Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Population Explosion In The IBM Neighborhood - FPC And New Genetic Maps

Mary Schaeffer , Michael Gerau , Hector Sanchez-Villeda

  USDA-ARS, Division of Plant Sciences, University of Missouri-Columbia

The first versions of IBM neighbors maps were created to provide on a single framework those genetically mapped loci that would facilitate anchoring and orienting BAC contigs along the maize chromosomes. The Neighbors algorithm is straightforward and sequentially projects selected genetic maps, initially SSR maps, onto a selected framework, in the most recent version these are the high resolution IBM2 maps. Having proved highly useful, the algorigthm has since been used to provide a consensus, IBM neighbors representation of most all mapped loci, in particular where there are proven mapping probes. One of these includes loci mapped by members of the community using the Community IBM, or CIMDE, mapping service; the cIBM maps now uses an expanded 580 locus framework to facilitate better incorporation into the Neighbors map. Another, the many mutants, incorporated into the Genetic 2005 maps; these maps now include the UMC 98 RFLP frame to facilitate projection onto IBM2. In addition, we devised a strategy that uses the FPC maps both (1) to refine orders of the projected maps and (2) to add map coordinates for loci mapped by overgo probings of anchored BAC contigs. All results are provided to MaizeGDB where they are linked both to the FPC representation of contigs at Arizona, and the evolving maize sequence presentation at Cold Spring Harbor. A useage example will be presented.