Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
Dheepakkumaran Jayaraman , Charles R. Yesudas , Samreen Kazi , Rabia Bashir , Ahmed J Afzal , David A. Lightfoot
Genomes like Glycine max (soybean) that have been highly conserved following increases in ploidy (by duplication or hybridization) present challenges for genome analysis. At http://soybeangenome.siu.edu the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, BAC fingerprint database and genetic map associated genomic data (1). Duplicated regions have been identified and catalogged with a-d suffix to marker anchor names and contig names that communicate ploidy (ctg>8000 are tetraploid, ctg>9000 are octoploid). DNA sequence data has been used to separate DNA marker anchors from homologs of DNA marker anchors in BAC pools. In recent additions, about 3,840 minimum tiling path (MTP4) BIBAC clones provided BAC end sequences (BES) to decorate the physical map. MTP2 and MTP4 clones were added to the database as separate tracks. Additional marker anchors were developed for contigs still in Queue. Linkage analysis placed one hundred of the 1,053 new microsatellite markers on the genetic map with contigs and associated features. SoyGD will represent the new build 5 for the physical map that is in progress based on the 76,749 fingerprinted clones available to the public. New QTL data has been incorporated from the newly release Essex by Forrest and Hartwig by Flyer RIL populations. Gene expression data has been added to the gene models represented in SoyGD. This work was supported by NSF project #9878635 and USB 2218-5218.
(1) Shultz et al., 2006. Browsing the soybean genome. Nucleic Acids Res. Database Issue.