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United States Department of Agriculture

Agricultural Research Service

Title: Imap: a Database-Driven Utility to Integrate and Access the Genetic and Physical Maps of Maize

Authors
item Fang, Z - AGRONOMY DEPT-UMC
item Cone, K - BIO SCIENCES-UMC
item Sanchez-Villeda, H - AGRONOMY DEPT-UMC
item Schaeffer, Mary
item McMullen, Michael
item Schroeder, S - AGRONOMY DEPT-UMC
item Gardiner, J - AGRONOMY DEPT-UMC
item Davis, G - AGRONOMY DEPT-UMC
item Havermann, S - AGRONOMY DEPT-UMC
item Coe Jr, Edward

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 8, 2003
Publication Date: November 1, 2003
Citation: FANG, Z., CONE, K., SANCHEZ-VILLEDA, H., POLACCO, M.L., MCMULLEN, M.D., SCHROEDER, S., GARDINER, J., DAVIS, G., HAVERMANN, S., COE JR, E.H. IMAP: A DATABASE-DRIVEN UTILITY TO INTEGRATE AND ACCESS THE GENETIC AND PHYSICAL MAPS OF MAIZE. BIOINFORMATICS. 2003. V. 19(16). P. 2105-2117.

Interpretive Summary: A representation of information about the order of the DNA and of genes in corn (maize, Zea mays L.) has been produced as a part of the Maize Mapping Project (MMP). The MMP is developing resources that will aid comprehension of the genome of corn. The volume and complexity of the data require a visual representation of the integrated genetic and physical information. The iMap (integrated map) web view of the data provides an essential tool for scientists who are studying fundamental processes of the corn plant, and for those who are studying methods to direct corn into greater productivity, improved quality, or new uses, and will increase the pace of advance in these areas.

Technical Abstract: Because of unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize (Zea mays L.) is required for storing, integrating, accessing, and visualizing the underlying data. The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display the integrated mapping information, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer), and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers, and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig is retrieved via popup windows that feature links to external data resources. Searches can be conducted for genetic locus, probe, or sequence accession number; search results include relevant map positions, anchored BAC contigs, and direct links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org. The entire iMap utility package is available from the authors for non-commercial use.

Last Modified: 4/19/2014
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