Since the early years when the first genetic markers were identified as being linked to disease resistance in tomato, there have been steady increases in developing molecular markers for genome mapping and MAS for numerous traits. Public and private sector breeders, as well as molecular marker service-providing companies, have placed increasing demands for new markers linked to additional genes influencing disease, pest, and abiotic stress resistances, fruit quality including flavor and nutritional value, and numerous other traits. More than 250,000 ESTs derived from more than 23 tomato cDNA libraries have been sequenced (Moore et al. 2002), and more than 30,000 unigenes have been defined (Van der Hooven et al. 2002; http://www.sgn.cornell.edu, http://www.ncbi.nlm.nih.gov). These unigenes represent a large set of candidate sequences for encoding critical developmental and physiological processes. With the sequencing of the tomato euchromatic portion of the genome (Mueller et al. 2005b), many additional candidate genes will be identified. High-throughput technologies of genomics, proteomics, and metabolomics enable the simultaneous quantification of the products of these genes during development (Alba et al. 2004; Fei etal. 2004) or in different plant tissues (Lemaire-Chamley et al. 2005). Techniques, such as comparative mapping, and tools, such as COS markers, facilitate synteny studies and expedite gene and QTL characterization (Fulton et al. 2002b). These studies will provide necessary data for hypothesis testing to rapidly elucidate the genes underlying favorable QTLs or mutations and subsequently incorporate them into cultivars.
Thousands of SNPs will be discovered that can be used for genome mapping, MAS, and positional cloning. Once a target gene has been characterized, it will be important to find new allelic variants within the large germplasm collections. An increased knowledge of gene function and regulation, as well as the development of more precise and efficient MAS, will help to avoid introgression oflarge segments and undesirable loci into elite lines. Mutational and trans-genic tools, such as mutation libraries in a uniform genetic background (Menda et al. 2004), and techniques to screen for genetic lesions in specific genes (Comai and Henikoff 2006) will aid in the description of desirable alleles. Thanks to a wealth of novel tools and techniques, to its vast natural polymorphism at intra- and inter-specific levels, and to consumer demands for nutritious foods (Weimer 1999), tomato will retain its status as a valuable model crop for the foreseeable future.
Acknowledgement. This work was partly supported by the Research and Development Program for New Bio-Industry Initiatives, NIH, USDA, CSU Agricultural Research Initiative (CSU-ARI), CSU Program for Education and Research in Biotechnology (CSUPERB), California State University Fresno College of Science & Mathematics, California Pepper Commission, New Mexico Agricultural Experiment Station, and grants from the National Institutes of Health GM S06 GM08136 and USDA CSREES 2003-34287-13411. We thank Dr. D. Shibata (Kazusa DNA Research Institute) for helpful discussion on metabolomics.
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