Functional Genomics of Tomato Fruit Quality: Bridging the Gap between QTLs and Genes

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PI: Harry J. Klee (University of Florida - Gainsville)CoPIs: Zhangjun Fei and James J. Giovannoni (Boyce Thompson Institute/USDA-ARS) and Denise Tieman (University of Florida - Gainsville)Collaborator: Alisdair Fernie (Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany)Fruits are major components of the human diet, contributing a large portion of vitamins, minerals, antioxidants, and fiber. While flavor and nutrient composition have clear and profound human benefit, they are difficult traits to modify due to their complex metabolic and regulatory pathways. Synthesis of nutritional and flavor compounds is the result of coordinated activity of multiple biochemical pathways, requiring integration of developmental, physiological and environmental cues. Effective manipulation of these traits requires knowledge of the pathways and the regulatory systems that control them. This project exploits the exceptional diversity within the Solanaceae to identify networks regulating synthesis of flavor and nutrition compounds. For many metabolic pathways, all of the genes encoding biosynthetic activities are known. Yet virtually nothing is known about how those genes are regulated to control metabolic output. The focus of this project is on three specific metabolic pathways responsible for synthesis of major flavor and nutrition chemicals: synthesis of folic acid, carotenoids and a family of phenylalanine-derived flavor and fragrance volatiles. In each case multiple, as yet unidentified genetic loci regulating metabolite flux through these pathways have been identified from wild tomato relatives. This project will specifically identify the genes responsible for that regulation and their mechanisms of action. In order to most effectively accomplish these goals, several valuable community resources will be developed. Gene expression profiling of fruit from lines containing defined segments of the wild tomato relative, Solanum pennellii, will be performed, providing quantitative information for gene expression and gene mapping. Also, BAC end sequencing of a S. pennellii library will be performed, facilitating rapid isolation of orthologous sequences by the entire research community. All sequence data will be available through GenBank and all metabolite, gene expression, and SNP data will be accessible through the Tomato Functional Genomics Database (TFGD, www.ted.bti.cornell.edu). All clone and germplasm resources can be ordered online at http://ted.bti.cornell.edu/cgibin/TFGD/order/home.cgi.This research project integrates genomics, metabolomics, informatics, genetics and biochemistry to achieve a deep understanding of how to manipulate important, multigenic quality traits in plants. This systems approach to a problem provides an excellent training environment for undergraduate and graduate students as well as postdoctoral scientists. The project integrates with ongoing highly successful minority training programs at both institutions. The achievable goals of better and healthier foods are highly appealing to students, industry and the public at large.