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United States Department of Agriculture

Agricultural Research Service

Title: Ibm2 2005 Neighbors-45,000 Locus Resource for Maize

Authors
item Schaeffer, Mary
item Sanchez-Villeda, Hector - UNIVERSITY OF MISSOURI
item McMullen, Michael
item Coe Jr, Edward

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2005
Publication Date: January 5, 2006
Citation: Schaeffer, M.L., Sanchez-Villeda, H., Mcmullen, M.D., Coe Jr, E.H. 2006. Ibm2 2005 neighbors--45,000 locus resource for maize. XIV Plant and Animal Genome Conference. p. 372.

Technical Abstract: Candidate gene discovery by chromosome walking depends upon a high resolution mapping capability to localize the trait or phenotype of interest to a small region. Towards that end, we have generated an extensive update of the IBM2 consensus map resource maintained at MaizeGDB (www.maizegdb.org). We now include over 9,000 total loci that have been genetically mapped, and are mostly associated with sequenced probes. Key new genetic maps include the insertion deletion polymorphism IDP maps of Pat Schnable; EST maps from Genoplante, Falque M et al. 2005 Genetics 170:1957-1966); the Genetic 2005 maps of Ed Coe. In addition, we add many loci whose location is entirely based on overgo hybridization of BACs, which, in turn, have been anchored by other loci onto a chromosome position. These physically mapped loci include 15,700 overgos related to Cornsensus, EST-UniGenes overgos (Gardiner J et al. 2000. Plant Physiol. 134:1317-1326); and 18,800 SOG, cereal overgos (Andrew Paterson). Locus orders within a BAC contig and on the maize chromosome are provided by Cari Soderlund www.genome.arizona.edu/fpc/maize). The tool for generating neighbors imports curated maps directly from MaizeGDB and projects them sequentially onto an evolving framework, beginning with IBM2. IBM2 is currently the best resolved genetic map for maize: it is based on a 302 member mapping panel of inter-mated B73 x Mo17 inbreds developed by Mike Lee and includes 2,000 loci where some 80% have statistically well-supported order (MaizeGDB; Davis G. et al. submitted). Software development was funded by the University of Missouri-Columbia and NSF grant DBI 9872655.

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