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Description:
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Neighbors 2008 maps were computed using the same algorithm as for previous versions, with manual review of values for chromosome ends. Unlike the 2005 version, this consensus genetic map includes only loci mapped in recombination experiments, and it excludes loci that were only mapped to the FPC maps. The frame for the IBM2 Neighbors is the IBM2 map used to anchor the B73 FPC contigs, in turn used to select the minimum tiling path for the B73 genome sequence project. This 2008 Neighbors includes some 15,000 loci, most with sequence-based probes, and some 10,000 had statistically defendable orders on source maps. These latter are separately represented in the Neighbors Frame maps. Contributions to Neighbors come from many sources. New locus additions come from the Genetic 2008 map provided by Ed Coe (1033 new loci); the ISU IBM Map7 provided by Pat Schnable (4647 new loci); NAM diversity maps from Mike McMullen (1045 new loci); and SSR B73 x Mo17 Davis (117 new loci). We used IBM2 FPC0507, a hybrid genetic-physical map, to position some 508 loci whose orders are not statistically well-defended on source maps, but are ordered on the July 2005 agarose FPC build (from Cari Soderlund, www.genome.arizona.edu/fpc/maize). In choosing the frame for the computation both the resolution power of a mapping panel, and the actual numbers of resolved coordinates were considered (for example, 3 loci with a coordinate of 21.1 on a particular chromosome map are counted only once). |
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