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Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox

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Abstract

Main conclusion

Presented here is the first Echinochloa colona leaf transcriptome. Analysis of gene expression before and after herbicide treatment reveals that E. colona mounts a stress response upon exposure to herbicide.

Herbicides are the most frequently used means of controlling weeds. For many herbicides, the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. In this study, changes in gene expression in response to herbicide exposure in imazamox-sensitive (S) and- resistant (R) junglerice (Echinochloa colona L.) biotypes was examined. As no reference genome is available for this weed, a reference leaf transcriptome was generated. Messenger RNA was isolated from imazamox-treated- and untreated R and S plants and the resulting cDNA libraries were sequenced on an Illumina HiSeq2000. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both biotypes. Differentially expressed transcripts included transcription factors, protein-modifying enzymes, and enzymes involved in metabolism and signaling. A literature search revealed that members of the families represented in this analysis were known to be involved in abiotic stress response in other plants, suggesting that imazamox exposure induced a stress response. A time course study examining a subset of transcripts showed that expression peaked within 4–12 h and then returned to untreated levels within 48 h of exposure. Testing of plants from two additional biotypes showed a similar change in gene expression 4 h after herbicide exposure compared to the resistant and sensitive biotypes. This study shows that within 48 h junglerice mounts a stress response to imazamox exposure.

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Abbreviations

ALS:

Acetolactate synthase

NIS:

Non-ionic surfactant

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Acknowledgements

Funding provided by BASF for the research is greatly appreciated. The authors appreciate the use of the facilities and equipment at USDA-ARS for this research. The authors would like to thank Dr. Chuan-yu Hsu for assistance in optimizing the RNA extraction protocol and Linda Ballard and Dr. Brian Scheffler for their assistance in submitting the transcriptome.

Author information

Author notes

  1. Alice A. Wright

    Present address: Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA

  2. Rajkumar Sasidharan

    Present address: Solvuu, Inc, New York, NY, 10017, USA

Authors and Affiliations

  1. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA

    Alice A. Wright, Daniel G. Peterson & David R. Shaw

  2. BASF, Research Triangle Park, NC, 27709, USA

    Rajkumar Sasidharan, Liisa Koski & Marianela Rodriguez-Carres

  3. Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, 38776, USA

    Vijay K. Nandula

  4. Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA

    Jeffery D. Ray

  5. Department of Plant and Soil Sciences, Mississippi State University, Stoneville, MS, 38776, USA

    Jason A. Bond

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  1. Alice A. Wright
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Correspondence to Alice A. Wright.

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Wright, A.A., Sasidharan, R., Koski, L. et al. Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox. Planta 247, 369–379 (2018). https://doi.org/10.1007/s00425-017-2784-7

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  • DOI: https://doi.org/10.1007/s00425-017-2784-7

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