Agrobacterium Protocols M E T H O D S I N M O L E C U L a R B I O L O G Y™

Agrobacterium Protocols M E T H O D S I N M O L E C U L A R B I O L O G Y™

John M. Walker, SERIES EDITOR

371. Biological Aging: Methods and Protocols, edited by 349349. YAC Protocols, Second Edition, edited by Alasdair Trygve O. Tollefsbol, 2007 MacKenzie, 2006 370. Adhesion Protein Protocols, Second Edition, edited 348348. Nuclear Transfer Protocols: Cell Reprogramming by Amanda S. Coutts, 2007 and Transgenesis, edited by Paul J. Verma and Alan 369. Electron Microscopy: Methods and Protocols, Trounson, 2006 Second Edition, edited by John Kuo, 2007 347.347 Glycobiology Protocols, edited by Inka Brockhausen- 368. Cryopreservation and Freeze-Drying Protocols, Schutzbach, 2006 Second Edition, edited by John G. Day and Glyn 346.346 Dictyostelium discoideum Protocols, edited by Stacey, 2007 Ludwig Eichinger and Francisco Rivero-Crespo, 2006 367. Mass Spectrometry Data Analysis in Proteomics, 345.345 Diagnostic Bacteriology Protocols, Second Edition, edited by Rune Mattiesen, 2007 edited by Louise O'Connor, 2006 366. Cardiac Gene Expression: Methods and Protocols, 344.344 Agrobacterium Protocols, Second Edition: edited by Jun Zhang and Gregg Rokosh, 2007 Volume 2, edited by Kan Wang, 2006 365. Protein Phosphatase Protocols: edited by Greg 343.343 Agrobacterium Protocols, Second Edition: Moorhead, 2007 Volume 1, edited by Kan Wang, 2006 364. Macromolecular Crystallography Protocols: 342.342 MicroRNA Protocols, edited by Shao-Yao Ying, 2006 Volume 2, Structure Determination, edited by Sylvie 341.341 Cell–Cell Interactions: Methods and Protocols, Doublié, 2007 edited by Sean P. Colgan, 2006 363. Macromolecular Crystallography Protocols: 340.340 Protein Design: Methods and Applications, Volume 1, Preparation and Crystallization edited by Raphael Guerois and Manuela López de la of Macromolecules, edited by Sylvie Doublié, 2007 Paz, 2006 362. Circadian Rhythms: Methods and Protocols, 339.339 Microchip Capillary Electrophoresis: Methods edited by Ezio Rosato, 2007 and Protocols, edited by Charles S. Henry, 2006 361. Target Discovery and Validation Reviews 338.338 Gene Mapping, Discovery, and Expression: and Protocols: Emerging Molecular Targets Methods and Protocols, edited by M. Bina, 2006 and Treatment Options, Volume 2, edited by 337.337 Ion Channels: Methods and Protocols, edited by Mouldy Sioud, 2007 James D. Stockand and Mark S. Shapiro, 2006 360. Target Discovery and Validation Reviews 336.336 Clinical Applications of PCR, Second Edition, and Protocols: Emerging Strategies for Targets edited by Y. M. Dennis Lo, Rossa W. K. Chiu, and K. C. and Biomarker Discovery, Volume 1, edited by Allen Chan, 2006 Mouldy Sioud, 2007 335.335 Fluorescent Energy Transfer Nucleic Acid 359. Quantitative Proteomics, edited by Salvatore Sechi, Probes: Designs and Protocols, edited by Vladimir 2007 V. Didenko, 2006 358. Metabolomics: Methods and Protocols, edited by 334.334 PRINS and In Situ PCR Protocols, Second Wolfram Weckworth, 2007 Edition, edited by Franck Pellestor, 2006 357. Cardiovascular Proteomics: Methods and Protocols, 333.333 Transplantation Immunology: Methods and edited by Fernando Vivanco, 2006 Protocols, edited by Philip Hornick and Marlene Rose, 2006 356. High-Content Screening: A Powerful Approach to Systems Cell Biology and Drug Discovery, edited by 332.332 Transmembrane Signaling Protocols, Second Ken Guiliano, D. Lansing Taylor, and Jeffrey Haskins, Edition, edited by Hydar Ali and Bodduluri Haribabu, 2006 2006 355. Plant Proteomics: Methods and Protocols, edited 331331. Human Embryonic Stem Cell Protocols, edited by by Hervé Thiellement, Michel Zivy, Catherine Kursad Turksen, 2006 Damerval, and Valerie Mechin, 2006 330330. Embryonic Stem Cell Protocols, Second Edition, 354. Plant–Pathogen Interactions: Methods and Volume II: Differentiation Models, edited by Kursad Protocols, edited by Pamela C. Ronald, 2006 Turksen, 2006 353. DNA Analysis by Nonradioactive Probes: Methods 329329.Embryonic Stem Cell Protocols, Second Edition, and Protocols, edited by Elena Hilario and John. F. Volume I: Isolation and Characterization, edited by MacKay, 2006 Kursad Turksen, 2006 32328.8 New and Emerging Proteomic Techniques, edited 35352.2 Protein Engineering Protocols, edited by Kristian Müller and Katja Arndt, 2006 by Dobrin Nedelkov and Randall W. Nelson, 2006 327.327 Epidermal Growth Factor: Methods and Protocols, 351351. C. elegans: Methods and Applications, edited by Kevin Strange, 2006 edited by Tarun B. Patel and Paul J. Bertics, 2006 326.326 In Situ Hybridization Protocols, Third Edition, 350350. Protein Folding Protocols, edited by Yawen Bai and Ruth Nussinov 2006 edited by Ian A. Darby and Tim D. Hewitson, 2006 M E T H O D S I N M O L E C U L A R B I O L O G Y™

Agrobacterium Protocols

Second Edition Volume 1

Edited by Kan Wang Center for Plant Transformation, Plant Science Institute, and Department of Agronomy, Iowa State University, Ames, Iowa © 2006 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Methods in Molecular BiologyTM is a trademark of The Humana Press Inc. All papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher.

This publication is printed on acid-free paper. f ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials.

Cover design by Patricia F. Cleary

Cover illustration: Agrobacterium cells attaching to plant tissue surface. Artwork provided by Dr. Kan Wang. For additional copies, pricing for bulk purchases, and/or information about other Humana titles, contact Humana at the above address or at any of the following numbers: Tel.: 973-256-1699; Fax: 973-256-8341; E-mail: [email protected]; or visit our Website: www.humanapress.com Photocopy Authorization Policy: Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Humana Press Inc., provided that the base fee of US $30.00 per copy is paid directly to the Copyright Clearance Center at 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [1-58829-536-2/06 $30.00 ]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 EISBN 1-59745-130-4 Library of Congress Cataloging in Publication Data

Agrobacterium protocols / edited by Kan Wang.— 2nd ed. p. ; cm. — (Methods in molecular biology ; 343) Includes bibliographical references and index. ISBN 1-58829-536-2 (alk. paper) 1. Agrobacterium. 2. Agricultural biotechnology. [DNLM: 1. Rhizobium radiobacter—genetics—Laboratory Manuals. 2. Rhizobium radiobacter—isolation & purification—Laboratory Manuals. 3. Bacteriological Techniques—methods—Laboratory Manuals. 4. Genetic Techniques—Laboratory Manuals. QW 25 A281 2006] I. Wang, Kan, 1957- II. Series: Methods in molecular biology (Clifton, N.J.) ; v. 343. QR82.R45A37 2006 631.5’233—dc22 2005029677 To Marc Van Montagu and Jeff Schell (1935–2003), my PhD mentors, for their inspiration and encouragement. Preface

Agrobacterium tumefaciens is a soil bacterium that for more than a century has been known as a pathogen causing the plant crown gall disease. Unlike many other pathogens, Agrobacterium has the ability to deliver DNA to plant cells and permanently alter the plant genome. The discovery of this unique feature 30 years ago has provided plant scientists with a powerful tool to genetically transform plants for both basic research purposes and for agricultural development. Compared to physical transformation methods such as particle bombard- ment or electroporation, Agrobacterium-mediated DNA delivery has a number of advantages. One of the features is its propensity to generate a single or a low copy number of integrated transgenes with defined ends. Integration of a single transgene copy into the plant genome is less likely to trigger “gene silencing” often associated with multiple gene insertions. When the first edition of Agrobacterium Protocols was published in 1995, only a handful of plants could be routinely transformed using Agrobacterium. Agrobacterium-mediated transformation is now commonly used to introduce DNA into many plant species, including monocotyledon crop species that were previously considered non-hosts for Agrobacterium. Most remarkable are recent developments indicating that Agrobacterium can also be used to deliver DNA to non-plant species including bacteria, fungi, and even mammalian cells. While the list of organisms that can be infected by Agrobacterium has increased significantly over the past decade, the success in transformation also relies on culture responsiveness of the target cells/tissues subsequent to the co-cultivation with Agrobacterium. Essentially, the dynamic interactions between the two living organisms are critical for development of transformation methods. The second edition of Agrobacterium Protocols contains 80 chapters (two volumes) divided into 14 parts. Part I in Volume 1 (Agrobacterium Handling) provides six chapters describing basic techniques in Agrobacterium manipula- tion and strategies for vector construction, major components of plant transformation that are often neglected by many plant biologists. Part II in Volume 1 (Model Plants) consists of seven chapters describing various ways to introduce DNA into three major model plant species, Arabidopsis thaliana, Medicago truncatula, and Nicotiana. Although most plant laboratories transform these model plants on a routine basis, protocols from leading experts may further enhance their capabilities. Parts III through VI in Volume 1 and Parts I through

vii viii Preface

VII in Volume 2 collect 61 chapters covering protocols for 59 plant species. The plants are grouped according to their practical utilization rather than their botanical classification. The significant expansion of this section reflects the remarkable advancements in plant transformation technology during the past decade. Part VIII in Volume 2 (Non-plants) contains six chapters with protocols for introducing DNA into non-plant species such as bacteria, fungi, algae, and mammalian cells. The description of this unique capacity of Agrobacte- rium is a new addition to this edition. Agrobacterium Protocols provides a bench-top manual for tested protocols involving Agrobacterium-mediated transformation. All chapters are written in the same format as that used in the Methods in Molecular Biology series. Each chapter is contributed by authors who are leaders or veterans in the respective areas. The Abstract and Introduction sections provide outlines of protocols, the rationale for selection of particular target tissues, and overall transformation effi- ciency. The Materials section lists the host materials, Agrobacterium strains and vectors, stock solutions, media, and other supplies necessary for carrying out these transformation experiments. The Methods section is the core of each chapter. It provides a detailed step-by-step description of the entire transformation procedure from the preparation of starting materials to the harvest of transgenic plants. To ensure the reproducibility of each protocol, the Notes section supplies additional information on possible pitfalls in the protocol and alternative materials or methods for generating transgenic plants. Typically, most laboratories only work on one or a few plant species. Of course, each laboratory or individual researcher has his/her own favorite varia- tion or modification of any given plant transformation protocol. The protocols presented in this edition represent the most efficient methods used in the laboratories of these contributors. They are by no means the only methods for suc- cessful transformation of your plant of interest. The broad range of target tissue selection and in vitro culture procedures indicate the complexity in plant transformation. It is the intention of this book to facilitate the transfer of this rapidly developing technology to all researchers for use in both fundamental and ap- plied biology. I take this opportunity to thank all my colleagues whose time and effort made this edition possible. Special thanks go to my family for their unconditional love and support during the process of editing this book. Kan Wang Contents

Dedication ...... v Preface ...... vii Contributors ...... xiii Contents for Volume 2 ...... xix

PART I AGROBACTERIUM HANDLING 1 Culture and Maintenance of Agrobacterium Strains Arlene A. Wise, Zhenying Liu, and Andrew N. Binns ...... 3 2 Binary Vectors and Super-binary Vectors Toshihiko Komari, Yoshimitsu Takakura, Jun Ueki, Norio Kato, Yuji Ishida, and Yukoh Hiei ...... 15 3 Three Methods for the Introduction of Foreign DNA into Agrobacterium Arlene A. Wise, Zhenying Liu, and Andrew N. Binns ...... 43 4 Integration of Genes into the Chromosome of Agrobacterium tumefaciens C58 Lan-Ying Lee...... 55 5 Nucleic Acid Extraction from Agrobacterium Strains Arlene A. Wise, Zhenying Liu, and Andrew N. Binns ...... 67 6 Agrobacterium Virulence Gene Induction Stanton B. Gelvin ...... 77

PART II MODEL PLANTS 7 Arabidopsis thaliana Floral Dip Transformation Method Andrew Bent ...... 87 8 Agrobacterium Transformation of Arabidopsis thaliana Roots: A Quantitative Assay Stanton B. Gelvin ...... 105 9 Medicago truncatula Transformation Using Leaf Explants Viviane Cosson, Patricia Durand, Isabelle d’Erfurth, Adam Kondorosi, and Pascal Ratet ...... 115 10 Medicago truncatula Transformation Using Cotyledon Explants Elane Wright, Richard A. Dixon, and Zeng-Yu Wang ...... 129 11 Medicago truncatula Transformation Using Root Explants Cynthia Crane, Richard A. Dixon, and Zeng-Yu Wang ...... 137

ix x Contents

12 Nicotiana (Nicotiana tobaccum, Nicotiana benthamiana) Tom Clemente ...... 143 13 Generation of Composite Plants Using Agrobacterium rhizogenes Christopher G. Taylor, Beth Fuchs, Ray Collier, and W. Kevin Lutke ...... 155

PART III CEREAL CROPS 14 Barley (Hordeum vulgare L.) John Jacobsen, Ingrid Venables, Ming-Bo Wang, Peter Matthews, Michael Ayliffe, and Frank Gubler...... 171 15 Maize (Zea mays L.) Bronwyn R. Frame, Tina Paque, and Kan Wang ...... 185 16 Indica Rice (Oryza sativa, BR29 and IR64) Karabi Datta and Swapan Kumar Datta ...... 201 17 Japonica Rice Varieties (Oryza sativa, Nipponbare, and Others) Philippe Hervé and Toshiaki Kayano ...... 213 18 Rye (Secale cereale L.) Fredy Altpeter ...... 223 19 Sorghum (Sorghum bicolor L.) Zuo-yu Zhao...... 233 20 Wheat (Triticum aestivum L.) Yuechun Wan and Jeanne Layton ...... 245

PART IV INDUSTRIAL PLANTS 21 Canola (Brassica napus L.) Vinitha Cardoza and C. Neal Stewart, Jr...... 257 22 Cotton (Gossypium hirsutum L.) Keerti S. Rathore, Ganesan Sunilkumar, and LeAnne M. Campbell ...... 267 23 Indian Mustard [Brassica juncea (L.) Czern.] Ksenija Gasic and Schuyler S. Korban ...... 281 24 Sunflower (Helianthus annuus L.) Dalia M. Lewi, H. Esteban Hopp, and Alejandro S. Escandón ...... 291

PART V LEGUME PLANTS 25 Alfalfa (Medicago sativa L.) Deborah A. Samac and Sandra Austin-Phillips...... 301 26 Chickpea (Cicer arietinum L.) Kiran Kumar Sharma, Pooja Bhatnagar-Mathur, and Boddu Jayanand ...... 313 Contents xi

27 Clovers (Trifolium spp.) Aidyn Mouradov, Stephen Panter, Marcel Labandera, Emma Ludlow, Michael Emmerling, and German Spangenberg .. 325 28 Peas (Pisum sativum L.) Jan Grant and Pauline Cooper ...... 337 29 Peanut (Arachis hypogaea L.) Kiran Kumar Sharma and Pooja Bhatnagar-Mathur ...... 347 30 Pigeonpea (Cajanus cajan L. Millsp.) Kiran Kumar Sharma, Gopinath Sreelatha, and Sunitha Dayal ...... 359 31 Red Clover (Trifolium pratense) Michael L. Sullivan and Kenneth H. Quesenberry ...... 369 32 Soybean (Glycine max) Transformation Using Mature Cotyledonary Node Explants Paula M. Olhoft, Christopher M. Donovan, and David A. Somers ...... 385 33 Soybean (Glycine max) Transformation Using Immature Cotyledon Explants Tae-Seok Ko, Schuyler S. Korban, and David A. Somers...... 397 34 Tepary Bean (Phaseolus acutifolius) Mukund Zambre, Marc Van Montagu, Geert Angenon, and Nancy Terryn ...... 407

PART VI VEGETABLE PLANTS 35 Brassica oleracea Penny A. C. Sparrow, Philip J. Dale, and Judith A. Irwin ...... 417 36 Cucumber (Cucumis sativus L.) Wojciech Burza, Sabina Zuzga, Zhimin Yin, and Stefan Malepszy ...... 427 37 Eggplant (Solanum melongena L.) Joyce Van Eck and Ada Snyder ...... 439 38 Lettuce (Lactuca sativa L.) Ian S. Curtis...... 449 39 Tomato (Lycopersicum esculentum) Joyce Van Eck, Dwayne D. Kirk, and Amanda M. Walmsley ...... 459 Index ...... 475 Contributors

FREDY ALTPETER • University of Florida–IFAS, Agronomy Department, PMCB, Genetics Institute, Gainesvilles, FL GEERT ANGENON • Laboratory of Plant Genetics, Vrije Universiteit Brussel (VUB), Campus Etterbeek–Gebouw E, Brussels, Belgium SANDRA AUSTIN-PHILLIPS • Transgenic Plant Facility, Biotechnology Center, University of Wisconsin–Madison, Madison, WI MICHAEL AYLIFFE • CSIRO Plant Industry, Canberra, ACT, Australia ANDREW BENT • Department of Plant Pathology, University of Wisconsin– Madison, Madison, WI POOJA BHATNAGAR-MATHUR • Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra, Pradesh, India ANDREW N. BINNS • Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA WOJCIECH BURZA • Warsaw Agricultural University, Department of Plant Genetics Breeding and Biotechnology, Warsaw, Poland LEANNE M. CAMPBELL • Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX VINITHA CARDOZA • Department of Botany, University of Vermont, Burlington, VT TOM CLEMENTE • Department of Agronomy & Horticulture, Center for Biotechnology, Plant Science Initiative, University of Nebraska–Lincoln, Lincoln, NE RAY COLLIER • Donald Danforth Plant Science Center, St. Louis, MO PAULINE COOPER • New Zealand Institute for Crop & Food Research Ltd., Christchurch, New Zealand VIVIANE COSSON • Institut des Sciences du Végétal, CNRS, Gif sur Yvette, Cedex, France CYNTHIA CRANE • Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK IAN S. CURTIS • Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, The United Kingdoms ISABELLE D’ERFURTH • Institut des Sciences du Végétal, CNRS, Gif sur Yvette, Cedex, France PHILIP J. DALE • Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, The United Kingdoms

xiii xiv Contributors

KARABI DATTA • International Rice Research Institute, Plant Breeding, Genetics, and Biotechnology Division, Tissue Culture and Genetic Engineering Laboratory, Metro Manila, Philippines SWAPAN KUMAR DATTA • Department of Botany, Calcutta University, Kolkata, India SUNITHA DAYAL • Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India RICHARD A. DIXON • Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK CHRISTOPHER M. DONOVAN • Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN PATRICIA DURAND • Institut des Sciences du Végétal, CNRS, Gif sur Yvette, Cedex, France MICHAEL EMMERLING • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia ALEJANDRO S. ESCANDÓN • Institute of Floriculture (CIRN), Instituto de Genética INTA, Castelar CC25 (1712), Castelar, Provincia de Buenos Aires, Argentina BRONWYN R. FRAME • Center for Plant Transformation, Plant Science Institute, Iowa State University, Ames, IA BETH FUCHS • Donald Danforth Plant Science Center, St. Louis, MO KSENIJA GASIC • Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, IL STANTON B. GELVIN • Department of Biological Sciences, Purdue University, West Lafayette, IN JAN GRANT • New Zealand Institute for Crop & Food Research Ltd., Christchurch, New Zealand FRANK GUBLER • CSIRO Plant Industry, Canberra, ACT, Australia PHILIPPE HERVÉ • International Rice Research Institute, Plant Breeding, Genetics and Biotechnology Division, Metro Manila, Philippines YUKOH HIEI • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan H. ESTEBAN HOPP • Institute of Biotechnology (CICVyA), Instituto de Genética INTA,Castelar CC25 (1712), Castelar, Provincia de Buenos Aires, Argentina JUDITH A. IRWIN • Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, The United Kingdoms Contributors xv

YUJI ISHIDA • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan JOHN JACOBSEN • CSIRO Plant Industry, Canberra, ACT, Australia BODDU JAYANAND • Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India NORIO KATO • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan TOSHIAKI KAYANO • National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan DWAYNE D. KIRK • School of Biological Sciences, Monash University, Melbourne, Victoria, Australia TAE-SEOK KO • Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN TOSHIHIKO KOMARI • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan ADAM KONDOROSI • Institut des Sciences du Végétal, CNRS, Gif sur Yvette, Cedex, France SCHUYLER S. KORBAN • Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, IL MARCEL LABANDERA • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia JEANNE LAYTON • Monsanto Company, St. Louis, MO LAN-YING LEE • Department of Biological Sciences, Purdue University, West Lafayette, IN DALIA M. LEWI • Institute for Genetics Ewald A. Favret (CICVyA), Instituto de Genética INTA, Castelar CC25 (1712), Castelar, Provincia de Buenos Aires, Argentina ZHENYING LIU • Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA EMMA LUDLOW • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia W. KEVIN LUTKE • Tissue Culture and Transformation Facility, Donald Danforth Plant Science Center, St. Louis, MO STEFAN MALEPSZY • Warsaw Agricultural University, Department of Plant Genetics Breeding and Biotechnology, Nowoursynowska, Warsaw, Poland PETER MATTHEWS • CSIRO Plant Industry, Canberra, ACT, Australia xvi Contributors

AIDYN MOURADOV • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia PAULA M. OLHOFT • BASF Plant Science, Research Triangle Park, NC STEPHEN PANTER • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia TINA PAQUE • Center for Plant Transformation, Plant Science Institute, Iowa State University, Ames, IA KENNETH H. QUESENBERRY • Department of Agronomy, University of Florida, Gainesville, FL PASCAL RATET • Institut des Sciences du Végétal, CNRS, Gif sur Yvette, Cedex, France KEERTI S. RATHORE • Institute for Plant Genomics & Biotechnology, and Department of Soil & Crop Sciences, Texas A&M University, College Station, TX DEBORAH A. SAMAC • USDA-ARS-Plant Science Research Unit and Department of Plant Pathology, University of Minnesota, St. Paul, MN KIRAN KUMAR SHARMA • Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India ADA SNYDER • The Boyce Thompson Institute for Plant Research, Inc., Ithaca, NY DAVID A. SOMERS • Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN GERMAN SPANGENBERG • Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria, Australia PENNY A. C. SPARROW • Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, The United Kingdoms GOPINATH SREELATHA • Genetic Transformation Laboratory, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India C. NEAL STEWART, JR. • Department of Plant Sciences, University of Tennessee, Knoxville, TN MICHAEL L. SULLIVAN • U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI GANESAN SUNILKUMAR • Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX Contributors xvii

YOSHIMITSU TAKAKURA • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan CHRISTOPHER G. TAYLOR • Donald Danforth Plant Science Center, St. Louis, MO NANCY TERRYN • Institute Plant Biotechnology for Developing Countries, University of Ghent, Gent, Belgium JUN UEKI • Plant Innovation Center, Japan Tobacco Inc., Iwata, Shizuoka, Japan JOYCE VAN ECK • The Boyce Thompson Institute for Plant Research, Inc., Ithaca, NY MARC VAN MONTAGU • Institute Plant Biotechnology for Developing Countries, University of Ghent, Gent, Belgium INGRID VENABLES • CSIRO Plant Industry, Canberra, ACT, Australia AMANDA M. WALMSLEY • School of Biological Sciences, Monash University, Melbourne, Victoria, Australia YUECHUN WAN • Monsanto Company, Agracetus Campus, Middleton, WI KAN WANG • Center for Plant Transformation, Plant Science Institute, and Department of Agronomy, Iowa State University, Ames, IA MING-BO WANG • CSIRO Plant Industry, Canberra, ACT, Australia ZENG-YU WANG • Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK ARLENE A. WISE • Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA ELANE WRIGHT • Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK ZHIMIN YIN • Institute of Plant Genetics, Polish Academy of Sciences, Poland MUKUND ZAMBRE • Institute Plant Biotechnology for Developing Countries, University of Ghent, Gent, Belgium ZUO-YU ZHAO • Crop Genetics Research and Development, Pioneer Hi-Bred International, Inc., A DuPont Company, Johnston, IA SABINA ZUZGA • Warsaw Agricultural University, Department of Plant Genetics Breeding and Biotechnology, Warsaw, Poland Contents for Volume 2

Preface Contributors Contents for Volume 1

PART I ROOT PLANTS 1 Carrot (Daucus carota L.) Owen Wally, Jayaraj Jayaraman and Zamir K. Punja 2 Cassava (Manihot esculenta Crantz) Weston Msikita, Uzoma Ihemere, Dimuth Siritunga, and Richard T. Sayre 3 Potato (Solanum tuberosum L.) Steve Millam 4 Sweet Potato [Ipomoea batatas (L.) Lam.] Guo-qing Song and Ken-ichi Yamaguchi

PART II TURF GRASSES 5 Bermudagrass (Cynodon spp.) Yaxin Ge and Zeng-Yu Wang 6 Perennial Ryegrass (Lolium perenne L.) Fredy Altpeter 7 Switchgrass (Panicum virgatum L.) Mariya N. Somleva 8 Tall Fescue (Festuca arundinacea Schreb.) Yaxin Ge and Zeng-Yu Wang 9 Turf Grasses Chip Longo, Colin Lickwar, Qian Hu, Kimberly Nelson-Vasilchik, David Viola, Joel Hague, Joel M. Chandlee, Hong Luo, Albert P. Kausch

PART III WOODY SPECIES 10 American Elm (Ulmus americana) Andrew E. Newhouse, Franziska Schrodt, Charles A. Maynard, William A. Powell 11 Cork Oak Trees (Quercus suber L.) Rubén Álvarez, Mariano Toribio, Millán Cortizo, and Ricardo-Javier Ordás Fernández

xix xx Contents for Volume 2

12 Eucalyptus Zenn-Zong Chen, Cheng-Kuen Ho, In-Suk Ahn, and Vincent L. Chiang 13 Pine (Pinus radiata) Jan Grant, Tracy Dale and Pauline Cooper 14 Poplar (Populus spp.) Richard Meilan and Caiping Ma 15 Rubber Tree (Hevea brasiliensis Muell. Arg) Perumal Venkatachalam, Radha Jayashree, Karumamkandathil Rekha, Sreedharannair Sushmakumari, Sankaren Sobha, Parukkuttyamma Kumari Jayasree, Radha Gopikkuttanunithan Kala, and Arjunan Thulaseedharan

PART IV TROPIC PLANTS 16 Banana (Musa sp.) Juan B. Pérez Hernández, Serge Remy, Rony Swennen, and László Sági 17 Citrus Vladimir Orbovi´c and Jude W. Grosser 18 Coffee (Coffea sp.) Thierry Leroy, Edgardo Alpizar, Magali Dufour, and Hervé Etienne 19 Papaya (Carica papaya L.) Yun J. Zhu, Maureen M. M. Fitch, and Paul H. Moore 20 Pineapple [Ananas comosus (L.) Merr.] Lourdes Yabor, Patricia Espinosa, Ariel D. Arencibia, and José C. Lorenzo 21 Sugarcane (Saccharum spp.) Ariel D. Arencibia and Elva R. Carmona

PART V NUTS AND FRUITS 22 American Chestnut [Castanea dentata (Marsh.) Borkh.] Charles A. Maynard, Linda D. Polin, Sharon LaPierre, Ronald E. Rothrock, and William A. Powell 23 Apple (Malus u domestica) Abhaya M. Dandekar, Gianni Teo, Sandra L. Uratsu, and David Tricoli 24 Blueberry (Vaccinium corymbosum L.) Guo-Qing Song and Kenneth C. Sink Contents for Volume 2 xxi

25 Grapevine (Vitis vinifera L.) Alain Bouquet, Laurent Torregrosa, Pat Iocco, and Mark R. Thomas 26 Strawberry (Fragaria u ananassa) Bruno Mezzetti and Elisa Costantini 27 Walnut (Juglans) Chuck Leslie, Sandra L. Uratsu, Gale McGranahan, and Abhaya M. Dandekar

PART VI ORNAMENTAL PLANTS 28 Carnation (Dianthus caryophylus L.) Chalermsri Nontaswatsri and Seiichi Fukai 29 Chrysanthemum (Dendranthema u grandiflora) Jaime A. Teixeira da Silva 30 Orchids (Cymbidium spp., Oncidium, and Phalaenopsis) Ming-Tsair Chan, Yuan-Li Chan and Sanjaya 31 Petunia (Petunia hybrida) W. Kevin Lutke 32 Rose (Rosa hybrida L.) Schuyler S. Korban, Ksenija Gasic, and Xiangqian Li

PART VII MEDICINAL PLANTS 33 Ginseng (Panax ginseng) Yong Eui Choi 34 Hemp (Cannabis sativa L.) Mistianne Feeney and Zamir K. Punja 35 Opium Poppy (Papaver somniferum) Julie A. Chitty, Robert S. Allen, and Philip J. Larkin

PART VIII NON-PLANTS 36 Actinomycetes (Streptomyces lividans) Clarence I. Kado and Brian Kelly 37 Filamentous Fungi (Magnaporthe grisea and Fusarium oxysporum) Chang Hyun Khang, Sook-Young Park, Hee-Sool Rho, Yong-Hwan Lee, and Seogchan Kang 38 Green Alga (Chlamydomonas reinhardtii) Manchikatla V. Rajam and S. Vinod Kumar 39 Mammalian Cells Tzvi Tzfira, Talya Kunik, Yedidya Gafni, and Vitaly Citovsky xxii Contents for Volume 2

40 Mushroom (Agaricus bisporus) C. Peter Romaine and Carl Schlagnhaufer 41 Yeast (Saccharomyces cerevisiae) Paul J. J. Hooykaas, Amke den Dulk-Ras, Paul Bundock, Jalal Soltani, Haico van Attikum, and G. Paul van Heusden Index