Poster: Genomics Resources

Abs # 927: The soybean integrated physical and genetic map: status report, access and educational tools.

Presenter:	Lightfoot, David A, ga4082@siu.edu
Authors	Lightfoot, David A (A)   Meksem, Khalid  (A)   Zhang, Hongbin  (B)
Affiliations:	(A): Southern Illinois University (B): Texas A & M University
Web Site:	http://www.siu.edu/~pbgc

A marker anchored physical map of the soybean genome has been constructed. Wu et al., (Plant Cell; 2003) describe a December 2002 version of the soybean physical map built from 78001 BAC (9.8 fold genomes) fingerprints to form 2,905 contigs encompassing 1,451 Mbp with 279 micro satellite anchors and 109 RFLP anchors locating 708 contigs to loci and homoeologous loci. There are three sets of tools available to access the datasets. One route of access is provided by genetic markers (www.siu.edu/~pbgc/htmls/search.html). The genetic map location of a marker on the USDA linkage group can be viewed at www.siu.edu/~pbgc/htmls/link.htm. The sequences associated with a contig represent a second route of entry to the physical map. NCBI buttons next to a marker allows the DNA sequences associated with that marker to be displayed. These include primer sequences, allele sequences, BAC end sequences and sequence tagged sites linked to clone plate addresses within that contig.. A third route of access is provided by the plate addresses for clones that can be used to view individual BAC fingerprints at http://hbz.tamu.edu/-PhysicalMapping/Soy Map for investigator driven contig assembly A downloadable FPC database is available so that individuals can generate their own builds and merges using fingerprint data. The databases are being incorporated into a GMOD genome browser format. Community members can build their own overlapping clone tiles, framework EST maps, compare genomes, deconvolute genome sequence and target locations for new DNA markers. An RET supplement has allowed for development of a lab manual, a kit and a workshop to help High-school teachers present concepts from genomics in the classroom. This work was supported by NSF project #9872635.