SoyBase Database

SoyBase is a database created by the United States Department of

Agriculture. It contains genetic information about soybeans. It
SoyBase
includes genetic maps, information about Mendelian genetics and Content
molecular data regarding genes and sequences. It was started in Description SoyBase the
1990 and is freely available to individuals and organizations
USDA-ARS
worldwide.
soybean
genetics and
History genomic
database
SoyBase was instituted by the Corn Insects and Corn Genetics
Data types Nucleic Acid,
Research Unit (CICGRU) in Ames, Iowa as a central repository
captured Protein,
for the soybean genetics community's published information.[1]
Originally, the database concentrated on genetic information such Expression,
as genetic linkage maps and other Mendalian information. Metabolism,
SoyBase genetic maps are a manually-curated composite of all Epigenetics
published mapping and QTL studies, and thus provide a species Organisms Glycine max,
level view of markers and QTL. Glycine soja
(soy, soya,
In 2010[2] the soybean genome sequence was released along with
gene models and many other types of genome annotations that soybean)
were integrated in to SoyBase. SoyBase genetic linkage maps Contact
were integral to the assembly of the soybean genome. Research center USDA
In 2018 the database received approximately 63,000 page requests Agricultural
from 2,600 users per month from 130 countries. About 40 Research
organizations in the United States and 82 foreign educational Service
institutions access SoyBase yearly. SoyBase supplies data to U.S. Laboratory Corn Insects
and foreign government organizations and corporate entities. and Crop
Genetics
Data submission and release policy Research Unit
Primary citation PMID 20008513
Data is accepted from the original source generators only. Users (https://pubmed.
that independently identify data for inclusion into the database can
ncbi.nlm.nih.gov/
contact SoyBase directly. A number Excel-based spreadsheet
20008513)
templates are available to facilitate the inclusion of data into
SoyBase. Access
Data format Various
All data in SoyBase are available without restrictions. A number of
data sub-setting and download tools are provided, and when Website soybase.org (htt
needed ad hoc subsets of the data can be requested from the ps://soybase.or
SoyBase Curator. g/)
Miscellaneous
Search tool License Public domain-
US Government
The SoyBase Database Search Tool uses a text entry box for Versioning None
queries. Results are returned as text and as displays. Results
Data release Continuously
display soybean genetic (and genomic) data using Generic Model
frequency
Organism Database (GMOD) open-source software. In addition to
SoyBase, objects identified by exact lexical matches to the query Curation policy Professionally
term, the tool also uses a soybean-specific ontology to identify curated
biologically-related SoyBase objects.

Some SoyBase sequence data and annotations are available

through an InterMine instance (SoyMine), which is a collaboration
with the Legume Information System Project.[3]

Graphical displays
Genetic maps contain information on markers (SSR, RFLP, SNP,
etc.), genes, and biparental and Genome-wide Association Study
(GWAS) Quantitative Trait Loci (QTL). Soybean genetic maps are
displayed using the CMap comparative genetic map viewer.
Soybean genomic sequence and gene model data are displayed
using the GBrowse sequence viewer. Other genome annotations in
this viewer include epigenetic data such as DNA methylation and
gene expression data of various soybean strains subjected to
different treatments and from different soybean tissues/cultivars.
Metabolic data and biochemical pathway information is displayed
using Pathway Tools. Soybean metabolic pathway information
(SoyCyc) was inferred by the Plant Metabolic Network[4] project
and was used to populate PathwayTools displays.

References The SoyBase Toolbox.

1. Grant, David; Nelson, Rex T.; Cannon, Steven B.;

Shoemaker, Randy C. (2010). "SoyBase, the USDA-ARS soybean genetics and genomics
database" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808871). Nucleic Acids
Research. 38 (Suppl 1) (Database issue): D843–D846. doi:10.1093/nar/gkp798 (https://doi.o
rg/10.1093%2Fnar%2Fgkp798). PMC 2808871 (https://www.ncbi.nlm.nih.gov/pmc/articles/P
MC2808871). PMID 20008513 (https://pubmed.ncbi.nlm.nih.gov/20008513).
2. Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica; et al. (2010). "Genome sequence
of the palaeopolyploid soybean" (https://doi.org/10.1038%2Fnature08670). Nature. 463
(7278): 178–183. Bibcode:2010Natur.463..178S (https://ui.adsabs.harvard.edu/abs/2010Nat
ur.463..178S). doi:10.1038/nature08670 (https://doi.org/10.1038%2Fnature08670).
PMID 20075913 (https://pubmed.ncbi.nlm.nih.gov/20075913). S2CID 4372224 (https://api.se
manticscholar.org/CorpusID:4372224).
3. Dash, S.; Campbell, J.D.; Cannon, E.K.; et al. (2016). "Legume information system
(LegumeInfo. org): a key component of a set of federated data resources for the legume
family" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702835). Nucleic Acids Research.
44 (D1): D1181–D1188. doi:10.1093/nar/gkv1159 (https://doi.org/10.1093%2Fnar%2Fgkv11
59). PMC 4702835 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702835).
PMID 26546515 (https://pubmed.ncbi.nlm.nih.gov/26546515).
4. Schlapfer, P.; Zhang, P.; Wang, C.; et al. (2010). "Genome-Wide Prediction of Metabolic
Enzymes, and Gene Clusters in Plants" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC537
3064). Plant Physiology. 173 (4): 2041–2059. doi:10.1104/pp.16.01942 (https://doi.org/10.11
 04%2Fpp.16.01942). PMC 5373064 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC537306
4). PMID 28228535 (https://pubmed.ncbi.nlm.nih.gov/28228535).

External links
Plant Metabolic Network project (https://www.plantcyc.org/)
Generic Model Organism Database project (http://gmod.org/wiki/Main_Page)
Legume Federation project (https://www.legumefederation.org/en/)
Legume Information System (https://legumeinfo.org/)
United States Department of Agriculture (https://www.usda.gov/)
InterMine (http://intermine.org/)

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