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United States Department of Agriculture

Agricultural Research Service

Research Project: 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 Soybean Breeder's Toolbox: Updated Features and New Data

Authors
item GRANT, DAVID
item NELSON, REX
item CANNON, STEVEN
item Shoemaker, Randy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 9, 2009
Publication Date: January 13, 2009
Citation: Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. Soybase and The Soybean Breeder's Toolbox: Updated Features and New Data [abstract]. Plant and Animal Genome Conference. Poster No. P364.

Technical Abstract: The Soybean Breeder’s Toolbox is constantly being upgraded and improved with new genetic and genomic data and tools. The genetic, physical and sequence map displays are based on viewers developed by the GMOD project, and have been extended by us to provide additional functionality. The Soybean Breeders Toolbox (SBT) contains much of the data originally collected in SoyBase. Genetic and physical maps are shown using the comparative map viewer CMap. This viewer allows side-by-side displays of multiple physical or genetic maps for comparing homoeologous regions of the genome or the genetic and physical maps. Markers and QTL on the genetic maps and BACs and FPC contigs on the physical map are linked to additional detailed textual data in the SBT. Controlled vocabularies for soybean growth, development and phenotypic traits are being developed and integrated with the Plant Ontology Consortium and Plant Trait Ontologies. Soybean ontologies are linked as appropriate to genes and QTL in the SBT, thus allowing the SBT to be searched by trait or developmental stage as well as by the more usual gene or QTL name. Along with recently reported QTL and the final FPC-based Williams 82 physical map the SNP-based markers developed by Hyten et al. (2008) have been added to the SBT. These new sequence-based genetic markers allow detailed integration of the genetic and sequence maps. The JGI soybean genomic sequence is viewed using GBrowse. Data tracks include the genomic sequence, sequenced genetic markers, soybean BACs, repetitive sequences, unigene sets, and automated gene calls.

Last Modified: 9/10/2014