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Thomas Brutnell

Adjunct Professor of Biological Sciences
Director, Enterprise Rent-A-Car Institute for Renewable Fuels
PhD, 1995 Yale University

Office: 975 N. Warson Road St. Louis, MO
Phone: 314-587-1485
Additional: Website
Headshot of Thomas Brutnell


Research summary

C4 photosynthesis and gene discovery in model plants for second generation lignocellulosic feedstocks

Research description

The Brutnell lab is located at the Donald Danforth Plant Science Center in St. Louis, Missouri.

A major thrust of the research in the Brutnell lab focuses on the use of new model grasses as drivers for lignocellulosic feedstock development and to improve productivity of major cereal crops. This includes developing genetic resources for Setaria viridis and Brachypodium distachyon. S. viridis is a small, self-pollinating diploid and is a member of the panicoid clade of grasses that includes maize, sugarcane, sorghum, Miscanthus and switchgrass. B. distachyon is also a small, self-pollinating diploid grass and is a member of the Pooideae clade that includes wheat, barley, rye and several turf grass and forage species. The genomes of both species have recently been sequenced and transformation technologies have been developed for each. Members of my group have contributed to the development of transformation technologies for S. viridis and we have helped annotate the S. viridis and B. distachyon genomes. We are currently developing genetic resources for both systems that include chemically- and radiation- mutagenized populations. We are also 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 to his research program is the development of reverse genetics tools for gene discovery in maize. Over the past ten years, members of the Brutnell lab have been mobilizing and mapping the maize transposable elements Ac and Ds insertions throughout the maize genome. They have 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. They have shown how these transposons can be used to fine map gene structure and have several targeted mutagenesis programs underway.

Finally, a fundamental biological challenge that Brutnell is trying to address in the lab is to understand the mechanisms that drive C4 photosynthetic differentiation. Using the forward and reverse genetics resources we have developed for S. viridis and Z. mays, we are now generating mutants in the genes necessary for the C4 carbon shuttle and using a combination of informatics and molecular approaches to define the regulatory networks driving their expression. These studies are targeted at understanding the function of genes involved in C4 photosynthesis and have applications in breeding/engineering improved photosynthetic traits in C4 grasses and in introducing novel C4 traits into C3 grasses.

Select Publications

Select Publications

Feldman, M.J., Paul, R.E., Banan, D., Barrett, J.F., Sebastian, J., Yee, M.-C., Jiang, H., Lipka, A.E., Brutnell, T.P., Dinneny, J.R., Leakey, A.D.B., Baxter, I. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4grass Setaria (2017) PLoS Genetics, 13 (6), art. no. e1006841,

Huang, P., Studer, A.J., Schnable, J.C., Kellogg, E.A., Brutnell, T.P. Cross species selection scans identify components of C4 photosynthesis in the grasses (2017) Journal of Experimental Botany, 68 (2), pp. 127-135.

Huang, P., Jiang, H., Zhu, C., Barry, K., Jenkins, J., Sandor, L., Schmutz, J., Box, M.S., Kellogg, E.A., Brutnell, T.P. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize (2017) Nature Plants, 3, art. no. 17054,

Nadal, M., Sawers, R., Naseem, S., Bassin, B., Kulicke, C., Sharman, A., An, G., An, K., Ahern, K.R., Romag, A., Brutnell, T.P., Gutjahr, C., Geldner, N., Roux, C., Martinoia, E., Konopka, J.B., Paszkowski, U. An N-acetylglucosamine transporter required for arbuscular mycorrhizal symbioses in rice and maize (2017) Nature Plants, 3, art. no. 201773,

Begemann, M.B., Gray, B.N., January, E., Gordon, G.C., He, Y., Liu, H., Wu, X., Brutnell, T.P., Mockler, T.C., Oufattole, M. Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases (2017) Scientific Reports, 7 (1), art. no. 11606,

Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W et al: Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nature Biotechnology 2016, 32(11):1158-1164.

Huang P, Brutnell TP: A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis. Current Opinion in Plant Biology 2016, 31:91-99.

Altpeter, F., Springer, N.M., Bartley, L.E., Blechl, A.E., Brutnell, T.P., Citovsky, V., Conrad, L.J., Gelvin, S.B., Jackson, D.P., Kausch, A.P., Lemaux, P.G., Medford, J.I., Orozco-Cárdenas, M.L., Tricoli, D.M., Van Eck, J., Voytas, D.F., Walbot, V., Wang, K., Zhang, Z.J., Neal Stewart, C. Advancing crop transformation in the era of genome editing (2016) Plant Cell, 28 (7), pp. 1510-1520.

Sebastian, J., Yee, M.-C., Viana, W.G., Rellán-Álvarez, R., Feldman, M., Priest, H.D., Trontin, C., Lee, T., Jiang, H., Baxter, I., Mockler, T.C., Hochholdinger, F., Brutnell, T.P., Dinneny, J.R. Grasses suppress shoot-borne roots to conserve water during drought (2016) Proceedings of the National Academy of Sciences of the United States of America, 113 (31), pp. 8861-8866.

Ding, Z., Zhang, Y., Xiao, Y., Liu, F., Wang, M., Zhu, X., Liu, P., Sun, Q., Wang, W., Peng, M., Brutnell, T., Li, P. Transcriptome response of cassava leaves under natural shade (2016) Scientific Reports, 6, art. no. 31673,

Salazar-Vidal, M.N., Acosta-Segovia, E., Sanchez-León, N., Ahern, K.R., Brutnell, T.P., Sawers, R.J.H. Characterization and transposon mutagenesis of the maize (Zea mays) Pho1 Gene Family (2016) PLoS ONE, 11 (9), art. no. e0161882,

Studer, A.J., Schnable, J.C., Weissmann, S., Kolbe, A.R., McKain, M.R., Shao, Y., Cousins, A.B., Kellogg, E.A., Brutnell, T.P. The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes (2016) Genome Biology, 17 (1), art. no. 223,

Huang, P., Shyu, C., Coelho, C.P., Cao, Y., Brutnell, T.P. Setaria viridis as a model system to advance millet genetics and genomics (2016) Frontiers in Plant Science, 7 (NOVEMBER2016), art. no. 1781,

Zhang Y, Ding Z, Ma F, Chauhan RD, Allen DK, Brutnell TP, Wang W, Peng M, Li P: Transcriptional response to petiole heat girdling in cassava. Scientific Reports 2015, 5:8414.

Zhang N, Gibon Y, Wallace JG, Lepak N, Li P, Dedow L, Chen C, So YS, Kremling K, Bradbury PJ et al: Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population. Plant Physiology 2015, 168(2):575-583.

Weissmann S, Ma F, Furuyama K, Gierse J, Berg H, Shao Y, Taniguchi M, Allen DK, Brutnell TP: Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants. Plant Cell 2015, 28(2):466-484.

Shyu C, Brutnell TP: Growth-defence balance in grass biomass production: The role of jasmonates. Journal of Experimental Botany 2015, 66(14):4165-4176.

Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C et al: Standards for plant synthetic biology: A common syntax for exchange of DNA parts. New Phytologist 2015, 208(1):13-19.

Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, Hill ST, McEntee CJ, Warnasooriya SN, Kumar I et al: A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria. Molecular Plant 2015, 8(10):1520-1535.

Ding Z, Weissmann S, Wang M, Du B, Huang L, Wang L, Tu X, Zhong S, Myers C, Brutnell TP et al: Identification of photosynthesis-associated C4 candidate genes through comparative leaf gradient transcriptome in multiple lineages of C3 and C4 species. PLoS ONE 2015, 10(10).

Brutnell TP, Bennetzen JL, Vogel JP: Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. In: Annual Review of Plant Biology. vol. 66; 2015: 465-485.

Kebrom, T.H., Brutnell, T.P. Tillering in the Sugary1 sweet corn is maintained by overriding the teosinte branched1 repressive signal (2015) Plant Signaling and Behavior, 10 (12), art. no. e1078954

Si Y, Liu P, Li P, Brutnell TP: Model-based clustering for RNA-seq data. Bioinformatics 2014, 30(2):197-205.

Warnasooriya SN, Brutnell TP: Enhancing the productivity of grasses under high-density planting by engineering light responses: From model systems to feedstocks. Journal of Experimental Botany 2014, 65(11):2825-2834.

Studer AJ, Gandin A, Kolbe AR, Wang L, Cousins AB, Brutnell TP: A limited role for carbonic anhydrase in C4 photosynthesis as revealed by a ca1ca2 double mutant in maize. Plant Physiology 2014, 165(2):608-617.

O'Connor SE, Brutnell TP: Editorial overview: Growing the future: Synthetic biology in plants. Current Opinion in Plant Biology 2014, 19:iv-v.

Mertz RA, Brutnell TP: Bundle sheath suberization in grass leaves: Multiple barriers to characterization. Journal of Experimental Botany 2014, 65(13):3371-3380.

Lori Tausta S, Li P, Si Y, Gandotra N, Liu P, Sun Q, Brutnell TP, Nelson T: Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes. Journal of Experimental Botany 2014, 65(13):3543-3555.

Jiang H, Barbier H, Brutnell T: Methods for performing crosses in Setaria viridis, a new model system for the grasses. Journal of visualized experiments : JoVE 2013(80).

Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S, Brutnell T, DeBolt S: Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and panicoid crop species. Frontiers in Plant Science 2013, 4(JUN).

Mauro-Herrera M, Wang X, Barbier H, Brutnell TP, Devos KM, Doust AN: Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae). G3 (Bethesda, Md) 2013, 3(2):283-295.

Weissmann S, Brutnell TP: Engineering C 4 photosynthetic regulatory networks. Current Opinion in Biotechnology 2012, 23(3):298-304.

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J et al: Reference genome sequence of the model plant Setaria. Nature Biotechnology 2012, 30(6):555-561.

Brutnell T, Frommer WB: Foods for thought. Scientist 2012, 26(6).

Honors & Awards

Selected honors and awards

International Research Initiative Scheme (IRIS) Award, Australia 2012

AAAS Fellow 2012