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

Abstract

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.

Evaluation of resistance to acetolactate synthase inhibiting herbicide in wild mustard (Sinapis arvensis L.)

“…3c). The results obtained demonstrate that ALS-based mutation (Asp-376-Glu) confers resistance in S. arvensis sub-populations (FHR2 and FHR3) and are in line with the results reported in the literature (Whaley et al, 2007;Zhang et al, 2011;Duhoux et al, 2015). Evolved ALS target-site resistance is most common in six positions , although other target positions have been reported in rare cases (McCourt et al, 2006).…”

“…Moreover, based on LD50 homozygous Raphanus raphanistrum for Asp-376-Glu were highly resistant to sulfonylurea herbicide chlorsulfuron (Duhoux et al, 2015). In addition, some studies emphasis that the homozygous Asp-376-Glu resistant plants treated with ALS herbicides are weaker than 122-Tyr, 197-Ser and 574-Leu in different resistant weeds (Warwick et al, 2005;Whaley et al, 2007;Ashigh et al, 2009;Duhoux et al, 2015).…”

“…In addition, some studies emphasis that the homozygous Asp-376-Glu resistant plants treated with ALS herbicides are weaker than 122-Tyr, 197-Ser and 574-Leu in different resistant weeds (Warwick et al, 2005;Whaley et al, 2007;Ashigh et al, 2009;Duhoux et al, 2015). Unfortunately, the mechanism of this pathway in ALS homozygous Glu-376 is not clear (Duhoux et al, 2015). Therefore, as stated above, homo/heterozygous Asp-376-Glu mutation in two resistant sub-populations (FHR2 and FHR3) represents a complex situation for resistance to mesosulfuron + iodosulfuron or even other sulfonylurea herbicides.…”

Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

“…Brassinosteroids (Zhou et al, 2015) and salicylate (Cui et al, 2010) directly regulate genes that are related to herbicide detoxification, and activation of auxin signaling (Kerchev et al, 2015) counteracts the cell death effects of photorespiration, which is involved in the responses to several herbicides (Serra et al, , 2015a(Serra et al, , 2015bVivancos et al, 2011). Analysis of transcriptomic, proteomic or metabolomic modifications also shows that herbicide treatments have major impacts on genes and proteins involved in stress and nutrition signaling pathways: ROS signaling, membrane stress signaling, photosystem and light stress signaling, endoplasmic reticulum stress signaling, drought and salinity signaling, nutritional starvation signaling, and cell death signaling (Duhoux et al, 2015;Faus et al, 2015;Gaines et al, 2014;Goossens et al, 2001;Horn et al, 2013;Li et al, 2015;Ozgur et al, 2014;Ramel et al, 2007Ramel et al, , 2009aSerra et al, 2013Serra et al, , 2015aSerra et al, , 2015bWalley et al, 2015;.…”

RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

“…It can top score unique RNA existence and quantity from novel genomes of ferns, mosses, algae, weeds and other hardy plants adapted to stress at a precise point of development and physiological stage. Analysis of genome-wide differential RNA expression provides canvassers with greater insights into biological pathways and molecular mechanisms that regulate cell fate, development, and changes during and due to abiotic stresses (Duhoux et al 2015). For mRNA analysis, the 3′ polyadenylated (poly(A) tail is hybridized with poly (T) oligos that are linked to magnetic beads.…”