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Past Publications


Busi, R., A. Porri, T. Gaines, and S. Powles. 2018. Pyroxasulfone resistance in Lolium rigidum is metabolism-based. Pesticide Biochemistry and Physiology, in press.

Oliveira, M., T. Gaines, A. Jhala, and S. Knezevic. 2017. Inheritance of mesotrione resistance in an Amaranthus tuberculatus (var. rudis) population from Nebraska, USA. Frontiers in Plant Science, in press.

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, in press.

Pan, Z., Baerson, S. R., Wang, M., Bajsa‐Hirschel, J., Rimando, A. M., Wang, X., Nanayakkara, N. P. D., Noonan, B. P., Fromm, M. E., Dayan, F. E., Khan, I. A., and Duke, S. O. (2018). A cytochrome P450 CYP71 enzyme expressed in Sorghum bicolor root hair cells participates in the biosynthesis of the benzoquinone allelochemical sorgoleone. New Phytologist 218:616-629.


Beckie, H., R. Blackshaw, J. Leeson, P. Stahlman, T. Gaines, and E. Johnson. 2017. Seed bank persistence, germination and early growth of glyphosate-resistant Kochia scoparia. Weed Research, in press. DOI: 10.1111/wre.12294

Giacomini, D., T. Gaines, R. Beffa, and P. Tranel. 2017. Optimizing RNA-seq studies to investigate herbicide resistance. Pest Management Science, in press. DOI: 10.1002/ps.4822.

Figueiredo, M., L. Leibhart, Z. Reicher, P. Tranel, S. Nissen, P. Westra, M. Bernards, G. Kruger, T. Gaines*, and M. Jugulam*. 2017. Metabolism of 2,4-dichlorophenoxyacetic acid contributes to resistance in a common waterhemp (Amaranthus tuberculatus) population. Pest Management Science, in press. DOI: 10.1002/ps.4811.

Chahal, P., S. Irmak, T. Gaines, K. Amundsen, M. Jugulam, P. Jha, I. Travlos, and A. Jhala. 2017. Control of photosystem (PS) II- and 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor-resistant Palmer amaranth (Amaranthus palmeri S. Wats.) in conventional corn. Weed Technology, in press.

Fernández-Escalada, M., A. Zulet-González, M. Gil-Monreal, A. Zabalza, K. Ravet, T. Gaines, and M. Royuela. 2017. Effects of EPSPS copy number variation (CNV) and glyphosate application on the aromatic and branched chain amino acid synthesis pathways in Amaranthus palmeri. Frontiers in Plant Science. 8: 1970. DOI: 10.3389/fpls.2017.01970.

Küpper, A., F. Peter, P. Zöllner, L. Lorentz, P. Tranel, R. Beffa, and T. Gaines*. 2017. Tembotrione detoxification in HPPD-inhibitor resistant Palmer amaranth (Amaranthus palmeri S. Wats.). Pest Management Science, in press. DOI: 10.1002/ps.4786.

Pettinga, D., J. Ou, E. Patterson, M. Jugulam*, P. Westra, and T. Gaines*. 2017. Increased Chalcone Synthase (CHS) expression is associated with dicamba resistance in Kochia scoparia. Pest Management Science, in press. DOI: 10.1002/ps.4778.

Vieira, B., S. Samuelson, G. Alves, T. Gaines, R. Werle, and G. Kruger. 2017. Distribution of glyphosate-resistant Amaranthus spp. in Nebraska. Pest Management Science, in press. DOI: 10.1002/ps.4781.

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, in press. DOI: 10.1093/jhered/esx087. In themed collection, ‘Genomics of Adaptation to Human Contexts.’

Oliveira, M., T. Gaines, F. Dayan, E. Patterson, A. Jhala, and S. Knezevic. 2017. Reversing resistance to tembotrione in an Amaranthus tuberculatus (var. rudis) population from Nebraska, USA with cytochrome P450 inhibitors. Pest Management Science (in press). DOI: 10.1002/ps.4697.

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.

Moretti, M., Van Horn, C., R. Robertson, K. Segobye, S. Weller, B. Young, W. Johnson, R.D. Sammons, D. Wang, X. Ge, A. d’Avignon, T. Gaines, P. Westra, A. Green, T. Jeffery, M. Lesperance, F. Tardif, P. Sikkema, J.C. Hall, M. McLean, M. Lawton, and B. Schulz. 2017. Glyphosate resistance in Ambrosia trifida: Part 2. Rapid response physiology and non-target site resistance. Pest Management Science (in press). DOI: 10.1002/ps.4569.

Van Horn, C., M. Moretti, R. Robertson, S. Weller, B. Young, W. Johnson, B. Schulz, P. Westra, A. Green, T. Jeffery, M. Lesperance, F. Tardif, P. Sikkema, J.C. Hall, M. McLean, M. Lawton, R.D. Sammons, and T. Gaines. 2017. Glyphosate resistance in Ambrosia trifida: Part 1. Novel rapid cell death response to glyphosate. Pest Management Science (in press). DOI: 10.1002/ps.4567.

Sarangi, D., A. Tyre, E. Patterson, T. Gaines, S. Irmak, S. Knezevic, J. Lindquist, and A. Jhala. 2017. Pollen-mediated gene flow from glyphosate-resistant common waterhemp (Amaranthus rudis Sauer): consequences for dispersal of resistance genes. Scientific Reports. 7: 44913. DOI: 10.1038/srep44913.

Küpper, A., E. Borgato, E. Patterson, A. Netto, M. Nicolai, S.J.P. Carvalho, S. NissenT. Gaines, and P. Christoffoleti. 2017. Multiple resistance to glyphosate and ALS inhibitors in Palmer amaranth (Amaranthus palmeri) identified in Brazil. Weed Science. 65: 317:326. DOI: 10.1017/wsc.2017.1.

Oliveira, M., A. Jhala, T. Gaines, S. Irmak, K. Amundsen, and S. Knezevic. 2017. Confirmation and control of 4-hydroxyphenylpyruvate dioxygenase inhibitor-resistant common waterhemp (Amaranthus rudis) in Nebraska. Weed Technology. 31: 67-79. DOI: 10.1017/wet.2016.4.

Busi, R., T. Gaines, and S. Powles. 2017. Phorate can reverse P450 metabolism-based herbicide resistance in Lolium rigidum. Pest Management Science. 73: 410-417. DOI: 10.1002/ps.4441.

Chen, X., Berim, A., Dayan, F. E., Gang, D. R. 2017. A (–)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia divinorum. Journal of Experimental Botany 68:1109-1122

Głąb, L., Sowiński, J., Bough, R. and Dayan, F. E. 2017. Allelopathic potential of Sorghum bicolor (L.) Moench in weed control: A comprehensive review. Advances in Agronomy, 145:43-95.

Chen, X., Berim, A., Dayan. F. E., Gang, D. R. 2017. A (-)-Kolavenyl diphosphate synthase catalyzes the first committed step of salvinorin A biosynthesis in Salvia divinorum. Journal of Experimental Botany, 68:1109-1122.

Romdhane, S., Devers-Lamrani, M., Martin-Laurent, F., Ben Jrad, A., Raviglione, D., Salvia, M. V., Besse-Hoggan, P., Dayan, F. E., Bertrand, C., and Barthelmebs, L. 2017. Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide. Environmental Science and Pollution Research. Available online.

Dayan, F.E., Barker, A. and Tranel, P.J., 2017. Origins and Structure of Chloroplastic and Mitochondrial Plant Protoporphyrinogen Oxidases: Implications for Evolution of Herbicide Resistance. Pest Management Science. Available online

Moraes, R. M., Cerdeira, A. L., Duke, S. O., Dayan, F. E., Cantrell, C. L., Queiroz, S. C. N. (2016) Pesticidas naturais Derivados de plantas: Descoberta e usos. In: de Almeida Halfeld-Vieira B, Marinho-Prado JS, de Lima Nechet K, Morandi MAB, Bettiol W (eds) Defensivos Agrícolas Naturais: Uso e Perspectivas. Embrapa, Brasília, DF, Brazil, pp 505-541


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.

^Li, Z., K. Kessler, M. Figueiredo, S. NissenT. Gaines, P. Westra, R. Van Acker, J.C. Hall, D. Robinson, N. Soltani, and P. Sikkema. 2016. Halosulfuron absorption, translocation, and metabolism in white and adzuki bean. Weed Science. 64: 705-711. DOI: 10.1614/WS-d-16-00029.1.

^Brunharo, C., E. Patterson, D. Carrijo, M. Melo, M. Nicolai, T. Gaines, S. Nissen, and P. Christoffoleti. 2016. Confirmation and mechanism of glyphosate resistance in Tall windmill grass (Chloris elata) from Brazil. Pest Management Science. 72: 1758-1764. DOI: 10.1002/ps.4205.

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.

Killeen, D. P., Larsen, L., Dayan, F. E., Gordon, K. C., Perry, N. B. and van Klink, J. W. 2016. Nortriketones: Antimicrobial trimethylated acylphloroglucinols from mānuka (Leptospermum scoparium). Journal of Natural Products, in press.

Carbonari, C., Latorre, D. O., Gomes, G. L. G. C., Velini, E. D., Owens, D. K., Pan, Z., and Dayan, F. E. 2016. Resistance to glufosinate is proportional to phosphinothricin acetyltransferase expression and activity in LibertyLink® and WideStrike® Cotton, Planta, in press.

Dayan, F. E. and Duke, S. O. 2016. Discovery of New Herbicide Modes of Action with Natural Phytotoxins. American Chemical Society Symposium Series 1204, 79-92

Duke, S. O. and Dayan, F. E. 2015. Natural toxins that affect plant amino acid metabolism, in Amino Acids in Higher Plants. Edited by D’Mello F. CAB International, Wallingford, UK, pp 448-460.

Duke, S.O., Scheffler, B. E., Boyette, C. D. and Dayan, F. E. 2016. Biotechnology in weed control. Kirk-Othmer Encyclopedia of Chemical Technology, John Wiley & Sons, Inc., New York, in press, accepted Feb.


Christoffoleti, P., M. Figueiredo, L. Peres, S. Nissen, and T. Gaines. 2015. Auxinic herbicides, mechanisms of action, and weed resistance: A look into recent plant science advances. Scientia Agricola. 72: 356-362. DOI: 10.1590/0103-9016-2014-0360

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.

Dayan, F. E., Owens, D. K., Corniani, N., Silva, F. M. L., Watson, S. B., Howell, J. and Shaner, D. L. 2015. Biochemical markers and enzyme assays for herbicide mode of action and resistance studies. Weed Science. 63, 23-63.

Ribeiro, D. N., Nandula, V. K., Dayan, F. E., Rimando, A. M., Duke, S. O., Reddy, K. N., and Shaw. D. R. 2015. Possible glyphosate resistance mechanisms in pitted morningglory (Ipomoea lacunosa L.), Journal of Agricultural and Food Chemistry, 63:23-63.

Dayan, F. E., Owens, D. K., Watson, S. B., Asolkar, R. N. and Boddy, L. G. 2015. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action, Frontiers in Plant Science, 6. doi: 10.3389/fpls.2015.00222.

Salas, R. A., Scott, R. C., Dayan, F. E., and Burgos, N. R. 2015. EPSPS gene amplification in glyphosate-resistant in Italian ryegrass (Lolium perenne ssp. multiflorum) populations from Arkansas, United States. Journal of Agricultural and Food Chemistry, 63: 5885-5893.

Silva, F. M. L., Duke, S. O., Dayan, F. E. and Velini, E. D. 2015. Low doses of glyphosate change the response of soybean to subsequent glyphosate treatments. Weed Technology, in press.

Duke, S. O., Owens, D. K., and Dayan, F. E. 2015. The growing need for biochemical bioherbicides. In AD Gross, JR Coats, SO Duke, JN Seiber, eds, Biopesticides: State of the Art and Future Opportunities, Vol 1172. American Chemical Society, pp 31-43.

Trivella, A., Stawingoga, M., Dayan, F. E., Cantrell, C. L., Mazellier, P., Richard, C. 2015. Photolysis of natural β-triketonic herbicides in water. Water Research, 78:28–36.

Maroli, A. S., Nandula, V. K., Dayan, F. E., Duke, S. O., Gerard, P., Tharayil, N. 2015. Metabolic profiling and enzyme analyses indicate a potential role of antioxidant systems in complementing glyphosate resistance in an Amaranthus palmeri biotype. Journal of Agricultural and Food Chemistry, 63:9199-9209.

2014 and prior

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. 2.

Sammons, R.D. and T. Gaines. Glyphosate resistance: State of knowledge. 2014. Pest Management Science. Early View article online, DOI: 10.1002/ps.3743.

Vila-Aiub, M., T. Gaines, S. Goh, H. Han, R. Busi, Q. Yu, and S. Powles. 2014. No fitness cost of glyphosate resistance endowed by massive EPSPS gene amplification in Amaranthus palmeri. Planta 239:793-801.

Busi, R., T. Gaines, M. Vila-Aiub, and S. Powles. 2014. Inheritance of evolved resistance to a novel herbicide (pyroxasulfone). Plant Science 217-218: 127-134.

Ribeiro, N. D., Pan, Z., Duke, S. O., Nandula, V. K., Baldwin, B. S., Shaw, D. and Dayan, F. E. 2014. Involvement of facultative apomixis in inheritance of EPSPS gene amplification in glyphosate-resistant Amaranthus palmeri. Planta, 239:199-212.

Dayan, F. E., Owens, D. K., Tranel, P. J., Preston, C. and Duke, S. O. 2014. Evolution of resistance to phytoene desaturase and protoporphyrinogen oxidase inhibitors – State of knowledge. Pest Management Science, 70: 1358-1366.

Silva, F. M. L., Donega , M. A., Cerdeira, A. L., Corniani, N., Velini, E. D., Cantrell, C. L., Dayan, F. E., Coelho, M. N., Shea, K., Duke, S. O. 2014. Roots of the invasive species Carduus nutans L. and C. acanthoides L. produce large amounts of aplotaxene, a possible allelochemical. Journal of Chemical Ecology, 40:276-284.

Dayan, F. E. and Duke, S. O. 2014. Natural compounds as next generation herbicides. Plant Physiology, 166:1090-1105.

Rocaboy-Faquet, E., Noguer, T., Romdhane, S., Bertrand, C., Dayan, F. E., Barthelmebs, L. 2014. Novel bacterial bioassay for a high throughput screening of 4-hydroxyphenylpyruvate dioxygenase inhibitors. Applied Microbiology and Biotechnology, 98:7243-7252.

Corniani, N., Velini, E. D., Silva, F. M. L., Nanayakkara, N. P. D., Witschel, M. and Dayan, F. E. 2014. Novel bioassay for the discovery of inhibitors of the 2-C-Methyl-d-erythritol 4-phosphate (MEP) and terpenoid pathways leading to carotenoid biosynthesis. PLoS ONE 9: e103704.

Garcia, A., Alarcon-Reverte, R., Watson, S. B., Abdallah, I., Dayan, F. E., Fischer, A. 2014. Concerted action of target-site mutations and high EPSPS activity in glyphosate-resistant junglerice (Echinochloa colona) from California. Pest Management Science, 71: 996-1007.

Busi, R., M. Vila-Aiub, H. Beckie, T. Gaines, D. Goggin, S. Kaundun, M. Lacoste, P. Neve, S. Nissen, J. Norsworthy, M. Renton, D. Shaner, P. Tranel, T. Wright, Q. Yu, and S. Powles. 2013. Herbicide resistant weeds: from research and knowledge to future needs. Evolutionary Applications 6:1218-1221.

Gaines, T., A. Wright, W. Molin, L. Lorentz, C. Riggins, P. Tranel, R. Beffa, P. Westra, and S. Powles. 2013. Identification of genetic elements associated with EPSPS gene amplification. PLoS ONE 8(6): e65819. doi:10.1371/journal.pone.0065819

Dayan, F. E. and Dayan E. A. 2013. Les porphyrines: Les couleurs de la vie. Pour La Science, 423: 66-72. (French adaptation of publication #86).

Owens, D. K., Nanayakkara, N. P. D. and Dayan, F. E. 2013. In planta mechanism of action of leptospermone: Impact of its physico-chemical properties on uptake, translocation, and metabolism. Journal of Chemical Ecology. 39: 262-270.

Uddin, M. R., Park, S. U., Dayan, F. E. and Pyon, J. Y. 2013. Herbicidal activity of formulated sorgoleone, a natural product of sorghum root exudate. Pesticide Management Science, 70:252-257.

Yang, S.-G., Hao, G.-F., Dayan, F. E., Tranel, P. J., and Yang, G.-F. 2013. Insight into the structural requirements of protoporphyrinogen oxidase inhibitors: Molecular modeling and CoMFA of diphenyl ether, isoxazole phenyl, and pyrazole phenyl ether. Chinese Journal of Chemistry, 31:1153-1158. This manuscript has been selected as a cover paper by this journal.

Busi, R., T. Gaines, M. Walsh, and S. Powles. 2012. Understanding the potential for resistance evolution to the new herbicide pyroxasulfone: field screening at high doses versus recurrent selection at low doses. Weed Research 52:489-499.

Gaines, T., A. Cripps, and S. Powles. 2012. Evolved resistance to glyphosate in junglerice (Echinochloa colona) from the tropical Ord River region in Australia. Weed Technology 26:480-484.

Gaines, T., S. Ward, B. Bukun, C. Preston, J. Leach, and P. Westra. 2012. Interspecific hybridization transfers a previously unknown glyphosate resistance mechanism in Amaranthus species. Evolutionary Applications 5:29-38.

Rimando, A. M., Pan, Z., Polashock, J., Dayan, F. E., Mizuno, C., Snook, M. E., Liu, C.-J., and Baerson, S. R. 2012. In planta production of the highly potent resveratrol analogue pterostilbene via stilbene synthase and O-methyltransferase co-expression. Plant Biotechnology Journal, 10, 269-283.

Dayan, F. E., Owens, D. K. and Duke, S. O. 2012. Rationale for a natural products approach to herbicide discovery. Pest Management Science, 68, 519-528.

Salas, R. A., Dayan, F. E., Pan, Z., Watson, S., Dickson, J., Scott, R. C., and Burgos, N.  2012. EPSPS gene amplification in glyphosate-resistant Italian ryegrass (Lolium perenne ssp multiflorum) from Arkansas, USA.  Pest Management Science, 68, 1223-1230.

Wang, R.-L., Staehelin, C., Dayan, F. E., Song, Y.-Y.,  Hu, L., Su, Y.-J., Zeng, R.-S.  Simulated acid rain accelerates litter decomposition and enhances the allelopathic potential of the invasive plant Wedelia trilobata (creeping daisy), Weed Science, 60, 462–467. 2012.

Cerdeira, A. L., Cantrell, C. L., Dayan, F. E., Byrd, J. D., and Duke, S. O. 2012. Tabanone, a new phytotoxic constituent of cogongrass (Imperata cylindrica).  Weed Science, 60, 212-218.

Dayan, F. E. and Zaccaro, M. L. 2012. Chlorophyll fluorescence as a marker for herbicide mechanisms of action.  Pesticide Biochemistry and Physiology, 102, 189–197.

Cantrell, C. L., Dayan, F. E. and Duke, S. O. 2012. Natural products as sources for new pesticides. Journal of Natural Products, 75, 1231-1242.

Dayan, F. E. and Dayan E. A. 2012. Ein ring fur die farben des lebens. Spektrum der Wissenschaft 6/12: 30-38. (German adaptation of publication #86).

Sumyanto, J., Dayan, F. E., Cerdeira, A. L.,Wang, Y.-H., Khan, I. A., and Moraes, R. M. 2012. Oligofructans content and yield of yacon (Smallanthus sonchifolius) cultivated in Mississippi.  Scientia Horticulturae, 148: 83-88.

Gaines, T., D. Shaner, S. Ward, J. Leach, C. Preston, and P. Westra. 2011. Mechanism of resistance of evolved glyphosate-resistant Palmer amaranth (Amaranthus palmeri). Journal of Agricultural and Food Chemistry 59:5886-5889.

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.

Bukun, B., T. Gaines, S. Nissen, P. Westra, G. Brunk, D. Shaner, B. Sleugh, and V. Peterson. 2009. Aminopyralid and clopyralid absorption and translocation in Canada thistle (Cirsium arvense). Weed Science 57:10-15.

Gaines, T., W. Henry, P. Byrne, P. Westra, S. Nissen, and D. Shaner. 2008. Jointed goatgrass (Aegilops cylindrica) by imidazolinone-resistant wheat hybridization under field conditions. Weed Science 56:32-36.

Westra, P., R. Wilson, S. Miller, P. Stahlman, G. Wicks, P. Chapman, J. Withrow, D. Legg, C. Alford, and T. Gaines. 2008. Weed population dynamics after six years under glyphosate and conventional herbicide-based weed control strategies. Crop Science 48:1170-1177.

Gaines, T., P. Byrne, P. Westra, S. Nissen, W. Henry, D. Shaner, and P. Chapman. 2007. An empirically derived model of field-scale gene flow in winter wheat. Crop Science 47:2308-2316.

Gaines, T., C. Preston, W. Henry, P. Byrne, and P. Westra. 2007. Adventitious presence of herbicide resistant wheat in certified and farm-saved seed lots. Crop Science 47:751-754.

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