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SoyBase


NAR Molecular Biology Database Collection entry number 919
Grant D., Nelson R.T., Schooler N. and Shoemaker R.C.
USDA-ARC-CICGR, G304 Agronomy Hall, Iowa State University, Ames, IA 50011, USA

Database Description

SoyBase, the USDA-ARS soybean genetics database, is a central repository where researchers can quickly find information on most aspects of soybean genetics, metabolism, and pathology. In 1993 SoyBase offered the first publicly available RFLP maps of the soybean genome as well as the first extensive collection of metabolic data in a plant genome database. SoyBase has since been expanded to contain almost all published data on soybean genetic research. A major milestone occurred in 2000 when a set of composite genetic maps was released. The current composite genetic maps contain more than 3800 mapped classical and molecular loci along with more than 950 QTL.

The major Classes of data in SoyBase are:
Map Collections: Classical genetic map and 35 molecular marker maps, including the composite genetic/molecular maps. Maps include molecular and whole plant phenotype markers and QTL.
Trait: Traits associated with entries in the GRIN and PVP databases, with links to genes, QTL, and pathology.
Reaction or Pathway: Clickable diagrams of more than 900 metabolic pathways showing kinetics, enzymes, metabolites and regulation. Data include detailed information for 900+ enzymes.
Pathology: Information on soybean diseases including causative organism, symptoms, differentials, distribution, and resistance mechanisms.
Nodulation: Plant and microbial processes and genes involved in nodulation of soybean.
Transformation: Summary of transformation in soybean, including methodology, transgenes, cultivar, and regeneration of plants.

Tools are provided at the SoyBase site for searching, downloading and analyzing the extensive soybean EST collection. Precomputed gene-specific clusters of ESTs are also available for searching by annotation or sequence and for download.

Recent Developments

Genetic maps in SoyBase are now displayed using CMap (part of the GMOD project), replacing the original ACeDB-based map displays. Among other improvements in the display, users can now easily compare multiple genetic maps side-by-side with common features indicated.

Acknowledgements

Ongoing funding of SoyBase is provided by the United States Department of Agriculture, Agriculture Research Service.

References

1. Schlueter JA, Dixon P, Granger C, Grant D, Clark L, Doyle JJ, Shoemaker RC (2004). Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876.
2. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005). Bridging model and crop legumes through comparative genomics. Plant Physiol. 137: 1189-1196.

Category: Plant databases
Subcategory: Other plants

Go to the abstract in the NAR 2010 Database Issue.
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