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United States Department of Agriculture

Agricultural Research Service

Title: The Soybean Breeder's Toolbox: Integration of Genetic and Molecular Data for Soybean

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

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 3, 2006
Publication Date: January 13, 2007
Citation: Nelson, R., Grant, D.M., Shoemaker, R.C. 2007. The soybean breeder's toolbox: integration of genetic and molecular data for soybean [abstract]. Plant and Animal Genome Conference. Paper No. P851.

Technical Abstract: Soybean genetic data has been compiled and stored in the soybean genetic database SoyBase. This data has been retrieved from an AceDB database and used to compile a new database called the Soybean Breeder’s Toolbox (SBT). The toolbox is a relational database utilizing the MySQL RDMS. The use of a relational database with a web accessible interface makes database queries easier to compose and also offers a mechanism to accept automated queries from other databases to facilitate information exchange. The Toolbox has been designed to accept specific queries for various data types as well as general browsing-type queries. An additional feature of the Toolbox is the use of CMap a comparative map viewer developed by the Generic Model Organism Database project (GMOD). CMap enables the user to display more than one genetic or physical map at a time allowing the comparison of multiple soybean linkage groups at a time. Since soybean is an ancient polyploid, this allows the visualization of the distribution of duplicated QTLs and loci among linkage groups. The ability to compare individual linkage groups will also allow the comparison of linkage groups from other legume species which have been mapped with homologous markers. This will allow the comparison of the distribution of homologs in other legumes and may shed light on the forces shaping legume genome evolution. The Toolbox will also be updated with data from the soybean physical map when it becomes available. A description of the database and representations of the interface will be presented.

Last Modified: 9/10/2014
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