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Molecular Weed Science

Associate Professor
C208 Plant Sciences
970-491-6824 office
970-491-1523 lab

Weed Science Lab





Research Interests:

My research goal is to support sustainable weed management that helps contribute to sustainable cropping systems.  To that end, I am interested in research to identify the molecular and genetic basis of complex herbicide resistance mechanisms; utilizing next-generation sequencing to study complex traits in weeds; and developing molecular markers for rapid resistance diagnostics.  Research projects in my lab study changes in evolutionary trajectories of weedy species due to human management (specifically herbicides and herbicide resistance evolution), and develop genomics and bioinformatics resources to study herbicide resistance traits in weedy species and crops.

Honors and Awards:

Highly Cited Researcher, 2019, Web of Science

Early Career Outstanding Scientist Award, 2019, Weed Science Society of America

Early Career Outstanding Scientist Award, 2019, Western Society of Weed Science

Classes Taught:

AB529: Pesticide Resistance Evolution and Management (Spring, Even)

AB 509, Herbicide Selectivity and Action (Fall, Even); co-taught with Franck Dayan

Dr. Gaines is also the Professional MS in Pest Management Program Adviser

Graduate Students I Advise:

Carlos Rigon – PhD in Weed Science

Crystal Sparks – PhD in Weed Science

Marcelo Figueiredo – PhD in Weed Science

Neeta Soni – PhD in Weed Science

Olivia Todd – PhD in Weed Science

Post-docs I Advise:

Eric Westra – Integrated Weed Management

Sarah Morran – Weed Genomics

Selected Publications:

Patterson, E., C. Saski, D. Sloan, P. Tranel, P. Westra, and T. Gaines*. 2019. The draft genome of Kochia scoparia and the mechanism of glyphosate resistance via transposon-mediated EPSPS tandem gene duplication. Genome Biology and Evolution, in press.

Soni, N., S. Nissen, P. Westra, J. Norsworthy, M. Walsh, and T. Gaines*. 2019. Seed retention of winter annual grass weeds at winter wheat harvest maturity shows potential for harvest weed seed control. Weed Technology, in press.

Westra, E., S. Nissen, T. Getts, P. Westra, and T. Gaines*. Survey reveals frequency of multiple resistance to glyphosate and dicamba in kochia (Bassia scoparia). 2019. Weed Technology. 33: 664-672.

Takano, H., E. Patterson, S. Nissen, F. Dayan, and T. Gaines*. 2019. Predicting herbicide movement across semi-permeable membranes using three phase partitioning. Pesticide Biochemistry and Physiology. 159: 22-26. DOI: 10.1016/j.pestbp.2019.05.009.

Gaines, T.*, E. Patterson, and P. Neve. 2019. Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance. New Phytologist. 223: 1770-1775. Tansley Insight. DOI: 10.1111/nph.15858.

Ravet, K., E. Patterson, H. Krähmer, K. Hamouzová, L. Fan, M. Jasieniuk, A. Lawton-Rauh, J. Malone, J.S. McElroy, A. Merotto, P. Westra, C. Preston, M. Vila-Aiub, R. Busi, P. Tranel, C. Reinhardt, C. Saski, R. Beffa, P. Neve*, and T. Gaines*. 2018. The power and potential of genomics in weed biology and management. Pest Management Science. 74: 2216-2225. DOI: 10.1002/ps.5048.

Küpper, A., H. Manmathan, D. Giacomini, E. Patterson, W. McCloskey, and T. Gaines*. 2018. Population genetic structure in glyphosate-resistant and -susceptible Palmer amaranth (Amaranthus palmeri) populations using genotyping-by-sequencing (GBS). Frontiers in Plant Science. 9: 29. DOI: 10.3389/fpls.2018.00029.

Figueiredo, M., L. Leibhart, Z. Reicher, P. Tranel, S. Nissen, P. Westra, M. Bernards, G. Kruger, T. Gaines*, and M. Jugulam*. 2018. Metabolism of 2,4-dichlorophenoxyacetic acid contributes to resistance in a common waterhemp (Amaranthus tuberculatus) population. Pest Management Science. 74: 2356-2362. DOI: 10.1002/ps.4811.

Küpper, A., F. Peter, P. Zöllner, L. Lorentz, P. Tranel, R. Beffa, and T. Gaines*. 2018. Tembotrione detoxification in HPPD-inhibitor resistant Palmer amaranth (Amaranthus palmeri S. Wats.). Pest Management Science. 74: 2325-2334. DOI: 10.1002/ps.4786.

Pettinga, D., J. Ou, E. Patterson, M. Jugulam*, P. Westra, and T. Gaines*. 2018. Increased Chalcone Synthase (CHS) expression is associated with dicamba resistance in Kochia scoparia. Pest Management Science. 74: 2306-2315. DOI: 10.1002/ps.4778.

Patterson, E., D. Pettinga, K. Ravet, P. Neve, and T. Gaines*. 2017. Glyphosate resistance and EPSPS gene duplication: Convergent evolution in multiple plant species. Journal of Heredity. 109: 117-125. DOI: 10.1093/jhered/esx087.

Patterson, E., M. Fleming, K. Kessler, S. Nissen, and T. Gaines*. 2017. A KASP genotyping method to identify northern watermilfoil, Eurasian watermilfoil, and their interspecific hybrids. Frontiers in Plant Science. 8: 752. DOI: 10.3389/fpls.2017.00752.

Gaines, T., A. Barker, E. Patterson, P. Westra, E. Westra, R. Wilson, P. Jha, V. Kumar, and A. Kniss. 2016. EPSPS gene copy number and whole-plant glyphosate resistance level in Kochia scoparia. PLoS One. 11:e0168295. DOI: 10.1371/journal.pone.0168295.

Powles, S. and T. Gaines. 2016. Exploring the potential for a regulatory change to encourage diversity in herbicide use. Weed Science. 64: 649-654. DOI: 10.1614/WS-D-15-00070.1.

Wiersma, A., T. Gaines*, C. Preston, J. Hamilton, D. Giacomini, C.R. Buell, J. Leach, and P. Westra. 2015. Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia. Planta. 241: 463-474. DOI: 10.1007/s00425-014-2197-9.

Gaines, T.*, L. Lorentz, A. Figge, J. Herrmann, F. Maiwald, M. Ott, H. Han, R. Busi, Q. Yu, S. Powles, and R. Beffa. 2014. RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum. The Plant Journal. 78: 865-876. DOI: 10.1111/tpj.12514. ISI Highly Cited Article.

Sammons, R.D. and T. Gaines. Glyphosate resistance: State of knowledge. 2014. Pest Management Science. 70: 1367-1377. DOI: 10.1002/ps.3743. ISI Highly Cited Article.

Gaines, T., W. Zhang, D. Wang, B. Bukun, S. Chisholm, D. Shaner, S. Nissen, W. Patzoldt, P. Tranel, A. Culpepper, T. Grey, T. Webster, W. Vencill, R. Sammons, J. Jiang, C. Preston, J. Leach, and P. Westra. 2010. Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proceedings of the National Academy of Sciences USA. 107:1029-1034. DOI: 10.1073/pnas.0906649107. ISI Highly Cited Article.

CSU Molecular Weed Science Lab

Speaking in Brazil August, 2018

CSU Weed Lab October 2019

CSU Weed Lab UFRRJ Visit March, 2019

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