Hee-Jong Koh · Suk-Yoon Kwon Michael Thomson Editors Current Technologies in Plant Molecular Breeding A Guide Book of Plant Molecular Breeding for Researchers C urrent Technologies in Plant Molecular Breeding H ee-Jong K oh • S uk-Yoon K won M ichael T homson E ditors C urrent Technologies in Plant Molecular Breeding A Guide Book of Plant Molecular Breeding for Researchers E ditors H ee-Jong K oh S uk-Yoon K won C ollege of Agriculture and Life Sciences P lant Systems Engineering Crop Science and Biotechnology Research Center S eoul National University K RIBB, D aejeon, K orea, Republic of S eoul, K orea, Republic of (South Korea) (South Korea) M ichael T homson P lant Breeding, Genetics, and Biotechnology I nternational Rice Research Institute L aguna, P hilippines I SBN 978-94-017-9995-9 ISBN 978-94-017-9996-6 (eBook) D OI 10.1007/978-94-017-9996-6 L ibrary of Congress Control Number: 2015946612 S pringer Dordrecht Heidelberg New York London © Springer Science+Business Media Dordrecht 2 015 T his work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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. T he use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. T he 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. P rinted on acid-free paper S pringer Science+Business Media B.V. Dordrecht is part of Springer Science+Business Media (www.springer.com) P refa ce P lant breeding, the science for plant genetic improvement, made great progress in the twentieth century with the rediscovery of Mendelian genetic principles in 1900. Most of the traditional breeding methods were established before the 1960s leading to the development of high-yielding varieties in cereal crops which brought the “Green Revolution” during the 1960s–1980s. Recent progress in biotechnology and genomics has expanded the breeders’ horizon providing a molecular platform on the traditional plant breeding, which is now known as “plant molecular breeding.” Under a new paradigm of plant breeding in the twenty-fi rst century, breeders try to create new variation through the direct manipulation of target genes instead of phenotype-b ased trait selection. Genetic resources are extended to the unrelated species because transgenic technologies break through the sexual limit for gene transfer. In addition, selection and genetic fi xation in the progeny can be performed by monitoring of genes and genomics information by which breeders can develop new varieties precisely and quickly. Although diverse technologies for molecular breeding have been developed and applied individually for plant genetic improvement, the common use in routine breeding programs seems to be limited probably due to the complexity and incom- plete understanding of the technologies. This book is intended to provide a guide for researchers or graduate students involved in plant molecular breeding by describing principles and application of recently developed technologies with actual case stud- ies for practical use. T his book is organized in nine chapters. In Chap. 1 , a brief history and perspec- tives of plant breeding are presented, including the directions of future development of breeding methods. In Chap. 2 , the basics on genetic analysis of agronomic traits are described, including how to construct molecular maps and how to develop DNA markers. In Chap. 3 , methods of detecting QTLs are illustrated, while in Chap. 4 , the application of molecular markers in actual plant breeding is described in detail with case studies. In Chap. 5 , genome sequencing and how to analyze the associa- tion between sequencing data and phenotype are introduced, including the epig- enome and its possible application to plant breeding. In Chap. 6 , genome-wide association studies are explained so that researchers can analyze the data following v vi Preface the manual including the introduction of software for analysis of population structure. In Chap. 7 , methods for mutation screening and targeted mutagenesis are described. In Chap. 8 , how to isolate the genes of interest and how to analyze the gene function are presented with case studies. In Chap. 9 , the basics of gene transfer in major crops and the procedures for commercialization of GM crops are explained. We attempted to cover most of the molecular tools applicable in plant breeding; however, due to the limitation of the book volume, we had to skip some skills that are still under development. Therefore, in this book, only key technologies which are currently used in plant breeding are mentioned. Since technologies per se are being advanced, we may add newly emerging ones with a chance given later. We hope this book would be a valuable reference for plant molecular breeders and, in addition, will become a cornerstone for the development of new technologies in plant molecular breeding for the future. W e are indebted to all the authors for their dedicated efforts and their time in writing the chapters despite the busy schedule. We are greatly thankful to Springer Publishing Co., Editorial Team, and particularly to Ms. Sophie Lim of Springer Korea for her support during the process of preparation and editing of the manu- scripts. Our thanks extend to Dr. Mi-ok Woo for her clerical assistance. S eoul, R epublic of Korea H ee-Jong K oh D aejeon, R epublic of Korea S uk-Yoon K won M etro Manila, P hilippines M ichael T homson C ontents 1 B rief History and Perspectives on Plant Breeding ................................. 1 J oohyun L ee, J oong H youn C hin, S ang N ag A hn, and H ee-Jong K oh 2 M ethods for Developing Molecular Markers ......................................... 15 H ee-Bum Y ang, W on-Hee K ang, S eok-Hyeon N ahm, and B young-Cheorl K ang 3 Q TL Identification .................................................................................... 51 H yun S ook L ee, S un-Goo H wang, C heol S eong J ang, and S ang N ag A hn 4 M arker-Assisted Breeding ........................................................................ 95 J ae B ok Y oon, S oon-Wook K won, T ae-Ho H am, S unggil K im, M ichael T homson, S herry L ou H echanova, K shirod K . J ena, and Y ounghoon P ark 5 G enomics-Assisted Breeding .................................................................... 145 I k-Young C hoi, H o-Jun J oh, G ibum Y i, J in H oe H uh, and T ae-Jin Y ang 6 C oncept of Genome-Wide Association Studies ....................................... 175 C hang-Yong L ee, T ae-Sung K im, S anghyeob L ee, and Y ong-Jin P ark 7 I dentification of Mutagenized Plant Populations ................................... 205 G eung-Joo L ee, D ong-Gwan K im, S oon-Jae K won, H ong-Il C hoi, and D ong S ub K im 8 I solation and Functional Studies of Genes .............................................. 241 M i-Ok W oo, K esavan M arkkandan, N am-Chon P aek, S oon-Chun J eong, S ang-Bong C hoi, and H ak S oo S eo 9 P lant Transformation Methods and Applications .................................. 297 Y oung H ee J oung, P il-Son C hoi, S uk-Yoon K won, and C hee H ark H arn I ndex ................................................................................................................. 345 vii C ontributors S ang N ag A hn D epartment of Crop Science, C hungnam National University, D aejeon, R epublic of Korea J oong H youn C hin I nternational Rice Research Institute (IRRI), M anila, P hilippines H o-Jun J oh D epartment of Plant Science, S eoul National University, S eoul, R epublic of Korea H ong-Il C hoi Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, J eongeup, R epublic of Korea I k-Young C hoi G reen-Bio Institute of Science and Technology, S eoul National University, S eoul, R epublic of Korea P il-Son C hoi O riental Pharmaceutical Development, N ambu University, G wangju, R epublic of Korea S ang-Bong C hoi D ivision of Bioscience and Bioinformatics, M yongji University, Y ongin, R epublic of Korea T ae-Ho H am D epartment of Agricultural Sciences, K orea National Open University, S eoul, R epublic of Korea C hee Hark H arn N ongwoo Bio Co., Y eoju, R epublic of Korea S herry L ou H echanova Plant Breeding, Genetics and Biotechnology Division , I nternational Rice Research Institute, M etro Manila, P hilippines J in H oe H uh D epartment of Plant Science and Plant Genomics and Breeding Institute, S eoul National University, S eoul, R epublic of Korea S un-Goo H wang D epartment of Applied Plant Sciences, K angwon National University, C huncheon, R epublic of Korea All of the co-authors equally contributed to this chapter. ix