A major thrust of this research will focus on the use of the model grass Setaria viridis as a driver for lignocellulosic feedstock development and to improve productivity of major cereal crops. S. viridis is a small, self-pollinating diploid species and is a member of the panicoid clade of grasses that includes maize, sugarcane, sorghum, Miscanthus and switchgrass. The rapid cycling time of Setaria coupled to emerging transformation (Lowe et al. PMID:27600536) and gene editing technologies (Lowder et al. PMID:26297141) promise to greatly reduce the barriers to gene discovery in the grasses.

The genome sequence of Setaria has helped in developing genetic resources and technologies for fine mapping chemically-mutagenized populations as recently demonstrated by Pu Huang, Hui Jiang and colleagues (Huang et al. PMID: 28418381). In collaboration with colleagues at the DOE-JGI, we are tapping high-throughput sequencing techniques to accelerate reverse and forward genetic screens and to develop a gene atlas for S. viridis using RNAseq technology.

Another important component of our research program is the development of reverse genetics tools for gene discovery in maize. Over the past ten years, members of the lab have mobilized and mapped the maize transposable elements Ac and Ds insertions throughout the maize genome. We also been developing genetic and molecular protocols for using Ac and Ds as insertional mutagens. These elements tend to insert at closely linked sites in the genome to create unstable genetic variation. These transposons can be used to fine map gene structure and have several targeted mutagenesis programs underway.  These transposon resources complement the emerging genome editing technologies, which together will provide the foundation for a sophisticated genetic analysis of the maize genome.

Finally, a fundamental biological challenge that the Brutnell lab is trying to address is to understand the mechanisms that drive C4 photosynthetic differentiation. Using the forward and reverse genetics resources they have developed for S. viridis and Z. mays, they are now generating mutants in the genes necessary for the C4 carbon shuttle and the differentiation of photosynthetic bundle sheath and mesophyll cells.  Using a combination of informatics and molecular approaches we are also defining the regulatory networks that drive cell fate specification.



  • Genome Wide Impact of mPing transposition on Rice Phenotypic Diversity, NSF-IOS 1027542
  •  A Systems-Level Analysis of Drought and Density Responses in the Model C4 Grass Setaria Viridis, DOE DE-SC0008769
  • Translational Dynamics of Leaf and Chloroplast Development in Maize, NSF-IOS 1339130
  • Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nurtrient Use Efficiency, and Interactions with the Soil Microbiome, DOE DE-SC0014395
  • Engineering C4 Photosynthesis in Maize to Enhance Nitrigen Utilization, USDA-NIFA 2016-67013-24585
  • Dissecting the Genetic Networks Underlying Kranz Anatomy in C4 Grasses, NSF-PGRP 1546882
  • Using Systems Approaches to Improve Photosynthesis and Water Use Efficiency in Sorghum, DOE DE-SC0018277