The Grass Regulome Initiative: Integrating Control of Gene Expression and Agronomic Traits Across the Grasses

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PI: Erich Grotewold (The Ohio State University (OSU))coPIs: John Gray (University of Toledo (UT),OH; subawardee) and Ramana Davuluri (The Ohio State University (OSU))Collaborator: Daniel Janies (The Ohio State University (OSU))An emerging theme in plant systems biology is establishing the architecture of regulatory networks and linking system components to agronomic traits. The goal of this project is to provide a concerted effort to perform comparative transcriptional genomics across several grass crops (maize, sorghum, sugarcane and rice), combining the development of experimental tools and bioinformatic resources to discover and display regulatory motifs. The Grass Regulatory Information Service (GRASSIUS, http://www.grassius.org/) will be implemented as a public web resource that integrates sequence and expression information on transcription factors (TFs), their DNA-binding properties, TF binding sites in the genome, the genes that TFs target for regulation and the regulatory motifs in which they participate. A method for the in vivo identification of direct targets for TFs, which should be applicable even in the absence of a complete genome sequence, will be developed and applied towards the identification of direct targets for a small subset of maize, rice, sorghum and sugarcane TFs. Together with the generation of a large centralized collection of plasmids harboring open reading frames for several TFs and antibodies to a subset of them, this project will facilitate the community-wide identification of protein-DNA interactions, essential for establishing the grass regulatory map. The experimental and computational integration of regulatory motifs with QTLs will provide an accelerated translation of findings derived from these studies to issues of agronomic relevance. Benefiting from the increasing amount of genome sequence available, this proposal integrates genetics, molecular biology, biochemistry, statistics, bioinformatics and computer sciences in establishing the architecture of the regulatory networks that control plant gene expression, in a pioneering effort to launch the comparative transcriptional genomics field to important grass crops. The interdisciplinary nature of this project provides a unique opportunity for training at various levels (undergraduate, graduate and post-doctoral) across several disciplines, training that will be complemented by the application of tools and resources developed here into the classroom at UT and OSU, in the existing OSU Functional Genomics Training Workshop, and through the development of a new workshop in Plant Regulatory Networks. The expansion of ongoing collaborations with international leaders in the field of grass genomics will further enhance the educational impact of this proposal, by offering students and postdocs an opportunity to advance their research abroad in areas of actual need, but for which modest research is ongoing nationally (e.g., sugarcane research). Finally, the development of Web-accessible public databases will continue to ensure that the findings derived from this project will have the broadest possible dissemination.