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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC MECHANISMS AND MOLECULAR GENETIC RESOURCES FOR MAIZE Title: A Visualization and Query Tool for Introgression Libraries

Authors
item Bottoms, Christopher -
item Flint-Garcia, Sherry
item McMullen, Michael

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: March 1, 2009
Publication Date: March 15, 2009
Citation: Bottoms, C., Flint Garcia, S.A., Mcmullen, M.D. 2009. A Visualization and Query Tool for Introgression Libraries. Maize Genetics Conference Abstracts. p.184.

Technical Abstract: Near isogenic lines are powerful resources to analyze phenotypic variation and are important in efforts to map-base clone genes underlying mutants and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. To make it more tractable, we created a tool to graphically display and query such data. This tool incorporates a web interface for displaying the location and extent of introgressions. For comparative purposes, each marker is associated with the genetic position of a reference map. Users can search for introgressions using marker names or chromosome number and map position. This search will result in a display that gives the names of the lines with an introgression at the given position. Upon selecting one of the lines, color-coded introgressions in all 10 chromosomes of the line are displayed graphically. Then, upon selecting a chromosome, the user is taken to a web page that shows all of the markers on the chromosome along with the introgressions. A feature in development is the option to download query results as text as well as high-resolution publication-quality images corresponding to those displayed on the screen. This tool will be used to display maize teosinte introgression libraries, which comprise over 600 lines with introgressions defined with >500 SNP loci. Using our tool will allow quick access to lines with introgressions of interest. It will furthermore provide the means for producing figures for publications.

Last Modified: 10/25/2014
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