Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

The Genome Browser For Soybean: Displaying A Sequence Framework And Physical Map.

Kay Shopinski⁵ , Jeffry L Shultz¹ , Nagayothi Lavu¹ , Javed Iqbal¹ , Christopher Town³ , Chencang Wu⁴ , Hongbin Zhang² , Khalid Meksem¹ , David A Lightfoot¹

¹  Southern Illinois University, Carbondale, IL62901.USA. ga4082@siu,edu, http://bioinformatics.siu.edu

²  Texas A&M Univ., College Station, TX USA

³  TIGR, Maryland USA

⁴  Pioneer Hibred, IO USA

⁵  USDA, Peoria, IL. USA

A deep marker anchored physical map of the soybean has been constructed and presented at http://bioinformatics.siu.edu. Tracks have been added to show data for markers, contigs, BACs, EST, BES, gene models and Syntenic genomes. One thousand additional microsatellite markers have been developed. Build 3 of the soybean physical map formed 2,905 contigs that encompassed 1,451 Mbp (4). Build four formed 2854 contigs (1, 2) that have been used in community directed merges to reduce to about 1,400. The minimum tiling path contained 9,546 BAC clones and 13,474 BESs identified >2,500 gene like sequences (<e-5)(3). Mapping with 313 EST probes has located gene paralogs. Gene rich islands were found near telomeric regions. Conserved synteny was measured with Arabidopsis thaliana and Medicago truncatulata. Maps are compared by C-MAP and through LIS at NCR This work was supported by NSF project #9878635 and USB 2218-5218.
(1) Shultz et al., 2003. Evaluating physical maps by clone location comparisons. Genome Lett. 2:109-118.
(2) Shultz et al., 2003. End sequencing of BACs comprising a provisional minimal-tiling path from a fingerprint physical map of soybean (Glycine max) cultivar Forrest. Genbank. CG826126 to CG812653 (13,473 sequences).
(3) Langin et al., 2004. Browsing the soybean genome. NAR Nov Database Issue
(4) Wu et al., 2004. A BAC and BIBAC-based Physical Map of the Soybean Genome. Genome Research 14:319-326.
(5) Wu et al., 2004. Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet. May [Epub].