DNA-BASED MARKERS IN PLANTS

Transcription

1 DNA-BASED MARKERS IN PLANTS

2 Advances in Cellular and Molecular Biology of Plants VOLUME 1 Editor-in-Chief Indra K. Vasil, Laboratory of Plant Cell and Molecular Biology, University of Florida, Gainesville, Florida, USA Editorial Advisory Board Robert T. Fraley, St. Louis, Missouri, USA Robert B. Goldberg, Los Angeles, California, USA Charles S. Levings, HI, Raleigh, North Carolina, USA Ronald L. Phillips, St. Paul, Minnesota, USA Jeff Schell, Cologne, Germany The titles published in this series are listed at the end of this volume.

3 DNA-based markers in plants Edited by RONALD L. PHILLIPS Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, U.S.A. and INDRA K. VASIL Laboratory of Plant Cell and Molecular Biology, University of Florida, Gainesville, Florida, U.S.A. SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.

4 Library of Congress Cataloging-in-Publication Data DNA-based markers in plants / edited by Ronald L. Phillips and Indra K. Vasil. p. cm. (Advances in cellular and molecular biology of plants. v. 1) Includes index. ISBN ISBN (ebook) DOI / Plant genome mapping. 2. Genetic polymorphisms. 3 Plant molecular genetics. I. Phillips, Ronald L. II. Vasil, I K. III. Series. QK D ' 3282 dc ISBN printed on acid-free paper All rights reserved 1994 Springer Science+Business Media Dordrecht Originally published by Kluwer Academic Publishers in 1994 Softcover reprint of the hardcover 1st edition in 1994 No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage and retrieval system, without written permission from the copyright owners

5 Contents General preface Preface Vll IX 1. Some concepts and new methods for molecular mapping in plants B. Burr 2. RFLP technology G. Kochert 3. Constructing a plant genetic linkage map with DNA markers N.D. Young 4. Mapping quantitative trait loci S.1. Knapp 5. Breeding multigenic traits C.W. Stuber 6. Nuclear DNA markers in systematics and evolution R. Whitkus, J. Doebley and J.F. Wendel 7. Introduction: molecular marker maps of major crop species R.L. Phillips and I.K. Vasil 8. Molecular maps of alfalfa E.C. Brummer, C.S. Echt, T.1.McCoy, K.K. Kidwell, T.c. Osborn, G.B. Kiss, G. Csanadi, K. Kalman, J. Gyorgyey, L. Okresz, A.E. Raczkevy, J.H. Bouton and G. Kochert v

6 VI Contents 9. An integrated RFLP map of Arabidopsis thaliana 159 H.M. Goodman, S. Hanley, S. Cartinhour, J.M. Cherry, B. Hauge, E. Meyerowitz, L. Medrano, S. Kempin, P. Stamm and M. Koornneef 10. RFLP maps of barley 163 A. Kleinhofs and A. Kilian 11. DNA-based marker maps of Brassica 199 C.F. Quiros, J. Hu and M.J. Truco 12. Genetic mapping in lettuce 223 R.W. Michelmore, R.V. Kesseli and E.J. Ryder 13. RFLP maps of maize 240 E.H. Coe and J.M. Gardiner 14. RFLP map of peanut 246 T. Halward, H.T. Stalker and G. Kochert 15. Phaseolus vulgaris: the common bean 261 C.E. Vallejos 16. RFLP map of the potato 271 C. Gebhardt, E. Ritter and F. Salamini 17. Rice molecular map 286 S.D. Tanksley 18. Generation of a genetic map for Sorghum bicolor 291 J.L. Bennetzen and A. Melake-Berhan 19. RFLP map of soybean 299 R.C. Shoemaker 20. Tomato molecular map 310 S.D. Tanksley 21. RFLP maps of bread wheat 327 G.E. Hart 22. Development of RFLP-based linkage maps in diploid and hexaploid oat (Avena sp.) 359 L.S. O'Donoughue, P.J. Rayapati, S.F. Kianian, M.E. Sorrells, S.D. Tanksley, M. Lee, H.W. Rines and R.L. Phillips List of contributors 375 Subject index 380

7 General preface The double helix architecture of DNA was elucidated in Twenty years later, in 1973, the discovery of restriction enzymes helped to create recombinant DNA molecules in vitro. The implications of these powerful and novel methods of molecular biology, and their potential in the genetic manipulation and improvement of microbes, plants and animals, became increasingly evident, and led to the birth of modern biotechnology. The first transgenic plants in which a bacterial gene had been stably integrated were produced in 1983, and by 1993 transgenic plants had been produced in all major crop species, including the cereals and the legumes. These remarkable achievements have resulted in the production of crops that are resistant to potent but environmentally safe herbicides, or to viral pathogens and insect pests. In other instances genes have been introduced that delay fruit ripening, or increase starch content, or cause male sterility. Most of these manipulations are based on the introduction of a single gene - generally of bacterial origin - that regulates an important monogenic trait, into the crop of choice. Many of the engineered crops are now under field trials and are expected to be commercially produced within the next few years. The early successes in plant biotechnology led to the realization that further molecular improvement of plants will require a thorough understanding of the molecular basis of plant development, and the identification and characterization of genes that regulate agronomically important multi genic traits. During the past ten years there has been a resurgence of molecular and related cellular studies in plants, including the molecular mapping of plant genomes. A great deal of interesting and useful information has been generated about the molecular basis of important plant processes. This series of volumes is intended to chronicle the most important advances in the cellular and molecular biology of plants, and to stimulate further interest and research in the plant sciences. The success and usefulness of these volumes depends on the timeliness of the subjects discussed, and the authoritative and insightful accounts provided by distinguished and internationally respected contributing authors. In this, I have been greatly aided by the advice of members of our Editorial Advisory Board and the editors of individual volumes, to whom lowe a debt of gratitude. I also Vll

8 Vlll General preface thank Dr. Ad. C. Plaizier of Kluwer Academic Publishers in helping me to launch this series, and his competent and helpful staff in the preparation of the volumes for publication. The various volumes already in press and in preparation have provided me the opportunity to know and work with many colleagues, and have helped me to improve my own understanding and appreciation of plant molecular biology. Indra K. Vasil

9 Preface As with numerous other technological advances, many insights have emerged from application of the new tools of molecular biology. The concept of DNAbased markers has revolutionized our ability to follow chromosome segments, including minute regions, and has led to new opportunities such as map-based cloning and directed plant breeding. Species with little genetic information available in the past now have hundreds of genetic markers. In some cases, the map from one specie.s can be transferred almost directly to another species, such as from tomato to potato. Additional genomic structure information, such as homoeologous chromosome identification, is forthcoming for several species. The suggestion of ancient polyploidy has been made even for maize, the most genetically studied plant species. The ancestral relationships of species and the pedigree relatedness of lines have been identified in hundreds of situations. This volume records the recently developed linkage maps of many important crop species. This recording, as impressive as it appears, will perhaps serve as a historical log of the development of the first molecular genetic marker maps for several species. The initial chapters provide aspects of the theory, technology, and applications of DNA-based markers. This book is intended to provide a solid base upon which students and researchers can build their understanding of genetic linkage and the applications of that knowledge. It also provides a statistical appreciation of DNA-based markers for the genetic dissection of qualitative and quantitative traits. Some of the newest ideas and concepts are expressed here for the first time. The locations of QTLs (Quantitative Trait Loci) for important agronomic and quality traits, as well as those that differentiate species, represent extremely useful knowledge.. Genomic markers for regions with major effects for such traits as disease resistance already are being used for gene cloning and breeding purposes. We recognize that genetic maps are a dynamic entity and will continue to expand and evolve over the years. At the same time, genetic map-based information is rigorous by its nature, and provides a set of basic tenets that should not change with future advancements. Thus, an understanding of the numerous basic tenets of mapping carefully described in these pages will establish a framework for future enhancement of the theory and applications of IX

10 x Preface this important and useful technology. Clearly, our ability to genetically manipulate more than just a few plant species has increased several orders of magnitude with the advent of DNAbased markers. The future will be exciting. We gratefully acknowledge the diligent efforts of each of the contributors to this volume for providing a clear statement of a difficult and still evolving subject. They represent pioneers in the field. Their interest and cooperation in making this volume a reality reflects a sincere and shared belief in the broad application of DNA-based markers in plants. Ronald L. Phillips Indra K. Vasil