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. 2010 Jan;38(Database issue):D843-6.
doi: 10.1093/nar/gkp798. Epub 2009 Dec 14.

SoyBase, the USDA-ARS soybean genetics and genomics database

David Grant  1 , Rex T Nelson, Steven B Cannon, Randy C Shoemaker
Affiliations

SoyBase, the USDA-ARS soybean genetics and genomics database

David Grant et al. Nucleic Acids Res. 2010 Jan.

Abstract

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated 'Williams 82' genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org.

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Figures

Figure 1.
Figure 1.
The main navigation aids that are present on all SoyBase pages, and which allow the user to quickly move between the sections of the web site. The main tabs (i.e. Maps or Resources) link immediately to the selected page. Entries on the second line can be used to move directly to a specific SoyBase page.
Figure 2.
Figure 2.
Homoeologous regions of soybean linkage groups C1 and C2 (chromosomes Gm04 and Gm06). Broad QTL classes are indicated by color. Only a subset of the QTL are shown so that potentially related QTL can easily be recognized.
Figure 3.
Figure 3.
Genome sequence view of a region of soybean chromosome Gm01. The tracks shown here are genetic markers, gene models from the 1.01 annotation (Soybean Genome Sequencing Consortium), and locations of Affymetrix probesets. For each of these tracks, a click on a feature provides a contextual menu with relevant links: to CMap from markers; to several sequence tools from gene models; and to PLEXdb (6) from Affymetrix probe sets. Many other annotation tracks are available, including intragenomic synteny blocks, the BAC-based FPC contigs that comprise the physical map, all of the fingerprinted and end-sequenced BACs, and EST contigs from both soybean and other legumes.
See this image and copyright information in PMC

References

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