Plant Molecular Biology

, Volume 87, Issue 4–5, pp 473–487 | Cite as

RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance

  • Arnaud Duhoux
  • Sébastien Carrère
  • Jérôme Gouzy
  • Ludovic Bonin
  • Christophe Délye


Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a polygenic adaptive trait driven by differential gene regulation in resistant plants. Little is known about its genetic determinism, which precludes NTSR diagnosis and evolutionary studies. We used Illumina RNA-sequencing to investigate transcriptomic differences between plants from the global major weed rye-grass sensitive or resistant to the acetolactate-synthase (ALS) inhibiting herbicide pyroxsulam. Plants were collected before and along a time-course after herbicide application. De novo transcriptome assembly yielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that were assigned putative annotations. Early effects of ALS inhibition consistent with the literature were observed in resistant and sensitive plants, proving LOLbase data were relevant to study herbicide response. Comparison of resistant and sensitive plants identified 30 candidate NTSR contigs. Further validation using 212 plants resistant or sensitive to pyroxsulam and/or to the ALS inhibitors iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase and one glutathione-S-transferase) were NTSR markers which combined expression levels could reliably identify resistant plants. This work confirmed that NTSR is driven by differential gene expression and involves different mechanisms. It provided tools and foundation for subsequent NTSR investigations.


RNA-Seq Herbicide Non-target-site resistance Transcriptomics Lolium Acetolactate synthase 



We thank Dr Valérie Le Corre (INRA Dijon, France) for assistance in statistical analyses, and Genotoul—Génopôle Toulouse Midi-Pyrénées for allowing access to computational facilities.

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Arnaud Duhoux
    • 1
  • Sébastien Carrère
    • 2
  • Jérôme Gouzy
    • 2
  • Ludovic Bonin
    • 3
  • Christophe Délye
    • 1
  1. 1.UMR1347 AgroécologieINRADijonFrance
  2. 2.UMR441 LIPMINRACastanet-TolosanFrance
  3. 3.Arvalis – Institut du VégétalParisFrance

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