The Soybean Genome Database (SoyGD): A Genomic Interactome Viewer Based On Cultivar Forrest

The many genomes of Glycine max (soybean) with sequence have allowed new analyses of presence and absence variations (PAVs), copy number variations (CNVs), small indels, SNPs, SNHs, residual heterozygosity, residual heterogeneity, linkats and protein protein interactomes to be made. For cultivar Forrest thirty thousand  polymorphic sequence tags were identified. Three sets of minimum tiling path (MTP) BAC clones  that each encompassed 90% of the genome were BAC end sequenced. Markers were aligned to the reference genome at the Soybean Genome Database (SoyGD) http://soybeangenome.siu.edu.  The genome browser attempts to integrate the data from soybean cultivar Forrest,  and a protein interactome viewer. New genome search tools are available at the web site.  Thousands of additional markers were developed. Duplicated regions of the genome that were identified and catalogued were separated into sets based on percent identity between homeologs.  DNA sequence data was used to separate DNA marker anchors from homologs of DNA markers and identify PAVs.  The MTP BACs were screened for functions by transformations. Predicted protein encoding genes from the genome sequence were used to develop a predicted protein-protein interactome and this is shown at SoyGD as a separate track below gene models. SNPs underlying traits were mapped to saturation. Candidate genes underlying disease resistance, seed yield and seed protein, oil or isoflavone content were detected, fine-mapped and tested in association studies using the tools assembled at SoyGD. SoyGD represents the build 5 for the NSF project #9878635