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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 Title: Fast neutron mutants database and web displays at SoyBase

Authors
item Grant, David
item Bolon, Yung Tsi
item Nelson, Rex
item Vance, Carroll
item Shoemaker, Randy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 15, 2011
Publication Date: January 15, 2011
Citation: Grant, D.M., Bolon, Y.E., Nelson, R., Vance, C.P., Shoemaker, R.C. 2011. Fast neutron mutants database and web displays at SoyBase [abstract]. Plant and Animal Genome Conference. Poster 389.

Technical Abstract: SoyBase, the USDA-ARS soybean genetics and genomics database, has been expanded to include data for the fast neutron mutants produced by Bolon, Vance, et al. In addition to the expected text and sequence homology searches and visualization of the indels in the context of the genome sequence viewer, SoyBase also offers two additional analysis tools that significantly enhance the utility of these data. Image Search: Photographs of mutant plants and plant parts are presented in a user-friendly browser. Images chosen for further analysis can be accumulated in a ‘shopping cart’ during browsing. All of the images in this list can be viewed together on a single page to facilitate comparisons between mutants with similar phenotypes. Integration with SoyCyc: Genes contained in FN-generated indels can be visualized on the cellular metabolism and pathway diagrams available at SoyCyc. This tool can be used to ‘paint’ the gene lists onto the metabolic pathways from the indel(s) in a single mutant. Alternatively the indels from up to five mutant lines can be simultaneously visualized on the pathway diagram. This will be particularly useful in instances where mutants have similar phenotypes but no deleted genes in common. In this case the underlying biochemical basis for the phenotype might become evident if the mutants all effect the same pathway although at different steps. As much as possible, the web pages and underlying database tables were designed to be mutant-source agnostic. This will allow similar displays and analysis tools for other types of mutant populations such as those generated by transposon insertions.

Last Modified: 12/21/2014
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