Christophe Délye

French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Agroécologie

Herbicides are currently pivotal to control weeds and sustain food security. Herbicides must efficiently kill weeds while being as harmless as possible for crops, even crops taxonomically close to weeds. To increase their selectivity toward crops, some herbicides are sprayed in association with safeners that are bioactive compounds exacerbating her...

Molecular detection of herbicide non-target-site-based resistance (NTSR) classically requires extensively validated NTSR genes. We assessed the feasibility of predicting NTSR phenotypes using expression data of NTSR transcriptional markers, i.e., transcripts which expression levels are statistically correlated to NTSR. Markers were sought by compar...

Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides whilst maintaining pesticide efficacy. This goal requires monitoring of the emergence and development of resistance to pesticides in crop pests. To this end, various methods for resistance diagnosis have been developed for differen...

Resistance to herbicides occurs in weeds as the result of evolutionary adaptation (Jasieniuk et al. 1996). Basically, two types of mechanisms are involved in resistance (Beckie and Tardif 2012; Délye 2013). Target-site resistance (TSR) is caused by changes in the tridimensional structure of the herbicide target protein that decrease herbicide bindi...

Resistance to herbicides in arable weeds is increasing rapidly worldwide and threatening global food security. Resistance has now been reported to all major herbicide modes of action despite the development of resistance management strategies in the 1990s. We review here recent advances in understanding the genetic bases and evolutionary drivers of...

Background Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify...

Assessing weed capacity to evolve herbicide resistance before resistance occurs in the field is of major interest for chemical weed control. We used herbicide selection followed by controlled crosses to provoke accelerated evolution of resistance to imazamox (imidazolinones) and tribenuron (sulfonyurea), two acetolactate-synthase (ALS) inhibitors t...

Ambrosia artemisiifolia L. (common ragweed) is a globally invasive, allergenic, troublesome arable weed. ALS-inhibiting herbicides are broadly used in Europe to control ragweed in agricultural fields. Recently, ineffective treatments were reported in France. Target site resistance (TSR), the only resistance mechanism described so far for ragweed, w...

BACKGROUND Monitoring resistance to Plant Protection Products (PPPs) is crucial for understanding the evolution of resistances in bioagressors, thereby allowing scientists to design sound bioagressor management strategies. Globally, resistance monitoring is implemented by a wide range of actors that fall into three distinct categories: academic, go...

Significance The emergence of noxious weeds poses a serious threat to agricultural production. Understanding their origin and evolution is therefore of major importance. Here we analyzed the intriguing case of teosinte, a wild relative of maize originating from Mexico that recently emerged as an invasive weed in maize fields in Europe. Patterns of...

Avant d'entamer le dossier, voici un petit glossaire à l'usage des gestionnaires de la résistance aux produits phytopharmaceutiques.

Pour limiter la diffusion de bioagresseurs résistants aux pratiques de contrôle, deux principes sont à retenir : diversité et efficacité des pratiques.

BACKGROUND Next Generation Sequencing (NGS) technologies offer tremendous possibilities for high‐throughput pesticide resistance diagnosis via massive genotyping‐by‐sequencing. Herein, we used Illumina sequencing combined with a simple, non‐commercial bioinformatics pipe‐line to seek mutations involved in herbicide resistance in two weeds. RESULTS...

The issue of cross‐ or multiple resistance to acetolactate synthase (ALS) inhibitors and the auxinic herbicide 2,4‐D was investigated in Papaver rhoeas L., a common and troublesome weed in winter cereals, in a broad‐scale study across four European countries. A combination of herbicide sensitivity bioassays and molecular assays targeting mutations...

Galium spurium(Rubiaceae) is a frequent troublesome dicotyledonous weed species, usually controlled with ALS inhibitors, synthetic auxins and their mixtures. In 2016, florasulam+2,4-D failed to adequately control this species in cereal fields (Phthiotida, central Greece) prompting the current study. Seeds from three G. spurium populations (G2, G3,...

Non-target-site-resistance (NTSR) to herbicides is a major cause for chemical control failure in a number of weeds. Studies investigating NTSR essentially considered grass weeds. Here, we investigated the transcriptomic bases of NTSR to ALS inhibitors in the global, allergenic weed Ambrosia artemisiifolia. Our objectives were to establish a transcr...

Las mutaciones Ile-1781-Leu, Ile-2041-Asp y Asp-2078-Gly confieren resistencia de punto a los herbicidas inhibidores de ACCasa y han sido encontradas en poblaciones de Lolium rigidum (LOL) en el occidente australiano y en poblaciones de Alopecurus myosuroides (ALOMY) en el continente europeo. Al inicio del proceso evolutivo en resistencias conferid...

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. thalianaAIRMs were identified in the major monocotyledonous weeds Alopecurus myosuroides a...

Le réseau R4P propose une classification unique des substances actives utilisées en santé végétale, qu’elles soient à usage herbicide, insecticide/ acaricide ou fongicide.

Prod 2018-236j SPE Pole EA GESTAD INRA

The four documented cases of field selection for herbicide resistance in weedy Setaria are described in this chapter. In each case, weed control failure was observed in practice in the field. In all cases, resistance was target-site-based resistance and was due to single nucleotide mutations causing amino-acid substitutions at codon 264 of psbA (ph...

Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 1...

EST-SSR markers obtained by 454 sequencing of A. artemisiifolia ESTs and showing consistent PCR amplifications and clear electrophoretic migration patterns. Loci in bold represent the markers selected in A. artemisiifolia. (DOCX)

Genetic diversity parameters at 26 nuclear SSR markers for 16 populations of Ambrosia artemisiifolia. N: number of individuals genotyped, A: average allelic richness after rarefaction, HO observed heterozygosity, HS expected heterozygosity, FIS inbreeding coefficient estimated taking into account the presence of null alleles. * FIS estimates signif...

Data maximum likelihood value (left) and deltaK method (right) results used to determine the most likely number of genetic clusters with 13 EST-SSR and 13 gSSR markers. (TIF)

gSSR markers obtained by 454 sequencing of enriched A. artemisiifolia gDNA and showing consistent PCR amplifications and clear electrophoretic migration patterns. Loci in bold represent the markers selected in A. artemisiifolia. (DOCX)

gSSR markers obtained by Illumina sequencing of raw A. artemisiifolia gDNA and showing consistent PCR amplifications and clear electrophoretic migration patterns. Loci in bold represent the markers selected in A. artemisiifolia. (DOCX)

Karyotype showing the 36 chromosomes of A. artemisiifolia in a telophase (left) and in the end of a prophase (right). The red arrows indicate the chromosomes. Gx100. (TIF)

Results of Bayescan FST outlier analysis on 14 gSSR (a) and 13 EST-SSR loci (b). The vertical bars correspond to threshold P-values of 0.05 (solid line) and 0.01 (dashed line) for the neutral model. (a) Data from all 16 populations. (b) Data from 11 European populations. (TIF)

Genetic structure of 16 populations of A. artemisiifolia analyzed using the 13 gSSR markers. (TIF)

Genetic structure of 16 populations of A. artemisiifolia analyzed using the 13 EST-SSR markers. (TIF)

Corn poppy (Papaver rhoeas) has long been associated with target-site and more recently non-target site resistance to ALS inhibitors (HRAC group B). Amounting evidence suggests that this species may also develop resistance to synthetic auxins (HRAC group O). The present study aimed at screening three P. rhoeas populations (F3B, F1D and F4C) from ce...

Safeners enable selective control of weeds in botanically related crops by enhancing or triggering herbicide degradation in crop plants via mechanisms very similar to mechanisms involved in weed non-target-site-based resistance (NTSR). To assess whether safeners could play a role in NTSR evolution, we investigated the eff ect of the safener cloquin...

Background: Managing herbicide-resistant weeds is becoming increasingly difficult. Here we adapted the weed dynamics model AlomySys to account for experimentally-measured fitness costs linked to mutants of target-site resistance to acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides in Alopecurus myosuroides. We ran simulations to test ho...

Following control failure by herbicides inhibiting acetolactate-synthase (ALS) in French wheat fields and vineyards, we aimed at confirming resistance evolution and investigating the evolutionary origin and spread of resistance in the tetraploid species Senecio vulgaris (common groundsel), a widespread, highly mobile weed. Sequencing two ALS homeol...

Background: Herbicide 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 fu...

Autogamy allows the reproduction of isolated plants so that these plants can produce a new population. On the other hand, allogamy tends to increase the genetic variability in plant populations and by processes of admixture, generates recombinant genotypes which can be adapted to new environments. Common ragweed (Ambrosia artemisiifolia, Asteracea...

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 Il...

This article investigates the possible existence of mechanisms counterbalancing the negative pleiotropic effects on development and reproduction that are conferred by alleles responsible for herbicide resistance in the weed Alopecurus myosuroides. We considered three herbicide-resistant, mutant acetyl-coenzyme A carboxylase (ACCase) alleles, Leu178...

Background: Herbicide 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 fu...

SPE EA Pôle GEAPSI & ECOLDUR CT1 (SPE (CD)

Background The Next Generation Sequencing (NGS) technologies offer tremendous possibilities for accurate detection of mutations endowing pesticide resistance. Yet, their use for this purpose has not emerged in crop protection. This study aims at promoting NGS use for pesticide resistance diagnosis. It describes a simple procedure accessible to virt...

PROD 2014-162 SPE GESTAD GEAPSI CT ? INRA

La résistance non liée à la cible (RNLC) est la menace principale pour le contrôle chimique des graminées adventices. Ses mécanismes, encore très largement inconnus, sont basés sur la régulation d’une partie des gènes impliqués dans la réponse de la mauvaise herbe au traitement herbicide. Cette étude vise à identifier des gènes de RNLC chez les ray...

Des gènes de résistance aux herbicides peuvent-ils préexister dans des populations de mauvaises herbes n’ayant jamais été traitées avec des herbicides ? Pour en savoir plus, une mutation conférant une résistance à des herbicides a été recherchée dans des parts d’herbiers contenant des spécimens de vulpin (Alopecurus myosuroides) collectés entre 178...

Nous avons assisté à une augmentation spectaculaire du nombre d’adventices résistantes à un herbicide ces 30 dernières années. Les mécanismes de résistance potentiellement les plus dangereux sous tendent la résistance non liée à la cible (RNLC) : la RNLC est polygénique, imprévisible et elle peut conférer des profils de résistance croisée à des her...

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic v...

Variation in the expression of numerous genes is at the basis of plant response to environmental stresses. Non-target-site-based resistance to herbicides (NTSR), the major threat to grass weed chemical control, is governed by a subset of the genes involved in herbicide stress response. Quantitative PCR assays allowing reliable comparison of gene ex...

Background and Aims Selective pressures exerted by agriculture on populations of arable weeds foster the evolution of adaptive traits. Germination and emergence dynamics and herbicide resistance are key adaptive traits. Herbicide resistance alleles can have pleiotropic effects on a weed's life cycle. This study investigated the pleiotropic effects...

Non-target-site-based resistance (NTSR) can confer unpredictable cross-resistance to herbicides. However, the genetic determinants of NTSR remain poorly known. The current, urgent challenge for weed scientists is thus to elucidate the bases of NTSR so that detection tools are developed, the evolution of NTSR is understood, the efficacy of the shrin...

QUESTION - Des gènes de résistance aux herbicides peuvent-ils déjà exister dans des populations de mauvaises herbes n'ayant jamais été traitées avec des herbicides ? Pour le savoir, une mutation conférant une résistance à des herbicides a été recherchée dans des parts d'herbiers contenant des spécimens de vulpin ( Alopecurus myosu roides ) collecté...

Papaver rhoeas, an annual plant species in the Papaveraceae family, is part of the biodiversity of agricultural ecosystems and also a noxious agronomic weed. We developed microsatellite markers to study the genetic diversity of P. rhoeas, using an enriched microsatellite library coupled with 454 next-generation sequencing. A total of 13,825 sequenc...

Non-target-site based resistance to herbicides is a major threat to the chemical control of agronomically noxious weeds. This adaptive trait is endowed by differences in the expression of a number of genes in plants that are resistant or sensitive to herbicides. Quantification of the expression of such genes requires normalising qPCR data using ref...

Figure S1. Primer specificity test. - melting curve generated for RUBISCO. Melting curves generated for RUBISCO (A), ACT (B), UBQ (C), EF1 (D), GAPDH (E), TUB (F), 25S (G), 26S (H) and 18S (I).

Table S1. Accession numbers of the sequences used for primer design. Table S2. Descriptive statistics of reference gene expression in black-grass based on the BestKeeper approach.

a b s t r a c t In two different locations of the Western Australian "wheatbelt", Lolium rigidum (rigid ryegrass) seeds were collected from organic fields (no herbicide use) and neighbouring conventional fields (persistent herbicide use), the latter infested with herbicide-resistant plants, to investigate the occurrence of gene flow among field pop...

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsate...

Délye C, Pernin F & Michel S (2011). ‘Universal’ PCR assays detecting mutations in acetyl-coenzyme A carboxylase or acetolactate synthase that endow herbicide resistance in grass weeds. Weed Research51, 353–362. Herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) or acetolactate synthase (ALS) are key for grass weed control. Yet, numerous...

Dans deux parcelles, l'emploi systématique d'herbicides inhibiteurs de l'ACCase, puis d'inhibiteurs de l'ALS, a sélectionné des plantes de vulpin résistantes à la plupart des substances ayant ces modes d'action (fénoxaprop, clodinafop, pinoxaden, quizalofop, iodosulfuron+mésosulfuron et pyroxsulame). Ces plantes ne contiennent pas de mutations de l...

Les inhibiteurs de l'acétolactate-synthase (ALS) sont actuellement la principale famille d'herbicides utilisés en France. La capacité de diagnostiquer rapidement la présence de plantes résistantes dans les parcelles contribue au maintien de leur efficacité. Des tests « ADN » ont été développés chez les coquelicots (Papaver rhoeas, Papaver dubium et...

To determine whether weed populations growing in neighbouring fields were genetically isolated, we investigated the genetic contamination of Alopecurus myosuroides populations in organic fields by populations in conventional fields. Herbicide resistance was used as a marker for gene flow to organic populations, which are not under herbicide selecti...

Complex genetic control of non-target-site-based resistance to herbicides inhibiting acetyl-coenzyme A carboxylase and acetolactate-synthase in Alopecurus myosuroides Huds. The genetic control of non-target-site-based resistance (NTSR) to three herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) and one inhibiting acetolactate-synthase (AL...

*The geographical structure of resistance to herbicides inhibiting acetyl-coenzyme A carboxylase (ACCase) was investigated in the weed Alopecurus myosuroides (black-grass) across its geographical range to gain insight into the process of plant adaptation in response to anthropogenic selective pressures occurring in agricultural ecosystems. *We anal...

To determine whether weed populations growing in neighbouring fields were genetically isolated, we investigated the genetic contamination of Alopecurus myosuroides populations in organic fields by populations in conventional fields. Herbicide resistance was used as a marker for gene flow to organic populations, which are not under herbicide selecti...

Repeated use of acetyl-CoA carboxylase (ACCase) inhibitors, especially fenoxaprop and clodinafop, since the late 1980s has selected for resistance in Alopecurus myosuroides Huds. (black-grass) in France. We investigated whether resistance to pinoxaden, a phenylpyrazoline ACCase inhibitor to be marketed in France, was present in French black-grass p...

Lolium species (ryegrasses) are genetically highly variable plants that are both forage crops and major weeds across the globe. As weeds, they rapidly evolve resistance under the selective pressure of acetolactate-synthase (ALS) inhibitors, the most resistance-prone herbicide group. Quick and accurate diagnosis is therefore of importance to prevent...

Target-site-based resistance to acetyl-CoA carboxylase (ACCase) inhibitors in Alopecurus myosuroides Huds. is essentially due to five substitutions (Isoleucine-1781-Leucine, Tryptophan-2027-Cysteine, Isoleucine-2041-Asparagine, Aspartate-2078-Glycine, Glycine-2096-Alanine). Recent studies suggested that cross-resistance patterns associated with eac...

Acetolactate synthase (ALS) inhibitors are the most resistance-prone herbicide group. Rapid resistance diagnosis is thus of importance for their optimal use. We formulate rules to use the derived cleaved amplified polymorphic sequence method to develop molecular tools detecting a change at a given codon, the nature of which is unknown. We applied t...

Pleiotropic effects associated with genes endowing resistance to herbicides are generally predicted to reduce plant fitness. Quantifying these effects is necessary to develop management strategies against herbicide‐resistant weeds. We assessed the pleiotropic effects associated with three mutant alleles of the herbicide target enzyme acetyl‐coenzym...

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