Co-PIs: Thomas Brutnell and Todd Mockler (Danforth Plant Science Center); Peng Liu (Iowa State University); Chris Myers, Robert Turgeon, Qi Sun, and Klaas van Wijk (Cornell University); and Joyce van Eck (Boyce Thompson Institute)

C4-type plants such as maize and several promising biofuel feedstocks have more efficient carbon-fixation, water and nitrogen use, and performance in high temperatures and light intensities, in comparison to C3-type plants such as rice and wheat. The traits conferring these C4 advantages are (1) cooperation of two distinct photosynthetic cell types (mesophyll and bundle sheath) for carbon fixation and photosynthesis, (2) enhanced movement of metabolites between cooperating cells, and (3) high density of leaf venation. These C4 traits are produced from genetic resources already present in less-efficient C3 plants, but regulated in more efficient patterns. Although C4 plants have evolved at least 50 times independently in various taxonomic groups, the molecular basis of the more efficient C4 regulatory system is insufficiently understood to extend its advantages to other crops and biofuel feedstocks.

A systems-level analysis of RNAs, proteins, metabolites, anatomy and physiology of corresponding developmental stages of maize (C4) and rice (C3) leaves has identified many of the molecular resources that produce the C4 traits. It has also revealed that additional corresponding data about small regulatory RNAs, epigenetic differences among cell types, protein modifications and several other "data channels" are needed to understand the production and regulation of these traits. In addition, more sophisticated computational approaches are needed to integrate the many "channels" of RNA, protein, anatomical and small molecule information that produce complex traits. This project will (1) obtain the missing data channels for C4 leaf developmental stages (2) utilize novel computational approaches for the integration of data channels and the modeling of regulatory networks that can be tested experimentally, and (3) test the regulatory basis for several C4 biochemical cellular traits by genetic and transgenic manipulation. This analysis will identify the regulatory points that are potential targets for the introduction of C4 traits in C3 species. Beyond producing a practical and profound understanding of C4 photosynthesis, the computational tools and systems resources developed by this project can be applied to other studies of plant development, biochemistry, physiology and productivity.

The impact of this project will be broadened through the novel BrachyBio! Outreach Program (, which introduces high school students to authentic plant genetics research, while providing the plant research community with a web-accessible collection of indexed mutant stocks of Brachypodium distachyon (C3) and Setaria viridis (C4). Project outcomes will be available through a project-specific public website (C3-C4DB,, and curated into the Gramene public database ( Data will also be deposited at the NIH NCBI and the European Bioinformatics Institute (EBI;

National Science Foundation (NSF)
Division of Molecular and Cellular Biosciences (MCB)
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Karen C. Cone
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Yale University
New Haven
United States
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