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: (cid:129) Jinguo Hu, Gerald Seiler & Chittaranjan Kole: Sunfl ower (cid:129) Kristin D. Bilyeu, Milind B. Ratnaparkhe & Chittaranjan Kole: Soybean (cid:129) Robert Henry & Chittaranjan Kole: Sugarcane (cid:129) Kevin Folta & Chittaranjan Kole: Berries (cid:129) Jan Sadowsky & Chittaranjan Kole: Vegetable Brassicas (cid:129) James M. Bradeen & Chittaranjan Kole: Potato (cid:129) C.P. Joshi, Stephen DiFazio & Chittaranjan Kole: Poplar (cid:129) Anne-Françoise Adam-Blondon, José M. Martínez- Zapater & Chittaranjan Kole: Grapes (cid:129) Christophe Plomion, Jean Bousquet & Chittaranjan Kole: Conifers (cid:129) Dave Edwards, Jacqueline Batley, Isobel Parkin & Chittaranjan Kole: Oilseed Brassicas (cid:129) Marcelino Pérez de la Vega, Ana María Torres, José Ignacio Cubero & Chittaranjan Kole: Cool Season Grain Legumes (cid:129) Yi-Hong Wang, Tusar Kanti Behera & Chittaranjan Kole: Cucurbits (cid:129) Albert G. Abbott & Chittaranjan Kole: Stone Fruits (cid:129) 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 crosses to realize optimum genetic polymorphism required for mapping and breeding. Genetic divergence has been evaluated using the available tools at a particular point of time. We included discussions on phenotype- based strategies employing morphological markers, genotype-based strategies employing molecular markers; the statistical procedures utilized; their utilities for evaluation of genetic divergence among genotypes, local landraces, species and genera; and also on the effects of breeding pedigrees and geographical locations on the degree of genetic diversity. Association mapping using molecular markers is a recent strategy to utilize the natural genetic variability to detect marker-trait association and to validate the genomic locations of genes, particularly those controlling the quantitative traits. Association mapping has been employed effectively in genetic studies in human and other animal models and those have inspired the plant scientists to take advantage of this tool. We included examples of its use and implication in some of the volumes that devote to the plants for which this technique has been successfully employed for assessment of the degree of linkage disequilibrium related to a particular gene or genome, and for germplasm enhancement. Genetic linkage mapping using molecular markers have been discussed in many books, reviews and book series. However, in this series, genetic mapping has been discussed at length with more elaborations and examples on diverse markers including the anonymous type 2 markers such as RFLPs, RAPDs, AFLPs, etc. and the gene-specifi c type 1 markers such as EST-SSRs, SNPs, etc.; various mapping populations including F, backcross, 2 Preface to the Series ix recombinant inbred, doubled haploid, near-isogenic and pseudotestcross; computer software including MapMaker, JoinMap, etc. used; and different types of genetic maps including preliminary, high-resolution, high-density, saturated, reference, consensus and integrated developed so far. Mapping of simply inherited traits and quantitative traits controlled by oligogenes and polygenes, respectively has been deliberated in the earlier literature crop-wise or crop group-wise. However, more detailed information on mapping or tagging oligogenes by linkage mapping or bulked segregant analysis, mapping polygenes by QTL analysis, and different computer software employed such as MapMaker, JoinMap, QTL Cartographer, Map Manager, etc. for these purposes have been discussed at more depth in the present volumes. The strategies and achievements of marker-assisted or molecular breeding have been discussed in a few books and reviews earlier. However, those mostly deliberated on the general aspects with examples drawn mainly from major plants. In this series, we included comprehensive descriptions on the use of molecular markers for germplasm characterization, detection and maintenance of distinctiveness, uniformity and stability of genotypes, introgression and pyramiding of genes. We have also included elucidations on the strategies and achievements of transgenic breeding for developing genotypes particularly with resistance to herbicide, biotic and abiotic stresses; for biofuel production, biopharming, phytoremediation; and also for producing resources for functional genomics. A number of desirable genes and QTLs have been cloned in plants since 1992 and 2000, respectively using different strategies, mainly positional cloning and transposon tagging. We included enumeration of these and other strategies for isolation of genes and QTLs, testing of their expression and their effective utilization in the relevant volumes. Physical maps and integrated physical-genetic maps are now available in most of the leading crop and model plants owing mainly to the BAC, YAC, EST and cDNA libraries. Similar libraries and other required genomic resources have also been developed for the remaining crops. We have devoted a section on the library development and sequencing of these resources; detection, validation and utilization of gene-based molecular markers; and impact of new generation sequencing technologies on structural genomics. As mentioned earlier, whole genome sequencing has been completed in one model plant (Arabidopsis) and seven economic plants (rice, poplar, peach, papaya, grapes, soybean and sorghum) and is progressing in an array of model and economic plants. Advent of massively parallel DNA sequencing using 454-pyrosequencing, Solexa Genome Analyzer, SOLiD system, Heliscope and SMRT have facilitated whole genome sequencing in many other plants more rapidly, cheaply and precisely. We have included x Genetics, Genomics and Breeding of Tomato extensive coverage on the level (national or international) of collaboration and the strategies and status of whole genome sequencing in plants for which sequencing efforts have been completed or are progressing currently. We have also included critical assessment of the impact of these genome initiatives in the respective volumes. Comparative genome mapping based on molecular markers and map positions of genes and QTLs practiced during the last two decades of the last century provided answers to many basic questions related to evolution, origin and phylogenetic relationship of close plant taxa. Enrichment of genomic resources has reinforced the study of genome homology and synteny of genes among plants not only in the same family but also of taxonomically distant families. Comparative genomics is not only delivering answers to the questions of academic interest but also providing many candidate genes for plant genetic improvement. The ‘central dogma’ enunciated in 1958 provided a simple picture of gene function—gene to mRNA to transcripts to proteins (enzymes) to metabolites. The enormous amount of information generated on characterization of transcripts, proteins and metabolites now have led to the emergence of individual disciplines including functional genomics, transcriptomics, proteomics and metabolomics. Although all of them ultimately strengthen the analysis and improvement of a genome, they deserve individual deliberations for each plant species. For example, microarrays, SAGE, MPSS for transcriptome analysis; and 2D gel electrophoresis, MALDI, NMR, MS for proteomics and metabolomics studies require elaboration. Besides transcriptome, proteome or metabolome QTL mapping and application of transcriptomics, proteomics and metabolomics in genomics-assisted breeding are frontier fi elds now. We included discussions on them in the relevant volumes. The databases for storage, search and utilization on the genomes, genes, gene products and their sequences are growing enormously in each second and they require robust bioinformatics tools plant-wise and purpose- wise. We included a section on databases on the gene and genomes, gene expression, comparative genomes, molecular marker and genetic maps, protein and metabolomes, and their integration. Notwithstanding the progress made so far, each crop or model plant species requires more pragmatic retrospect. For the model plants we need to answer how much they have been utilized to answer the basic questions of genetics and genomics as compared to other wild and domesticated species. For the economic plants we need to answer as to whether they have been genetically tailored perfectly for expanded geographical regions and current requirements for green fuel, plant-based bioproducts and for improvements of ecology and environment. These futuristic explanations have been addressed fi nally in the volumes.