Bioinformatics and microgenomics integration for discovering cell specific gene regulation in a complex plant genome

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The blue print instructions for a functional organism are encoded by its genome, studied by the fast growing fields of genomics (molecular methods) and bioinformatics (computational methods). To date an amazing eleven higher plant genomes have been sequenced. Among these, the average number of genes is about 40,000, ranging from 25,000 in Arabidospis (a small 'model plant') to 66,000 in soybean (the economically most important legume crop plant in the world). Gene sequences alone do not provide sufficient information for a functional plant - the genes need flanking sequences, promoters (sometimes called "gene switches"), which regulate when and where the gene will be expressed. These promoters contain specific sequence motifs to which gene regulating proteins, transcription factors, can bind. The basic set of genes may by and large be the same in all plants, but it is the regulation of the genes that make each species unique. Where and when genes are switched on and off, and more interestingly how, is still not a matter of simple prediction even in model organisms, and both experimental and computational analysis methods are needed to address the problem at a large scale. The proposed research is unique in that it integrates high speed computing (bioinformatics) with molecular techniques (micro-genomics) to find the molecular mechanisms behind cell specific gene regulation. Our model system is soybean, which has long been in the forefront of functional genomics research, with the genome sequence recently released and a multitude of other genetic and genomic resources available. We will identify which promoter motifs are responsible for subsets of soybean genes being specifically expressed in several different cell types. The results will be available in an online database where links can be made between the molecular mechanism of cell specific transcriptional regulation and the resulting cell type. This research has invaluable impact by increasing our basic knowledge of plant development and function, by making progress for biotechnology and crop improvement strategies and by training highly qualified graduate students in this exciting and rapidly expanding field.