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
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
Giovannoni of ARS'
Plant, Soil and Nutrition Laboratory in Ithaca, N.Y., in collaboration with
Cornell, the University of Florida, and
Virginia Tech University's Virginia
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.