Exploitation of Tomato as a Model for Comparative and Functional Genomics

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The Solanaceae, which includes tomato, potato, eggplant and pepper, comprises the third most valuable crop family in the U.S. Tomato is the centerpiece for genetic and molecular research for the Solanaceae, due in part to features that make it an attractive research system. These features include 2N chromosome number, a modest-sized genome (about 950 Mb), tolerance of inbreeding, amenability to genetic transformation, and an existing collection of well-characterized genetic resources. During the course of the project, a physical map will be constructed for the nuclear genome of tomato. This physical map will comprise overlapping, ordered Bacterial Artificial Chromosomes (BACs). The physical map will be superimposed onto the tomato genetic map using a common set of genes. Together, the physical and genetic maps will provide a detailed road map of tomato chromosomes and allow scientists to more easily identify new gene functions. They will also allow comparison of the organization of the tomato genome with that of other related species (e.g. petunia, pepper, potato and eggplant) and the well-studied model plant Arabidopsis. Gene silencing approaches will be employed to study disease resistance and fruit development, two aspects of plant biology for which tomato is a model system. Finally, a series of genetic and genomic resources will be developed and disseminated to other researchers. These will include: 1) a non-redundant tomato unigene set; 2) tomato cDNA microarrays; 3) DNA, associated data sets from mapping populations, and seeds; 4) a set of ordered tomato BAC clones; and 5) new solanaceous BAC libraries. To facilitate distribution of genomic information for tomato and related species in a comparative genomic context, we will continue development of the Solanaceae Genome Network database. This is a genomics database that ties together information about sequence, genetic and physical maps among solanaceous species, and anchors this information against the Arabidopsis genome sequence.