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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC MECHANISMS AND MOLECULAR GENETIC RESOURCES FOR MAIZE

Location: Plant Genetics Research

Title: IView: Introgression library visualization and query tool

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

Submitted to: BMC Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 9, 2010
Publication Date: October 7, 2010
Citation: Bottoms, C., Flint Garcia, S.A., McMullen, M.D. 2010. IView: Introgression library visualization and query tool. BMC Bioinformatics. 11(6):S28.

Interpretive Summary: Near-isogenic lines (NIL), genetic stocks with small specific chromosome regions of one variety placed into another variety (an introgression), are powerful genetic resources to analyze phenotypic variation and are important to clone genes for underlying mutations and traits according to their position on the gentic map underlying mutations and traits. A large number of NILs make up what is known as an "introgression library": a collection of lines each with a distinct "introgressed" chromosome fragment from one particular variety into another. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. We have created a tool to graphically display and query NILs for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with the genetic position of a reference genetic map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines with an introgression at the specified position. Upon selecting one of the lines, color-coded introgression in all chromosomes of the line are displayed graphically. The user can download a high-quality image of any of the displayed chromosomes by clicking on the desired chromosome. This tool will be useful for geneticists and breeders to make introgression data from their stocks of germplasm searchable, to enhance the ability to use NILs for genetic research and crop improvement.

Technical Abstract: Near-isogenic lines (NIL) are powerful genetic resources to analyze phenotypic variation and are important to map-base clone genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. We have created a tool to graphically display and query NILs for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. 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 positions. This search results in a display of lines with an introgression at the specified position. Upon selecting one of the lines, color-coded introgression in all chromosomes of the line are displayed graphically. The user can download a high-quality image of any of the displayed chromosomes by clicking on the desired chromosome. An example of our tool in use can be found at http://www.panzea.org/IView. This site displays maize teosinte introgression libraries, comprising 896 lines with introgressions defined with >500 SNP loci. This tool will be useful for those wanting to make introgression data from their stock of germplasm searchable.

Last Modified: 7/25/2014
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