Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance

Joshua S. Yuan; Laura L.G. Abercrombie; Yongwei Cao; Matthew D. Halfhill; Xin Zhou; Yanhui Peng; Jun Hu; Murali R. Rao; Gregory R. Heck; Thomas J. Larosa; R. Douglas Sammons; Xinwang Wang; Priya Ranjan; Denita H. Johnson; Phillip A. Wadl; Brian E. Scheffler; Timothy A. Rinehart; Robert N. Trigiano; C. Neal Stewart

doi:10.1614/WS-D-09-00037.1

Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance

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

Computational and Predictive Biology

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59 Scopus citations

Abstract

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 nontarget-site resistance candidate genes for follow-on functional genomics analysis.

Original language	English
Pages (from-to)	109-117
Number of pages	9
Journal	Weed Science
Volume	58
Issue number	2
DOIs	https://doi.org/10.1614/WS-D-09-00037.1
State	Published - Apr 2010

Keywords

Bioinformatics
Herbicide resistance
Phylogeography
Systems biology
Transcriptomics

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10.1614/WS-D-09-00037.1

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Yuan, J. S., Abercrombie, L. L. G., Cao, Y., Halfhill, M. D., Zhou, X., Peng, Y., Hu, J., Rao, M. R., Heck, G. R., Larosa, T. J., Sammons, R. D., Wang, X., Ranjan, P., Johnson, D. H., Wadl, P. A., Scheffler, B. E., Rinehart, T. A., Trigiano, R. N., & Stewart, C. N. (2010). Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance. Weed Science, 58(2), 109-117. https://doi.org/10.1614/WS-D-09-00037.1

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title = "Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance",

abstract = "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 nontarget-site resistance candidate genes for follow-on functional genomics analysis.",

keywords = "Bioinformatics, Herbicide resistance, Phylogeography, Systems biology, Transcriptomics",

author = "Yuan, {Joshua S.} and Abercrombie, {Laura L.G.} and Yongwei Cao and Halfhill, {Matthew D.} and Xin Zhou and Yanhui Peng and Jun Hu and Rao, {Murali R.} and Heck, {Gregory R.} and Larosa, {Thomas J.} and Sammons, {R. Douglas} and Xinwang Wang and Priya Ranjan and Johnson, {Denita H.} and Wadl, {Phillip A.} and Scheffler, {Brian E.} and Rinehart, {Timothy A.} and Trigiano, {Robert N.} and Stewart, {C. Neal}",

year = "2010",

month = apr,

doi = "10.1614/WS-D-09-00037.1",

language = "English",

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Yuan, JS, Abercrombie, LLG, Cao, Y, Halfhill, MD, Zhou, X, Peng, Y, Hu, J, Rao, MR, Heck, GR, Larosa, TJ, Sammons, RD, Wang, X, Ranjan, P, Johnson, DH, Wadl, PA, Scheffler, BE, Rinehart, TA, Trigiano, RN & Stewart, CN 2010, 'Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance', Weed Science, vol. 58, no. 2, pp. 109-117. https://doi.org/10.1614/WS-D-09-00037.1

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AU - Abercrombie, Laura L.G.

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AU - Halfhill, Matthew D.

AU - Zhou, Xin

AU - Peng, Yanhui

AU - Hu, Jun

AU - Rao, Murali R.

AU - Heck, Gregory R.

AU - Larosa, Thomas J.

AU - Sammons, R. Douglas

AU - Wang, Xinwang

AU - Ranjan, Priya

AU - Johnson, Denita H.

AU - Wadl, Phillip A.

AU - Scheffler, Brian E.

AU - Rinehart, Timothy A.

AU - Trigiano, Robert N.

AU - Stewart, C. Neal

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AB - 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 nontarget-site resistance candidate genes for follow-on functional genomics analysis.

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ER -

Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance

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Keywords

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