Délye C, Gardin JAC, Boucansaud K, Chauvel B & Petit C (2011). Non‐target‐site‐based resistance should be the centre of attention for herbicide resistance research: Alopecurus myosuroides as an illustration. Weed Research51, 433–437. Summary Non‐target‐site‐based resistance (NTSR) mechanisms can confer unpredictable resistance to herbicides with different chemistries or modes of action. In two French fields, 18% and 40% individual plants of Alopecurus myosuroides (black‐grass), respectively, were resistant via NTSR to all the most effective herbicides approved for A. myosuroides control in wheat (fenoxaprop, clodinafop, pinoxaden, iodosulfuron+mesosulfuron and pyroxsulam) and to the broad‐leaf‐selective herbicide quizalofop. Pinoxaden and pyroxsulam had never been applied to these populations. In the absence of new herbicide modes of action, this renders a purely chemical control of A. myosuroides in winter cereals much more complex in these fields. A segregation analysis showed that multi‐resistant phenotypes were endowed by multiple NTSR genes, underlining the complexity of NTSR. Yet, despite the threat posed to weed control, our lack of knowledge on NTSR is obvious. NTSR should therefore become the priority in herbicide resistance research.

BackgroundHerbicide resistance in agrestal weeds is a global problem threatening food security. Non-target-site resistance (NTSR) endowed by mechanisms neutralising the herbicide or compensating for its action is considered the most agronomically noxious type of resistance. Contrary to target-site resistance, NTSR mechanisms are far from being fully elucidated. A part of weed response to herbicide stress, NTSR is considered to be largely driven by gene regulation. Our purpose was to establish a transcriptome resource allowing investigation of the transcriptomic bases of NTSR in the major grass weed Alopecurus myosuroides L. (Poaceae) for which almost no genomic or transcriptomic data was available.ResultsRNA-Seq was performed from plants in one F2 population that were sensitive or expressing NTSR to herbicides inhibiting acetolactate-synthase. Cloned plants were sampled over seven time-points ranging from before until 73 h after herbicide application. Assembly of over 159M high-quality Illumina reads generated a transcriptomic resource (ALOMYbase) containing 65,558 potentially active contigs (N50 = 1240 nucleotides) predicted to encode 32,138 peptides with 74 % GO annotation, of which 2017 were assigned to protein families presumably involved in NTSR. Comparison with the fully sequenced grass genomes indicated good coverage and correct representation of A. myosuroides transcriptome in ALOMYbase. The part of the herbicide transcriptomic response common to the resistant and the sensitive plants was consistent with the expected effects of acetolactate-synthase inhibition, with striking similarities observed with published Arabidopsis thaliana data. A. myosuroides plants with NTSR were first affected by herbicide action like sensitive plants, but ultimately overcame it. Analysis of differences in transcriptomic herbicide response between resistant and sensitive plants did not allow identification of processes directly explaining NTSR. Five contigs associated to NTSR in the F2 population studied were tentatively identified. They were predicted to encode three cytochromes P450 (CYP71A, CYP71B and CYP81D), one peroxidase and one disease resistance protein.ConclusionsOur data confirmed that gene regulation is at the root of herbicide response and of NTSR. ALOMYbase proved to be a relevant resource to support NTSR transcriptomic studies, and constitutes a valuable tool for future research aiming at elucidating gene regulations involved in NTSR in A. myosuroides.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1804-x) contains supplementary material, which is available to authorized users.

We investigated whether specific ALS-inhibitor response marker-genes (AIRMs) identified in the model dicotyledonous plant Arabidopsis thaliana (Brassicaceae) were conserved across phylogenetically very distant species. The most probable homologs of the 533 A. thaliana AIRMs were identified in the major monocotyledonous weeds Alopecurus myosuroides and Lolium sp. (Poaceae) using recently established transcriptome resources. Expression patterns of above 70% of the grass AIRMs homologs matched those of their A. thaliana counterparts. Pathways of response to acetolactate-synthase (ALS)-inhibiting herbicides seem therefore strongly conserved, even across very distant plant species. This opens new perspectives for unravelling the genetic determinants of non-target-site resistance (NTSR) to ALS inhibitors, especially those governing NTSR regulation that remains fully unknown to date. Model plants could be used in a first step to discover the genes involved in ALS-inhibitor response pathways. Subsequent studies comparing sequence and expression of weed homologs of these genes should expedite the identification of candidates for the role of genes governing NTSR sensing and regulatory pathways.