GENETICS, GENOMICS AND BREEDING OF TOMATO Genetics, Genomics and Breeding of Crop Plants Series Editor Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA Books in this Series: Published or in Press: • Jinguo Hu, Gerald Seiler & Chittaranjan Kole: Sunfl ower • Kristin D. Bilyeu, Milind B. Ratnaparkhe & Chittaranjan Kole: Soybean • Robert Henry & Chittaranjan Kole: Sugarcane • Kevin Folta & Chittaranjan Kole: Berries • Jan Sadowsky & Chittaranjan Kole: Vegetable Brassicas • James M. Bradeen & Chittaranjan Kole: Potato • C.P. Joshi, Stephen DiFazio & Chittaranjan Kole: Poplar • Anne-Françoise Adam-Blondon, José M. Martínez- Zapater & Chittaranjan Kole: Grapes • Christophe Plomion, Jean Bousquet & Chittaranjan Kole: Conifers • Dave Edwards, Jacqueline Batley, Isobel Parkin & Chittaranjan Kole: Oilseed Brassicas • Marcelino Pérez de la Vega, Ana María Torres, José Ignacio Cubero & Chittaranjan Kole: Cool Season Grain Legumes • Yi-Hong Wang, Tusar Kanti Behera & Chittaranjan Kole: Cucurbits • Albert G. Abbott & Chittaranjan Kole: Stone Fruits • Byoung-Cheorl Kang & Chittaranjan Kole: Peppers and Eggplants GENETICS, GENOMICS AND BREEDING OF TOMATO Editors Barbara E. Liedl West Virginia State University Gus R. Douglass Institute Agricultural and Environmental Research Station Institute, WV USA Joanne A. Labate USDA-ARS Plant Genetic Resources Unit Geneva, NY USA John R. Stommel USDA-ARS Vegetable Laboratory BARC-West Beltsville, MD USA Ann Slade Arcadia Bioscience Seattle, WV USA Chittaranjan Kole Department of Genetics and Biochemistry Clemson University Clemson, SC USA p, A SCIENCE PUBLISHERS BOOK GL--Prelims with new title page.indd ii 4/25/2012 9:52:40 AM CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2013 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 20130321 International Standard Book Number-13: 978-1-4665-6325-4 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information stor- age or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copy- right.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that pro- vides licenses and registration for a variety of users. For organizations that have been granted a pho- tocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Dedication This book is dedicated to Professor Steven D. Tanksley, Liberty Hyde Bailey Professor of Plant Breeding Cornell University and CEO/Chief Scientifi c Offi cer of Nature Source Genetics for his innovative research to identify and study genes responsible for the variation found in tomato and a variety of other crops. His work with tomato began with his graduate work at the University of California-Davis under the guidance of Dr. Charles M. Rick, plant geneticist and botanist. The work in his early career to develop molecular markers and a saturated linkage map for tomato served as a critical resource for his and other laboratories to ask the larger questions about tomatoes and in other plant species. In 1993, scientists in his lab successfully cloned the fi rst gene in tomato using a technique known as map-based cloning. His lab was also responsible for demonstrating that quantitatively inherited traits scattered across the genome can be dissected into Mendelian factors, called quantitative trait loci. This work has laid the ground work for understanding the inheritance of complex traits but opened up research avenues researchers in all areas of the life sciences. He was also involved in the international group responsible for sequencing the vi Genetics, Genomics and Breeding of Tomato tomato genome. He has been recognized for his numerous accomplishments including being elected to the National Academy of Sciences and receiving awards such as Alexander von Humboldt Foundation Award, Martin Gibbs Medal of the ASPP, Wolf Foundation Prize in Agriculture and the Kumho Award in Plant Molecular Biology and Technology. His enduring legacy will not be only the bounty of research he has published and directed, but also the undergraduate, graduate and post graduate students from around the world as well as collaborators from all fi elds that have benefi tted from his teaching, expertise, philosophy and passion for plants, particularly tomato. Preface to the Series Genetics, genomics and breeding has emerged as three overlapping and complimentary disciplines for comprehensive and fi ne-scale analysis of plant genomes and their precise and rapid improvement. While genetics and plant breeding have contributed enormously towards several new concepts and strategies for elucidation of plant genes and genomes as well as development of a huge number of crop varieties with desirable traits, genomics has depicted the chemical nature of genes, gene products and genomes and also provided additional resources for crop improvement. In today’s world, teaching, research, funding, regulation and utilization of plant genetics, genomics and breeding essentially require thorough understanding of their components including classical, biochemical, cytological and molecular genetics; and traditional, molecular, transgenic and genomics-assisted breeding. There are several book volumes and reviews available that cover individually or in combination of a few of these components for the major plants or plant groups; and also on the concepts and strategies for these individual components with examples drawn mainly from the major plants. Therefore, we planned to fi ll an existing gap with individual book volumes dedicated to the leading crop and model plants with comprehensive deliberations on all the classical, advanced and modern concepts of depiction and improvement of genomes. The success stories and limitations in the different plant species, crop or model, must vary; however, we have tried to include a more or less general outline of the contents of the chapters of the volumes to maintain uniformity as far as possible. Often genetics, genomics and plant breeding and particularly their complimentary and supplementary disciplines are studied and practiced by people who do not have, and reasonably so, the basic understanding of biology of the plants for which they are contributing. A general description of the plants and their botany would surely instill more interest among them on the plant species they are working for and therefore we presented lucid details on the economic and/or academic importance of the plant(s); historical information on geographical origin and distribution; botanical origin and evolution; available germplasms and gene pools, and genetic and cytogenetic stocks as genetic, genomic and breeding resources; and viii Genetics, Genomics and Breeding of Tomato basic information on taxonomy, habit, habitat, morphology, karyotype, ploidy level and genome size, etc. Classical genetics and traditional breeding have contributed enormously even by employing the phenotype-to-genotype approach. We included detailed descriptions on these classical efforts such as genetic mapping using morphological, cytological and isozyme markers; and achievements of conventional breeding for desirable and against undesirable traits. Employment of the in vitro culture techniques such as micro- and megaspore culture, and somatic mutation and hybridization, has also been enumerated. In addition, an assessment of the achievements and limitations of the basic genetics and conventional breeding efforts has been presented. It is a hard truth that in many instances we depend too much on a few advanced technologies, we are trained in, for creating and using novel or alien genes but forget the infi nite wealth of desirable genes in the indigenous cultivars and wild allied species besides the available germplasms in national and international institutes or centers. Exploring as broad as possible natural genetic diversity not only provides information on availability of target donor genes but also on genetically divergent genotypes, botanical varieties, subspecies, species and even genera to be used as potential parents in