RESEARCH-PGR: Elucidating Maize Gene Regulatory Networks to Accelerate Translational Genomics

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Maize is one of the most widely grown cereal crops that supports growing populations across the world. Through improvements in agriculture over the last century, corn yields have increased significantly across the U.S. Despite these advances, agriculture currently faces significant environmental challenges, from increasing water stress to spread of new diseases. New breeding approaches are thus needed to produce resilient plants and to maintain the health and productivity of maize agriculture. Major new advances in this arena come from recent discoveries in maize genetics and genomics: Researchers have identified key factors in the genome that serve as "master regulators" to control expression of important traits. Currently, little is known about when or where these factors function or how they control traits. The project uses all-new technologies to find and characterize hidden sites of expression control in the genome, and tests their function. The breakthroughs from this research will provide new ways to generate crop resilience and will improve the breeding potential of maize. Through public websites, outcomes from the project are made available to other researchers, growers and breeders, thereby ensuring a coordinated community effort to improve maize research and agriculture. Students and post-doctoral researchers are trained in crop genomics to maintain the strength, continuity and security of the scientific enterprise in the U.S. Elucidating gene regulatory networks involves linking the cis-regulatory code (cistrome) with the trans-acting factors through identifiying protein-DNA interactions. The cistrome hinges on where transcription initiation starts, which must be empirically defined. Differences in gene expression between inbred lines contribute to hybrid vigor, and are ultimately a consequence of cis- and trans-acting variations that affect the protein-DNA interaction space. Understanding these variations provides opportunities to accelerate crop breeding. Building on the team's previously developed tools to identify protein-DNA interactions, this interdisciplinary project has three main objectives: 1) Establish the genome-wide landscape of transcriptional initiation in maize, 2) develop a comprehensive catalog of maize gene regulatory interactions, and 3) incorporate functional transcription factor information to accelerate trait discovery. The project will continue to develop genome-wide tools necessary for plant gene regulatory network dissection, and build the knowledge necessary to enable similar studies in other crops. Data will be visualized through the Web-accessible knowledge base GRASSIUS (www.grassius.org) and MaizeGDB (www.maizegdb.org) to ensure the broadest possible dissemination of results. The interdisciplinary nature of the research will be integrated with the training of undergraduate students through the FIRE (Fostering Integration of Research and undergraduate Education) program, and recently graduated students from underrepresented groups through the SIGuE (Success In Graduate Education) program.