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SoyBase: A Comprehensive Database for Soybean Genetic and Genomic Data

  • David Grant
  • Rex T. Nelson
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

SoyBase, the USDA-ARS soybean genetics and genomics database, provides a comprehensive collection of data, analysis tools, and links to external resources of interest to soybean researchers. The SoyBase home page (https://soybase.org) contains the SoyBase Toolbox which provides quick access to a search of the SoyBase database or the SoyCyc metabolic pathways database, access to the data download page, a genome sequence BLAST tool, and direct links to the genetic and sequence maps. An extensive navigation menu and site description provides facile access to all sections of SoyBase. Comprehensive information for a number of data types is available at SoyBase including the current genetic maps, the soybean reference genome sequence with tracks covering genetic markers, genome organization, gene annotation and expression, and gene knockout mutants. SoyBase includes an extensive RNA-Seq gene atlas and innovative tools for identifying fast neutron-induced mutants. SoyBase is an actively curated database, with new data regularly being incorporated, including additions to the controlled vocabularies (ontologies) for soybean growth, development and phenotypic traits, soybean genes, and quantitative trait loci. New “omics” tools enable sophisticated queries on lists of genes. These features are all accessed using intuitive interfaces and are linked together wherever possible.

Notes

Acknowledgements

The SoyBase Development Group includes David Grant, Rex T. Nelson, Kevin Feeley, Nathan Weeks, Jacqueline D. Campbell, Victoria Carollo Blake, Wei Huang, and Steven B. Cannon.

Data in SoyBase were generously provided by many cooperators or were collected from the literature by SoyBase staff.

Funding: This work was supported by the US Department of Agriculture, Agricultural Research Service (USDA-ARS) CRIS Project 3625-21000-062-00D.

Conflict of interest: No conflicts of interest declared.

Disclaimer

This digital data set publication was prepared by an agency of the US Government. Neither the US Government nor any agency thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or misuse of the data, or for damage, transmission of viruses, or computer contamination through the distribution of these data sets or for the usefulness of any information, apparatus, product, or process disclosed in this report, or represents that its use would not infringe privately owned rights. Reference therein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the US Government or any agency thereof. Any views and opinions of authors expressed herein do not necessarily state or reflect those.

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.USDA-ARS, Corn Insects and Crop Genetics Research UnitIowa State UniversityAmesUSA
  2. 2.Department of AgronomyIowa State UniversityAmesUSA

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