MaizeCode - An Initial Analysis of Functional Elements in the Maize Genome

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PI: Thomas Gingeras (Cold Spring Harbor Laboratory)CoPIs: David Jackson, Robert Martienssen, W. Richard McCombie, Michael Schatz, and David Micklos (Cold Spring Harbor Laboratory), Doreen Ware (USDA-ARS/Cold Spring Harbor Laboratory); and Ken Birnbaum (New York University)Maize (corn) is one of the most economically and agriculturally important crops grown in the world. It has assumed this position after centuries of careful genetic breeding to enhance many of its growth and nutritional properties. The generation of high quality genome sequences paired with diverse molecular data allows scientists to better understand the effects of this selective breeding at both the genetic and epigenetic levels. The MaizeCODE project aims to create a comprehensive reference encyclopedia of highly useful genomic reference sequence resources for breeders and plant scientists to use to improve economically important crop traits like disease resistance and yield. In addition, this project will provide broad and comprehensive training opportunities for students, breeders and practicing scientists through specific courses and workshops that will address various approaches to obtain and analyze MaizeCODE data. The Education, Outreach, and Training (EOT) effort will prepare faculty from primarily undergraduate institutions (PUIs) to analyze MaizeCODE with undergraduate students and will provide travel awards for graduate students to attend MaizeCODE training at professional meetings. The EOT program will be unique in promoting Science, Technology, Engineering and Math (STEM) disciplines by anticipating and encouraging broad participation in primary data analysis by undergraduate and graduate students. Improved assemblies of the maize genome will provide a foundation for the identification of biochemically active and biologically functional elements encoded in this working-draft sequence. A comprehensive catalog of these elements will be a critical component in strategies to link genotype with important traits in maize, a classical genetic system. This is the overarching goal of the MaizeCODE project. The human ENCODE project is a model for such a comprehensive catalog. Building on the project team's leadership experience with ENCODE, this similarly integrated and multi-disciplinary project has three main objectives: 1) to develop high-quality working drafts for two inbred maze lines and one teosinte inbred line, 2) to identify regions of the maize genome that are transcribed, methylated, bound by specific modified histones in six cell types that are the major progenitors of the root and shoot systems (focusing on histone modification in three root cell types) and transcription factors in five unrelated tissues and 3) to store, collate, display and disseminate the data to the broader community of plant biologists worldwide. Given the wealth of "genome to phenome" studies in maize, and the emerging realization that much of the variation under selection acts at the level of gene regulation, it is expected that this project will have broad and significant impact on maize genetics research and breeding, with the potential to inform similar research in other grass crops. The project expects to extend significantly the functional annotations and the current understanding of the regulation of gene activity in maize, adding critical content to established databases and graphical genome display centers. Information generated in this project will be rapidly and broadly disseminated using publically available databases and the CyVerse (www.cyverse.org) online resource.