AN INFORMATICS INFRASTRUCTURE FOR FUNCTIONAL AND COMPARATIVE GENOMICS STUDIES IN SOYBEAN

¹ University of Minnesota, Computational Biology Centers, Mayo Box 43, 420 Delaware St., Minneapolis MN 55455 USA

² Department of Crop Sciences, University of Illinois

³ USDA-ARS and Department of Agronomy, Iowa State University

⁴ Deparment of Biology, Northern Arizona University

⁵ Biochemistry Department, University of Missouri, Columbia

⁶ Department of Plant Pathology, University of Minnesota, St. Paul MN, USA

⁷ USDA-ARS and Iowa State University

The functional genomics program for soybean is a collaborative effort to provide the knowledge and tools to expidite functional genomics research for the entire soybean community and those interested in all legumes. Efforts are underway to asses the feasibility of three functional genomics techniques for use in soybean: 1) high-density expression arrays, 2) microarrays, and 3) serial analysis of gene expression (SAGE). We are developing bioinformatics tools to assess expression patterns for various tissues and developmental stages of soybean. We report on a method for preliminary analysis of SAGE expression data. We also report on the design of an informatics infrastructure that integrates data from contigs of soybean EST and BAC-end sequences, soybean genetic maps, and Arabidopsis genome infrastructure that integrates data from contigs of soybean EST and BAC-end sequences, soybean genetic maps, and Arabidopsis genome sequence data to facilitate comparative genomics studies. This information base, to be available on the world-wide-web, will contain an infrastructure of soybean sequence data correlated to known map positions and will enable the soybean genome organization to be correlated with the complete Arabidopsis genome organization as each data source becomes available.