A Website Ripe with Data from ARS Tomato Studies

By Luis Pons
March 16, 2006

Landmark Agricultural Research Service (ARS) work on genes governing tomato ripening and nutritional content are the cornerstone of the Tomato Expression Database (TED), a Cornell University website funded by ARS and the National Science Foundation (NSF).

The site, part of the NSF's ongoing Tomato Genomics Project, gives researchers worldwide access to data they can use to develop new theories on tomato genetics--and to expand upon what's already known about this popular food.

The site comprises four sections created and maintained by molecular biologist James Giovannoni of ARS' U.S. Plant, Soil and Nutrition Laboratory in Ithaca, N.Y., in collaboration with Cornell, the University of Florida, and Virginia Tech University's Virginia Bioinformatics Institute.

Giovannoni has led breakthrough research by ARS and other institutions that identified key genes that control the ripening of tomatoes. The TED website provides large-scale tomato gene expression data generated from "microarrays" - collections of microscopic DNA samples on glass chips that allow scientists to assess thousands of genes in an organism.

One section within TED is a tomato microarray data-storage "warehouse," which serves as a source of downloadable raw research information.

TED's microarray expression database, meanwhile, offers information analyzed in Giovannoni's laboratory on gene expression related to fruit development and ripening. It also contains data that allows for genetic comparisons between normal and mutant tomatoes.

The site's digital expression database presents information that's similar, but based upon expressed tag sequences. These sequences identify genes through expression in RNA that's reflected in DNA. A fourth database, the tomato metabolite database, has information on the chemical composition of tomatoes, along with comparative gene-expression data. It's designed to help researchers develop and test hypotheses on how flavor and texture attributes of tomato fruit are regulated.

The TED site also allows users with a login ID and password to submit new data. According to Giovannoni, a recent NSF grant will allow for an expansion of the TED site.

ARS is the U.S. Department of Agriculture's chief scientific research agency.