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Title: CIMDE: A COMMUNITY IBM GENETIC MAPPING SERVICE

Author
item Schaeffer, Mary
item SANCHEZ-VILLEDA, HECTOR - UNIVERSITY OF MISSOURI
item HAVERMAN, SETH - UNIVERSITY OF MISSOURI
item McMullen, Michael
item DAVIS, GEORGIA - UNIVERSITY OF MISSOURI
item CONE, KAREN - UNIVERSITY OF MISSOURI
item COE, EDWARD - USDA-ARS-PGRU RETIRED

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 2/28/2005
Publication Date: 3/10/2005
Citation: Schaeffer, M.L., Sanchez-Villeda, H., Haverman, S., Mcmullen, M.D., Davis, G., Cone, K., Coe, E. 2005. Cimde: a community ibm genetic mapping service [abstract]. 2005 Maize Genetics Conference. 47:112.

Interpretive Summary:

Technical Abstract: CIMDE is a public genetic mapping service for any member of the community using the IBM-94 mapping population. This map population is a 94-line subset of the 302 high-resolution recombinant inbred lines that were derived from B73 and Mo17 inbreds; and were used to create a genetic resource for anchoring the BAC contigs (Arizona) to chromosomal locations. Seed for the IBM-94 are available from the Stock Center. DNA is available from the University of Missouri-Columbia < http://www.maizemap.org/dna_kits.htm>. The community may download scores for this population at MaizeGDB and compute their own maps; alternatively, they may submit scores to the CIMDE interface at the University of Missouri-Columbia and receive, sometime over the following 2 weeks, an approximate map coordinate. Either tab-delimited files or ‘hand entry’ of individual scores may be used to submit data. The submitter may use the interface to edit scores at any time, including weeks after submission. RI line identity is controlled by scoring data for 3 selected SSR markers. There are also controls for marker syntax. All data are stored in a local laboratory information management system described by Sanchez-Villeda et al 2003 Bioinformatics 19:2022-2030. There is no limit to the number of markers that may be submitted at one time. Map computation uses the build and place commands of Mapmarker; loci are ordered onto a framework of 250 loci previously mapped onto the high resolution IBM population. With permission of the submitters, map data submitted to the CIMDE interface is supplied to the MaizeGDB as the community cIBM map. This map is periodically incorporated into the IBM neighbors representation. At this time over 400 loci, from some 11 research groups, have been mapped by this tool. Current support is provided by the USDA-ARS and the University of Missouri-Columbia.