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Title: Herbicide injury induces dose-dependent DNA methylome alterations in Arabidopsis

item KIM, GUNJUNE - Virginia Tech
item Clarke, Christopher
item LAROSE, HAILEY - Virginia Tech
item ZHANG, LIQING - Virginia Tech
item HAAK, DAVID - Virginia Tech
item ASKEW, SHAWN - Virginia Tech
item BARNEY, JACOB - Virginia Tech
item WESTWOOD, JAMES - Virginia Tech

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/19/2017
Publication Date: 7/20/2017
Publication URL:
Citation: Kim, G., Clarke, C.R., Larose, H., Zhang, L., Haak, D.C., Askew, S., Barney, J., Westwood, J.H. 2017. Herbicide injury induces dose-dependent DNA methylome alterations in Arabidopsis. PeerJ.

Interpretive Summary: Every year, more weeds develop resistance to the herbicide glyphosate, the most used herbicide in the history of agriculture. This emergence of herbicide resistance in weedy populations reduces the efficacy of glyphosate treatment, and has led to substantially lower earnings for growers. Currently, it is a mystery how weedy populations develop herbicide resistance so rapidly. We investigated whether changes in the structure of packaged DNA, known as epigenetics, have the potential to contribute to the development of herbicide resistance after sustained herbicide use. Genome sequencing coupled with measurements of DNA modifications revealed that plants undergo substantial epigenetic changes following glyphosate treatment. In general, the epigenetic changes were both dependent on dose and stress-specific. Taken together, these results support the hypothesis that epigenetic changes can contribute to the increase in resistance to herbicide treatment. This discovery and the publicly available data developed in the course of this work will be utilized by numerous other researchers who study plant stress. Additionally, this work justifies performing long-term research projects on the specific role of epigenetics in the development of herbicide resistance. This research may ultimately impact strategies for herbicide usage to improve the effective lifespan of agronomically valuable herbicides.

Technical Abstract: The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic changes, such as alterations in DNA methylation, are potential additional adaptive mechanisms for herbicide resistance. We performed methylC sequencing of Arabidopsis thaliana leaves that developed after either mock treatment or two different sub-lethal doses of the herbicide glyphosate, the most used herbicide in the history of agriculture. The herbicide injury resulted in 9205 differentially methylated regions (DMRs) across the genome. 5914 of these DMRs were induced in a dose-dependent manner, wherein the methylation levels were positively correlated to the severity of the herbicide injury, suggesting that plants can modulate the magnitude of methylation changes based on the severity of the stress. Of the 3680 genes associated with glyphosate-induced DMRs, only 7% were also implicated in methylation changes following biotic or salinity stress. These results demonstrate that plants respond to herbicide stressthrough changes in methylation patterns that are, in general, dose-sensitive and, at least partially, stress-specific.