Using SoyBase Tools to Identify Genes Potentially Involved in Quantitative Traits: the Soybean bZIP1 Transcription Factor and Water Use Efficiency

Understanding plant responses to stresses is crucial for crop improvement. Biological information as well as genetic and genomic data are often from plant models and can serve as starting points for experimentation in other species. Data from the model dicot Arabidopsis thaliana have frequently been used to identify gene homologs and point to interesting questions in many other species. Recently Sun et al. identified the bZIP1 transcription factor from Arabidopsis as a positive regulator of a number of abiotic stresses that could be associated with climate change such as drought and salinity tolerance. BLAST similarity matching at SoyBase using the Arabidopsis bZIP1 protein sequence against a database of all JGI gene calls for the soybean genome sequence identified five predicted genes with an e-value less than e-10. Using the SoyBase genome sequence browser (http://soybase.org -> Genome tab -> SoyBase browser) we identified pairs of sequenced-based genetically mapped markers that flanked each of the gene models. These markers were then used to identify regions on the genetic map (http://soybase.org -> Maps tab) that include the gene calls. Examination of the genetic maps indicated that three of these genes are located within or very near QTL regions for “water use efficiency” (WUE) and “drought index”. Since the Arabidopsis bZIP1 protein is a transcription factor, these gene models may prove to be excellent candidates as master controllers for soybean water response regulation. This exercise demonstrates the considerable power SoyBase tools provide the user to engage in cross-species comparisons and to rationally identify potential gene candidates for many quantitative traits. The gene models identified in this study and their relationships to the soybean genetic maps available at SoyBase will be presented.