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NAR Molecular Biology Database Collection entry number 870
Shultz J.L.1,10, Jayaraman D.1, Shopinski K.1,7, Iqbal M.J.1, Kazi S.1, Zobrist K.1,5, Bashir R.1, Yaegashi S.1,6, Lavu N.1, Afzal A.J.1, Yesudas C.R.1, Kassem M.A.1,8, Wu C.2,4, Zhang H.B.2, Town C.D.3, Meksem K.9 and Lightfoot D.A.1
1Genomics Core-Facility, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
2Department of Soil and Crop Sciences and Institute for Plant Genomics & Biotechnology, 2123 TAMU, Texas A&M University, College Station, Texas 77843-2123, USA
3The Institute for Genomic Research, Rockville, MD 20850, USA
4Current address, Pioneer Hi-Bred International Inc., Johnson City, IA, USA
5Current address, Monsanto, Chesterfield, MO, USA
6Current address, University of Tokyo, Japan Science and Technology Agency, Itabashi-Ku, Japan
7Current address, USDA, Peoria, IL, USA
8Current address, Kean State University, NJ, USA
9Current address, Plant and Animal Genomic Laboratory, SIUC, Carbondale, IL, USA
10Current address, United States Department of Agriculture, Stoneville, MS 38776, USA

Database Description

The Soybean Genome Database (SoyGD) genome browser integrates the publicly available physical map, BAC sequence database and genetic map associated genomic data at SoGD shows different builds of the soybean physical map and the associated minimum tile paths. High quality DNA markers that anchored contigs are shown. Since many DNA markers anchored sets of 2-8 different contigs each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. The minimum tiling path clones provide BAC end sequences (BES) to decorate the physical map with gene models, new marker anchors and new microsatellite markers. Paralogs from low copy gene families can be located. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.

Recent Developments

The new build 5 for the physical map based on the 76,749 MICF and 4,992 HICF fingerprinted clones from MTP4 will soon be available to the public. New QTL data has been incorporated from the newly release Essex by Forrest RIL population. All of the EST placed in SoyGD to date have been used for expression analysis and are related to responses of roots to biotic stresses strengthening the usefulness of SoyGD for the identification of candidates for genes underlying QTL and other genetic loci. Direct query of the data in SoyGD with users own data is possible over the Internet. Layering on the map fingerprint data from the Williams 82 cultivar is envisioned when the data are released.

In the near future the genome browser interface will be improved using as yet unpublished data in several ways; by showing sequences and gene predictions from 37,000 BESs; by showing the locations of additional microsatellite anchors, SNP anchors and BES-SSR anchors; by showing many well annotated contiguous sequenced regions of more than 100 kbp; by showing the locations of about 2,000 resistance gene analog positive clones (nucleotide binding leucine rich repeat paralogs), 700 receptor like kinases and 512 additional low-copy gene family paralogs. In addition to adding soybean data, the adoption of GBrowse tools that allow comparisons of synteny among genomes will be a priority.


This research was funded in part by a grant from the NSF 9872635, ISPOB 98-122-02 and 02-127-03 and USB 2228-5228. The SoyGD material was based upon work supported by the National Science Foundation under Grant No. 9872635. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. The continued support of SIUC, College of Agriculture and Office of the Vice Chancellor for Research to MJI and DAL is appreciated. The authors thank Dr. Q Tao for assistance with fingerprinting. We thank Chester Langin for his work on SoyGD from 2004-2005. We thank LIS for their C-Map representation of our GBrowse data.

Category: Plant databases
Subcategory: Other plants

Go to the abstract in the NAR 2006 Database Issue.
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