Skip to main content Accessibility help

Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of Non–Target-Site Glyphosate Resistance

  • Joshua S. Yuan (a1), Laura L. G. Abercrombie (a2), Yongwei Cao (a3), Matthew D. Halfhill (a2) (a4), Xin Zhou (a1), Yanhui Peng (a2), Jun Hu (a1) (a2), Murali R. Rao (a2), Gregory R. Heck (a3), Thomas J. Larosa (a3), R. Douglas Sammons (a3), Xinwang Wang (a5), Priya Ranjan (a2) (a6), Denita H. Johnson (a5), Phillip A. Wadl (a5), Brian E. Scheffler (a7), Timothy A. Rinehart (a8), Robert N. Trigiano (a5) and C. Neal Stewart (a2)...


The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis.


Corresponding author

Corresponding author's E-mail:


Hide All
Abercrombie, L. G., Anderson, C. M., Baldwin, B. G., et al. 2009. Permanent genetic resources added to Molecular Ecology Resources database 1 January 2009–30 April 2009. Mol. Ecol. Resourc. 9:13751379.
Ahmadian, A., Ehn, M., and Hober, S. 2006. Pyrosequencing: history, biochemistry and future. Clin. Chim. Acta. 363:8394.
Basu, C., Halfhill, M. D., Mueller, T. C., and Stewart, C. N. Jr. 2004. Weed genomics: new tools to understand weed biology. Trends Plant Sci. 9:391398.
Baucom, R. S. and Mauricio, R. 2008. Constraints on the evolution of tolerance to herbicide in the common morning glory: resistance and tolerance are mutually exclusive. Evolution. 62:28422854.
Bradshaw, L. D., Padgette, S. R., Kimball, S. L., and Wells, B. H. 1997. Perspectives on glyphosate resistance. Weed Technol. 11:189198.
Dauer, J. T., Mortensen, D. A., and VanGessel, M. J. 2007. Temporal and spatial dynamics of long-distance Conyza canadensis seed dispersal. J. Appl. Ecol. 44:105114.
Dill, G. M. 2005. Glyphosate-resistant crops: history, status and future. Pest Manag. Sci. 61:219224.
Dill, G. M., Cajacob, C. A., and Padgette, S. R. 2008. Glyphosate-resistant crops: adoption, use and future considerations. Pest Manag. Sci. 64:326331.
Duke, S. O. and Powles, S. B. 2008a. Glyphosate-resistant weeds and crops. Pest Manag. Sci. 64:317318.
Duke, S. O. and Powles, S. B. 2008b. Glyphosate: a once-in-a-century herbicide. Pest Manag. Sci. 64:319325.
Feng, P. C. C. and Chiu, T. 2005. Distribution of C14 glyphosate in mature glyphosate-resistant cotton from application to a single leaf or over-the-top spray. Pestic. Biochem. Physiol. 82:3645.
Feng, P. C. C., Chiu, T., and Sammons, R. D. 2003a. Glyphosate efficacy is contributed by its tissue concentration and sensitivity in velvetleaf (Abutilon theophrasti). Pestic. Biochem. Physiol. 77:8391.
Feng, P. C. C., Chiu, T., Sammons, R. D., and Ryerse, J. S. 2003b. Droplet size affects glyphosate retention, absorption, and translocation in corn. Weed Sci. 51:443448.
Feng, P. C. C., Pratley, J. E., and Bohn, J. A. 1999. Resistance to glyphosate in Lolium rigidum. II. Uptake, translocation, and metabolism. Weed Sci. 47:412415.
Feng, P. C. C., Sandbrink, J. J., and Sammons, R. D. 2000. Retention, uptake, and translocation of C14-glyphosate from track-spray applications and correlation to rainfastness in velvetleaf (Abutilon theophrasti). Weed Technol. 14:127132.
Feng, P. C. C., Tran, M., Chiu, T., Sammons, R. D., Heck, G. R., and Cajacob, C. A. 2004. Investigations into glyphosate-resistant horseweed (Conyza canadensis): retention, uptake, translocation, and metabolism. Weed Sci. 52:498505.
Fischer, A., Lenhard, A., Tronecker, H., et al. 2007. iGentifier: indexing and large-scale profiling of unknown transcriptomes. Nucleic Acids Res. 35:46404648.
Funke, T., Yang, Y., Han, H., Healy-Fried, M., Olesen, S., Becker, A., and Schonbrunn, E. 2009. Structural basis of glyphosate resistance resulting from the double mutation Thr97 → Ile and Pro101 → Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli . J. Biol. Chem. 284:98549860.
Goudet, J. 1995. FSTAT (Version 1.2): a computer program to calculate F-statistics. J. Heredity. 86:485486.
Gressel, J. 2009. Crops with target-site herbicide resistance for Orobanche and Striga control. Pest Manag. Sci. 65:560565.
Gressel, J. and Valverde, B. E. 2009. A strategy to provide long-term control of weedy rice while mitigating herbicide resistance transgene flow, and its potential use for other crops with related weeds. Pest Manag. Sci. 65:723731.
Halfhill, M. D., Good, L. L., Basu, C., Burris, J., Main, C. L., Mueller, T. C., and Stewart, C. N. Jr. 2007. Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (Conyza canadensis) hybrids. Plant Cell Reports. 26:303311.
Heap, I. 2010. International Survery of Herbicide Resistant Weeds. Accessed: February 15, 2010.
Hong, F. X., Breitling, R., McEntee, C. W., Wittner, B. S., Nemhauser, J. L., and Chory, J. 2006. RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics. 22:28252827.
Hu, J., Tranel, P. J., Stewart, C. N. Jr., and Yuan, J. S. 2009. Molecular and genomic mechanisms of non-target site herbicide resistance. Pages 149161. In Stewart, C. N. Jr. Genomics of Weedy and Invasive Plants. Ames, IA Blackwell Scientific.
Ito, K., Oleschuk, C. J., Westlake, C., Vasa, M. Z., Deeley, R. G., and Cole, S. P. C. 2001. Mutation of Trp1254 in the multispecific organic anion transporter, multidrug resistance protein 2 (MRP2) (ABCC2), alters substrate specificity and results in loss of methotrexate transport activity. J. Biol. Chem. 276:38,10138,114.
Kang, B-G., Ye, X., Osburn, L. D., Stewart, C. N. Jr., and Cheng, Z-M. 2010. Transgenic hybrid aspen overexpressing the Atwbc19 gene encoding an ATP binding cassette transporter confers resistance to four aminoglycoside antibiotics. Plant Cell Rep. In press.
Klein, M., Burla, B., and Martinoia, E. 2006. The multidrug resistance-associated protein (MRP/ABCC) subfamily of ATP-binding cassette transporters in plants. FEBS Lett. 580:11121122.
Koger, C. H. and Reddy, K. N. 2005. Role of absorption and translocation in the mechanism of glyphosate resistance in horseweed (Conyza canadensis). Weed Sci. 53:8489.
Langella, O. 2002. Populations, a Free Population Genetics Software.∼olivier-langella/+archive/ppa. Accessed: September 14, 2009.
Lee, H. S., Wang, J., Tian, L., et al. 2004. Sensitivity of 70-Mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnol. J. 2:4557.
Linton, K. J. and Higgins, C. F. 2007. Structure and function of ABC transporters: the ATP switch provides flexible control. Pflügers Arch. Eur. J. Physiol. 453:555567.
Liu, G., Sanchez-Fernandez, R., Li, Z. S., and Rea, P. A. 2001. Enhanced multispecificity of Arabidopsis vacuolar multidrug resistance-associated protein-type ATP-binding cassette transporter, AtMRP2. J. Biol. Chem. 276:86488656.
Ma, J. F. and Yamaji, N. 2008. Functions and transport of silicon in plants. Cell. Mol. Life Sci. 65:30493057.
Main, C. L., Mueller, T. C., Hayes, R. M., and Wilkerson, J. B. 2004. Response of selected horseweed (Conyza canadensis (L.) cronq.) populations to glyphosate. J. Agric. Food Chem. 52:879883.
Mallory-Smith, C. and Zapiola, M. 2008. Gene flow from glyphosate resistant crops. Pest Manag. Sci. 64:428440.
Margulies, M., Egholm, M., Altman, W. E., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437:376380.
Maurel, C., Verdoucq, L., Luu, D. T., and Santoni, V. 2008. Plant aquaporins: membrane channels with multiple integrated functions. Ann. Rev. Plant Biol. 59:595624.
Mentewab, A. and Stewart, C. N. Jr. 2005. Overexpression of an Arabidopsis thaliana ABC transporter confers kanamycin resistance to transgenic plants. Nat. Biotechnol. 23:11771180.
Mueller, T. C., Massey, J. H., Hayes, R. M., Main, C. L., and Stewart, C. N. Jr. 2003. Shikimate accumulates in both glyphosate sensitive and glyphosate resistant horseweed (Conyza canadensis L. Cronq.). J. Agric. Food Chem. 51:680684.
Nei, M. 1972. Genetic distance between populations. Amer. Nat. 106:283.
Owen, M. D. and Zelaya, I. A. 2005. Herbicide resistant crops and weed resistance to herbicides. Pest Manag. Sci. 61:301311.
Özvegy, C., Váradi, A., and Sarkadi, B. 2002. Characterization of drug transport, ATP hydrolysis, and nucleotide trapping by the human ABCG2 multidrug transporter modulation of subtrate specifically by a point of mutation. J. Biol. Chem. 277:47,98047,990.
Page, R. D. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12:357358.
Powles, S. B. 2008. Evolved glyphosate resistant weeds around the world: lessons to be learnt. Pest Manag. Sci. 64:360365.
Preston, C. 2009. Herbicide resistance: target site mutations. Pages 127148. In Stewart, C. N. Jr. Genomics of Weedy and Invasive Plants. Ames, IA Blackwell Scientific.
Preston, C. and Wakelin, A. M. 2008. Resistance to glyphosate from altered herbicide translocation patterns. Pest Manag. Sci. 64:372376.
Rao, M. R., Halfhill, M. D., Abercrombie, L. G., Ranjan, P., Abercrombie, J. M., Gouffon, J. S., Saxton, A. M., and Stewart, C. N. Jr. 2009. Phytoremediation and phytosensing of chemical contaminants, RDX and TNT: identification of the required target genes. Funct. Integr. Genom. 9:537547.
Ryerse, J. S., Downer, R. A., Sammons, R. D., and Feng, P. C. C. 2004. Effect of glyphosate spray droplets on leaf cytology in velvetleaf (Abutilon theophrasti). Weed Sci. 52:302309.
Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406425.
Sammons, R. D., Heering, D. C., Dinicola, N., Glick, H., and Elmore, G. A. 2007. Sustainability and stewardship of glyphosate and glyphosate-resistant crops. Weed Technol. 21:347354.
Sanchez-Fernandez, R., Davies, T. G. E., Coleman, J. O. D., and Rea, P. A. 2001. The Arabidopsis thaliana ABC protein superfamily, a complete inventory. J. Biol. Chem. 276:30,23130,244.
Scheiber, P., Tran, M., and Duncan, D. 2006. Tissue culture and transient transformation of marestail (Conyza canadensis (L.) Cronquist). Plant Cell Rep. 25:507512.
Schulz, B. and Kolukisaglu, H. U. 2006. Genomics of plant ABC transporters: the alphabet of photosynthetic life forms or just holes in membranes? FEBS Lett. 580:10101016.
Shaner, D. 2009. Role of translocation as a mechanism of resistance to glyphosate. Weed Sci. 57:118123.
Shendure, J., Porreca, G. J., Reppas, N. B., et al. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 309:17281732.
Shields, E. J., Dauer, J. T., VanGessel, M. J., and Neuman, G. 2006. Horseweed (Conyza canadensis) seed collected in the planetary boundary layer. Weed Sci. 54:10631067.
Smith, T. F., Gaitatzes, C., Saxena, K., and Neer, E. J. 1999. The WD repeat: a common architecture for diverse functions. Trends Biochem. Sci. 24:181185.
Stewart, C. N. Jr. 2009. Weedy and Invasive Plant Genomics. Ames, IA Wiley-Blackwell. 253.
Stewart, C. N. Jr., Tranel, P. J., Horvath, D. P., Anderson, J. V., Rieseberg, L. H., Westwood, J. H., Mallory-Smith, C. A., Zapiola, M. L., and Dlugosch, K. M. 2009. Evolution of weediness and invasiveness: charting the course for weed genomics. Weed Sci. 57:451462.
VanGessel, M. J. 2001. Glyphosate-resistant horseweed from Delaware. Weed Sci. 49:703705.
Vila-Aiub, M. M., Vidal, R. A., Balbi, M. C., Gundel, P. E., Trucco, F., and Ghersa, C. M. 2008. Glyphosate-resistant weeds of South American cropping systems: an overview. Pest Manag. Sci. 64:366371.
Wakelin, A. M. and Preston, C. 2006. A target-site mutation is present in a glyphosate-resistant Lolium rigidum population. Weed Res. 46:432440.
Williams, G. M., Kroes, R., and Munro, I. C. 2000. Safety evaluation and risk assessment of the herbicide Roundup and its active ingredient, glyphosate, for humans. Regul. Toxicol. Pharmacol. 31:117165.
Yuan, J. S., Galbraith, D. W., Dai, S. Y., Griffin, P., and Stewart, C. N. Jr. 2008. Plant systems biology comes of age. Trends Plant Sci. 13:165171.
Yuan, J. S., Tranel, P. J., and Stewart, C. N. Jr. 2007. Non-target site herbicide resistance: a family business. Trends Plant Sci. 12:613.
Zelaya, I. A., Owen, M. D. K., and VanGessel, M. J. 2004. Inheritance of evolved glyphosate resistance in Conyza canadensis (L.) Cronq. Theor. Appl. Genet. 110 (1):5870.
Zhou, X., Su, Z., Sammons, R. D., Peng, Y., Tranel, P. J., Stewart, C. N. Jr., and Yuan, J. S. 2009. Novel software package for cross-platform transcriptome analysis (CPTRA). BMC Bioinformatics. 10 (Suppl. 11):S16.
Zhu, J., Patzoldt, W. L., Shealy, R. T., Vodkin, L. O., Clough, S. J., and Tranel, P. J. 2008. Transcriptome response to glyphosate in sensitive and resistant soybean. J. Agric. Food Chem. 56:63556363.


Related content

Powered by UNSILO
Type Description Title
Supplementary materials

Yuan et al. supplementary material
Supplementary Material

 Unknown (2.4 MB)
2.4 MB

Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of Non–Target-Site Glyphosate Resistance

  • Joshua S. Yuan (a1), Laura L. G. Abercrombie (a2), Yongwei Cao (a3), Matthew D. Halfhill (a2) (a4), Xin Zhou (a1), Yanhui Peng (a2), Jun Hu (a1) (a2), Murali R. Rao (a2), Gregory R. Heck (a3), Thomas J. Larosa (a3), R. Douglas Sammons (a3), Xinwang Wang (a5), Priya Ranjan (a2) (a6), Denita H. Johnson (a5), Phillip A. Wadl (a5), Brian E. Scheffler (a7), Timothy A. Rinehart (a8), Robert N. Trigiano (a5) and C. Neal Stewart (a2)...


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed.