Minisymposium 23: Genome Annotation

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Abs # M2304: The Soybean Genome Database (SoyGD): A Tool For Integrated Legume Biology.

Presenter:	Lightfoot, David A       Contact Presenter
Authors	Lightfoot, David A (A)   Shultz, Jeffry L (B) (A)  Kazi, Samreen  (A)   Bashir, Rabia  (A)   Yesudas, Charles R (A)   Jayaraman, Dheepakkumaran  (A)   Iqbal, Javed M (D) (A)  Yaegashi, Satsuki  (E) (A)  Town, Chris  (C)   Koo, Hean  (C)
Affiliations:	(A): Southern Illinois University (B): USDA, Stoneville, MS (C): The Institute for Genomic Research, MD (D): Virginia Institute for Advanced Learning Research, VA (E): U. of Tokio
Web Site:	http://bioinformatics.siu.edu

The legume Glycine max (soybean) genome is being sequenced at DOE by the shotgun approach. The physical map will be critical to finishing that sequence and placing its features onto the genetic map. Map development is challenging because the genome represents a type of polyploid, with ~25% highly conserved following two increases in ploidy. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) browser integrates and serves the publicly available soybean physical map (1) with the genetic map and gene expression resources. Duplicated regions have been identified and catalogued with a-d suffix to marker anchor names and contig names that communicate ploidy. In recent additions, the minimum tiling path BIBAC clones provided ~20 Mbp of sequence from 21,174 BAC ends (BES) to decorate the physical map. MTP2 and MTP4 clones were added to the SoyGD as separate tracks. Gene family distribution and positional efffects on gene expression were explored by EST hybridization. There was strong selection for either divergence (and loss)or conservation in different families. Expressed genes clustered. Predicted gene models were developed for about 15% of the BES and candidate genes underlying disease resistance, seed yield and seed protein, oil or isoflavone content were detected and fine-mapped. In genome evolution analyses more than a thousand additional microsatellite marker anchors were developed (70% class II) for contigs, 353 on the map and about 700 in Queue. Linkage analysis placed one hundred of the 1,053 new microsatellite markers on the genetic map, unequivocally placing contigs and associated features. About half of the markers mapped to regions of the genome that formed gaps in earlier maps, suggesting marker clustering biases among class I microsatellites. SoyGD now shows the new build 5 for the physical map with less than 800 contigs. New QTL data has been incorporated from LIS and Soybase. Support was from NSF #9878635 and USB 2218-6218. (1) Shultz et al., 2006. Nucleic Acids Res. Database Issue D758-D765.