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An Online Toolkit for Soybean StudiesBy Luis Pons
September 25, 2006
Soybean breeders, producers and scientists have a new resource to tap.
Agricultural Research Service (ARS) scientists at Ames, Iowa, recently launched "The Soybean Breeder's Toolbox," an online database that allows exploration of the soybean's genetic makeup through easily retrieved information. ARS is the chief in-house scientific research agency of the U.S. Department of Agriculture (USDA).
The website is the new interface to SoyBase, a pioneering, ARS-supported plant-genetic database established in 1993. It can be accessed at http://soybase.org/.
According to ARS computational biologist Rex Nelson, who helped design the toolbox, this database offers easier remote access to information in SoyBase, as well as the use of complex queries to retrieve sets of related data.
The new site makes it possible to compare current soybean genetic maps and will allow study of maps from other legume species when they become available, according to Nelson, who is in the ARS Corn Insects and Crop Genetics Research Unit (CICGRU) at Ames, Iowa. The site uses an open-source, comparative map viewer program called CMap, which was created by the USDA-supported Generic Model Organism Database project.
In The Soybean Breeder's Toolbox, there is information about molecular markers on genetic maps, diseases and insects that attack soybean plants, and many other topics. Also included are data associated with soybean quantitative traits such as the resistance of different soybean genotypes to stresses that include bacterial, fungal and insect attacks and drought and flooding.
Nelson explained that the toolbox's easy linkage with other databases makes it easier to combine information from other databases into a single report. This helps researchers to quickly find genomic sequences associated with particular agronomic traits of interest. Ultimately, it can help make possible the development of varieties containing superior traits.
The website will be updated with new data as it is published and with new functions requested by people involved in soybean breeding and production.
CICGRU geneticists David Grant and Randy Shoemaker also assisted in getting The Soybean Breeder's Toolbox online. Grant is the curator for SoyBase.