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Title: IBM NEIGHBORS: CONSENSUS GENETIC MAP FOR PHYSICAL MAP SCAFFOLDING

Author
item Schaeffer, Mary
item SANCHEZ-VILLEDA, HECTOR - AGRONOMY-UNIV OF MISSOURI
item Coe Jr, Edward

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2003
Publication Date: 1/10/2004
Citation: Polacco, M.L., Sanchez-Villeda, H., Coe Jr, E.H. 2004. IBM neighbors: consensus genetic map for physical map scaffolding [abstract]. Plant and Animal Genome.

Interpretive Summary:

Technical Abstract: Anchoring BAC contigs onto a well-ordered genetic map is critical to assembly of the maize physical map. The best map for this purpose is the high resolution IBM map, based on the inter-mated B73 x Mo17 mapping population developed by Mike Lee (Lee et al. 2002, Plant Mol. Biol. 48:453-461; Sharopova et al. 2002, Plant Mol. Biol. 48:463-481). This population expands resolution of map order some 15-fold as compared to other public mapping populations used for maize. However, many genetically mapped anchor points have not been placed on this mapping population. To enhance the genetic scaffold for the physical map, we have developed an algorithm that relies on any map curated in MaizeGDB (www.maizegdb.org), with the only constraint that some of the loci have also been placed on either the IBM, or another map with loci in common with IBM maps. The algorithm weights map order based on statistical evidence for map position. The IBM2 neighbors contribution to the manual editing of the physical map may be viewed at Arizona by various displays (genome.arizona.edu/fpc/maize), and at Missouri as the iMap display (www.maizemap.org/iMapDB/iMap.html). The June 2003 version contained some 5700 loci, representing nearly 7000 RFLP, SNP (single nucleotide polymorphism), IDP (InDel; insertion deletion polymorphism), and SSR probes; it includes loci mapped onto the community IBM mapping population, a 94-line subset of the 302 used for high-resolution IBM maps. Incorporating the physical map into IBM neighbors not only refines order, but adds some 13,000 additional loci, largely maize cDNAs with Overgo probe associations with BACs. The software to create IBM neighbors is freely available on the internet, with source code, at www.maizemap.org/bioinformatics.htm. This project was supported by the NSF Grant #9872655.