editions of Plant Cell Culture Protocols, an Appendix of the composition of the most commonly used plant cell, tissue, and organ culture media is included. We would like to thank all the authors for their enthusiasm and the time devoted to prepare their chapters in which they are sharing the most invaluable richness: their expertise. Finally, we should make a special mention of gratitude to David Casey and John Walker, who always supported and guided us during this editorial journey. Mérida, Yucatán, Mexico Víctor M. Loyola-Vargas Irapuato, Guanajuato, Mexico Neftalí Ochoa-Alejo Contents Preface . .. v Contributors . xi PART I INTRODUCTION 1 An Introduction to Plant Tissue Culture: Advances and Perspectives . 3 Victor M. Loyola-Vargas and Neftalí Ochoa-Alejo PART II CELL CULTURE THE FUNDAMENTS 2 Micropropagation in the Twenty-First Century . 17 Jean Carlos Cardoso, Lee Tseng Sheng Gerald, and Jaime A. Teixeira da Silva 3 Cellular and Morpho-histological Foundations of In Vitro Plant Regeneration . 47 Diego Ismael Rocha, Lorena Melo Vieira, Andréa Dias Koehler, and Wagner Campos Otoni 4 Bacterial Endophytes in Plant Tissue Culture: Mode of Action, Detection, and Control ������������������������������������������������������������������������������������������������������� 69 Mona Quambusch and Traud Winkelmann 5 Digital Photography as a Tool of Research and Documentation in Plant Tissue Culture ���������������������������������������������������������������������������������������������������