Development of Tools for Tomato Functional Genomics: Application to Analysis of Fruit Development, Responses to Pathogens, and Genome Synteny with Arabidopsis

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Tomato has long served as a model system for plant genetics, development, pathology, and physiology, which has resulted in an accumulation of substantial information regarding the biology of this economically important organism. In recent years, the most widely studied aspects of tomato biology include development and ripening of fleshy fruits and characterization of responses to infection by microbial pathogens. Although Arabidopsis has surpassed some plant systems as a model for basic plant biology research, the areas of fruit ripening and pathogen response continue to thrive with tomato as the experimental organism of choice. In the case of fruit development, this is simply due to the fact that the developmental program which results in the dramatic expansion and ripening of carpels in tomato and in many other economically and nutritionally important species does not occur in Arabidopsis. With regard to plant defense, decades of applied and basic research on tomato have resulted in characterization of responses to numerous disease agents. In many cases, this has led to the identification and genetic characterization of loci that confer general or pathogen-specific resistance. In addition, many experimental tools and features of tomato make it an excellent model system in its own right including: extensive germplasm collections; numerous natural, induced and transgenic mutants and genetic variants; routine transformation technology; a dense RFLP map; numerous cDNA and genomic libraries; a small genome; relatively short life-cycle; and ease of growth and maintenance. The intense research efforts in fruit biology and defense responses and the available tools that make tomato an especially attractive model system have resulted in many important recent discoveries. Specific highlights which have had a broad impact on the field of plant biology include: control of gene expression by antisense/sense technology; functional characterization of numerous genes influencing fruit development and ripening; transgenic analysis of genes which impact susceptibility or response to pathogen attack; and isolation of more disease resistance genes than any other plant species.This project involves development of an integrated set of experimental tools for use in tomato functional genomics. The resources developed will be used to expand understanding of the molecular genetic events underlying fruit development and the response to pathogen infection and will be made available to the research community for analysis of diverse plant biological phenomena. Specific objectives include: (1) development of a tomato EST (Expressed Sequence Tag) database with emphasis on sequences expressed during fruit development and maturation and in pathogen-challenged tissues; (2) genome-wide gene expression analyses during fruit development and ripening and in response to pathogen infection; and (3) development of a tomato-Arabidopsis synteny map which will be used by members of this group and made publicly available for target gene isolation, candidate gene identification, and analysis of genome organization and evolution.