Joanne A. Labate1, Silvana Grandillo2, Theresa Fulton3, Stéphane Munos4, Ana L. Caicedo5, Iris Peralta6, Yuanfu Ji7, Roger T. Chetelat8, J. W. Scott7, Maria Jose Gonzalo9, David Francis9, Wencai Yang9, Esther van der Knaap9, Angela M. Baldo1'10, Brian Smith-White11, Lukas A. Mueller12, James P. Prince13, Nicholas E. Blanchard13, Dylan B. Storey13, Mikel R. Stevens14, MatthewD. Robbins9, Jaw-Fen Wang15, Barbara E. Liedl16, Mary A. O'Connell17, John R. Stommel18, Koh Aoki19, Yoko Iijima19, Ann J. Slade20, Susan R. Hurst20, Dayna Loeffler20, Michael N. Steine20, Dionne Vafeados20, Cate McGuire21, Carrie Freeman21, Anna Amen20, John Goodstal21, Daniel Facciotti21, Joyce Van Eck22, and Mathilde Causse4
1 USDA-ARS, Plant Genetic Resources Unit, Geneva, NY 14456, USA, e-mail: [email protected]
2 CNR-IGV, Institute of Plant Genetics, Portici, Via Universita 133, 80055, Portici, (NA), Italy
3 Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
4 Laboratory of Vegetable and Fruit Genetics and Breeding, INRA, UR 1052, BP94, 84143, Montfavet, France
5 Biology Department, University of Massachusetts, Amherst, MA 01003, USA
6 Department of Agronomy, National University of Cuyo, Almirante Brown 500, 5500, Chacras de Coria, Lujan, Mendoza, Argentina and IADIZA-CONICET, C.C. 507, 5500, Mendoza, Argentina
7 Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
8 C.M. Rick Tomato Genetics Resource Center, Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
9 Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA
10 USDA-ARS, Grape Genetics Research Unit, Geneva, NY 14456, USA
II National Center for Biotechnology Information, USA National Library of Medicine, NIH, Bethesda, MD 20894, USA
12 Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA
13 Department of Biology, California State University-Fresno, Fresno, CA 93740, USA
14 Department of Plant and Wildlife Sciences, Brigham Young University, 287 Widstoe Building, Provo, UT 84602, USA
15 AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, Taiwan 74199, ROC
16 Gus R. Douglass Institute, Agricultural and Environmental Research Station, West Virginia State University, Institute, WV 25112, USA
17 Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
18 USDA-ARS, Vegetable Laboratory, Bldg. 010A, BARC-West, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
19 Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, 292-0818, Japan
20 Arcadia Biosciences, 410 W. Harrison, Ste 150, Seattle, WA 98119, USA
21 Arcadia Biosciences, 202 Cousteau Place, Ste 200, Davis, CA 95616, USA
22 Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
Tomatoes (Solanum lycopersicum) are consumed as either fresh fruit by themselves, in salads, as ingredients in many recipes, or in the form of various processed products such as paste, whole peeled tomatoes, diced products, and various forms of juices and soups. The tomato is a favorite garden plant in many parts of the world, an important source of vitamins and nutrients (see Sect. 1.14), and an economically important agricultural commodity (see Sect. 1.3.3).
Tomato was among the first crops for which molecular markers (isozymes) were suggested for marker-assisted selection (MAS) in breeding (Rick and Fobes 1974; Tanksley and Rick 1980). Tanksley (1983) discussed the viability of using isozymes for MAS in tomato and concluded that DNA-based markers would probably be utilized for the next iteration of MAS in tomato.
The most daunting challenge of effectively implementing MAS in cultivated tomato has been the low frequency of easily identifiable molecular polymorphisms within S. lycopersicum (Stevens and Rob-bins 2007) (see Sect. 1.4). This impediment was rec-
Genome Mapping and Molecular Breeding in Plants, Volume 5
© Springer-Verlag Berlin Heidelberg 2007
ognized as quickly as the theoretical concepts of using MAS were developed (Tanksley 1983; Helentjaris etal. 1985). In 1985, Helentjaris etal. demonstrated that DNA-based molecular markers in the form of restriction fragment length polymorphisms (RFLPs) could effectively identify differences between cultivated tomato and wild tomato species. Two years later, Nienhuis etal. (1987) demonstrated that MAS could identify quantitative trait loci (QTL) associated with insect resistance derived from Solanum habrochaites in an interspecific cross.
The clear demonstration that polymorphic markers were relatively abundant between cultivated tomato and its wild relatives opened a new line of MAS utilizing DNA-based markers. Young et al. (1988) exploited the abundance of polymorphisms derived from linkage drag surrounding genes in-trogressed from S. peruvianum into tomato. They utilized near-isogenic lines (NIL) to identify two RFLP markers tightly linked to the Tm-2a viral resistance gene.
Tomato's importance as a crop and role as a model for genetics, fleshy fruit development, secondary metabolism, disease resistance, domestication, and evolution, has led to concerted efforts to develop genetic and genomic resources for this species. These efforts have rapidly advanced tomato genome mapping and MAS, and have culminated in the adoption of tomato as the model genome (see Sect. 1.6, 1.18) for the commercially important (e.g., potato, pepper, eggplant) Solanaceae family.
Tomato Evolution and Taxonomy
The tomato clade is an evolutionarily young group that has diversified to occupy a great variety of habitats. The age of the genus Solanum is estimated at ~12 million years (My) based on nuclear (18S rDNA) and chloroplast markers ribulose-bisphosphate car-boxylase large subunit (rbcL) and ATP Synthase B (atpB) (Wikström et al. 2001), and the radiation of the tomato clade has been estimated as ~7 My based on four nuclear genes (Nesbitt and Tanksley 2002). In this amount of time, tomato species have evolved to occupy various habitats along the western coast of South America, from central Ecuador to northern Chile, as well as the Galápagos Islands, ranging from sea level to above 3,000 m in altitude, within various grades of xeric to mesic environments (Taylor 1986). For evolutionary biologists, the group is a prime example of rapid evolution and adaptation to diverse environments and environmental stresses. For breeders, wild tomato species contain useful traits that can be introgressed into cultivated tomato, ranging from resistance to multiple pathogens to tolerance to drought, salinity, etc. (Bohn and Tucker 1940; Stevens and Rick 1986). Wild germplasm has played an important role in the modern breeding of cultivated tomato (Stevens and Rick 1986), fueling interest in the study of wild tomatoes and the evolution of the group as a whole.
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