CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES
Location: Corn Insects and Crop Genetics Research
Title: SoyBase and the legume information system: accessing information about the soybean and other legume genomes
Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: October 20, 2011
Publication Date: January 10, 2012
Citation: Cannon, S.B., Crow, J.A., Grant, D.M. 2012. SoyBase and the legume information system: accessing information about the soybean and other legume genomes. In: Wilson, R. editor. Designing Soybeans for 21st Century Markets. Urbana, IL: AOCS Press. p. 53-66.
Interpretive Summary: This review describes two websites relevant for soybean research: SoyBase, and the Legume Information System (LIS). The soybean genome sequence contains the vast majority of gene and regulatory sequences responsible for characteristics of a soybean plant. Together, these websites provide access to the genome sequence and many related pieces of information, allowing researchers to locate and track important traits, to reconstruct and investigate metabolic pathways, to describe plant growth characteristics, and to identify how genes respond in different conditions or parts of a soybean plant.
This review describes two websites relevant for soybean research: SoyBase, and the Legume Information System (LIS). SoyBase and LIS have different objectives and areas of emphasis. SoyBase holds a wide range of specialized data in support of soybean breeding and research activities, with the primary focus on genetic data (i.e., markers, maps, and QTL) and genomic data (i.e., genome sequence, gene predictions, gene expression information). Other significant soybean data sets are incorporated where possible, for example, information about fast-neutron mutant populations and metabolic pathways. LIS includes similar genetic and genomic data, but for a broad range of species. The primary objectives in LIS are, in the words of the site's mission statement, to “enable productive applied and basic research in the legumes by relating data from multiple crop and model species, and by helping researchers traverse among various data types.” To serve the needs for comparative cross-species analysis, LIS houses genetic map data for multiple species, and relates the sequence-based markers for each species to the genome sequences of the sequenced “reference” legume genomes (at the time of writing, soybean, Lotus, and Medicago). Sequence search tools are designed to display results with respect to the reference genomes and to other analysis resources such as UniProt. Additionally, LIS helps link and integrate resources at multiple online genetic databases.