Specific detection and quantification of virulent/avirulent Phytophthora infestans isolates using a real-time PCR assay that targets polymorphisms of the Avr3a gene.

Equipe 6International audienceMolecular tools that allow intraspecific quantification and discrimination of pathogen isolates are useful to assess fitness of competitors during mixed infections. However, methods that were developed for quantifying Phytophthora infestans are only specific at the species level. Here, we reported a TaqMan-based real-time PCR assay allowing, according to the specificity of the used probes, an accurate quantification of different proportions of two genetically distinct clones of P. infestans in mixed fractions. Indeed, in addition to a primer specific to P. infestans, two primers and two TaqMan(®) probes that target single-nucleotide polymorphisms located in the Avr3a/avr3a virulence gene sequence were designed. The reliability of the method was tested on serially diluted fractions containing plasmid DNA with either the Avr3a or the avr3a sequences at concentrations ranging from 10(2) to 10(8) copies per μl. Based on its specificity, sensitivity and repeatability, the proposed assay allowed a quantification of the targeted DNA sequence in fractions with a Avr3a/avr3a ratio in the range 1/99 to 99/1. The reliability of the test was also checked for counting zoospores. Applications for future research in P. infestans/host quantitative interactions were also discussed

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

International audienceStudying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration–drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies , such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations

De la génétique des populations à la gestion durable des résistances : intérêt de l'étude des populations sauvages des pathogènes des cultures. Cas de deux nématodes à kystes et de leur hôte sauvage commun

The sustainable management of genetic resistances to crop pathogens needs to consider their evolutionary potential. The evolutionary potential results both from the evolutionary history and the current population dynamics of pathogens, which can be affected by human activities occurring in agro-ecosystems. Therefore, they should be described and evaluated on wild pathogen populations free of human-mediated disturbances. The aim of this work is twofold (1) assessing the evolutionary history of two cysts nematodes, Heterodera schachtii and Heterodera betae, and their common wild host, Beta vulgaris ssp. maritima, in wild populations sampled on the coast from the South of Spain to Sweden; (2) investigating at a fine spatial scale the population genetic structure of H. schachtii .Results show that the colonization of the Atlantic coastline by the two nematodes was probably influenced by climatic fluctuations occurring since the Last Glacial Maximum, along with marine currents. Phylogeographical patterns of H. schachtii and the host-plant suggest a non-shared evolutionary history, which contrasts with the coastal recolonization of Europe observed in H. betae. The fine-scale study evidenced that wild populations of H. schachtii are genetically sub-structured at the level of the host plant, strongly isolated and characterized by small effective population sizes. All these results are discussed in the framework of the sustainable management of nematodes populations in cultivated fields.La gestion durable des variétés génétiquement résistantes aux pathogènes des cultures nécessite de tenir compte de leurs capacités évolutives. Celles-ci découlent de leur histoire évolutive et de la dynamique actuelle de leurs populations qui peut être modifiée par les activités humaines inhérentes au milieu agricole. La description et l’évaluation des capacités évolutives d’un pathogène ne sont donc possibles que sur des populations issues d’environnements non soumis à des perturbations d’origine anthropique. Les objectifs de ce travail sont donc (1) de reconstruire les histoires évolutives de deux nématodes à kystes, Heterodera schachtii et Heterodera betae et de leur hôte sauvage commun, Beta vulgaris ssp. maritima, à partir de populations sauvages distribuées sur le littoral du sud de l’Espagne à la Suède ; (2) de décrire, à une échelle plus fine, le fonctionnement et la structure génétique de populations sauvages d’H. schachtii.Nos résultats montrent que la colonisation de la côte Atlantique par les deux nématodes a probablement été influencée par les fluctuations climatiques survenues depuis le dernier Maximum Glaciaire et les courants marins. Les patrons phylogéographiques observés entre H. schachtii et la plante suggèrent des histoires évolutives disjointes contrairement à ceux observés chez H. betae. A fine échelle spatiale, les populations d’H. schachtii sont isolées entre elles, structurées à l’échelle de la plante hôte et présentent de petites tailles efficaces. Ces résultats sont discutés dans le contexte général de la protection des cultures

Automated construction of a French Entity Linking dataset to geolocate social network posts in the context of natural disasters

International audienceDuring natural disasters, automatic information extraction from Twitter posts is a valuable way to get a better overview of the field situation. This information has to be geolocated to support effective actions, but for the vast majority of tweets, spatial information has to be extracted from texts content. Despite the remarkable advances of the Natural Language Processing field, this task is still challenging for current state-of-the-art models because they are not necessarily trained on Twitter data and because high quality annotated data are still lacking for low resources languages. This research in progress address this gap describing an analytic pipeline able to automatically extract geolocatable entities from texts and to annotate them by aligning them with the entities present in Wikipedia/Wikidata resources. We present a new dataset for Entity Linking on French texts as preliminary results, and discuss research perspectives for enhancements over current state-of-the-art modeling for this task

What can be learned from wild populations of pests to better manage resistances in the fields?

Session 2: Agricultural Ecology Pests and PesticidesFollowing the ban of pesticide treatments, resistant varieties have emerged as one of the best environmental-friendly methods to control populations of parasitic nematodes. However, as host resistances exert strong selective pressures on parasites populations, they are likely to be overcome more or less rapidly, according to the effective sizes of parasite populations and to the level of gene flow among them. In agricultural landscapes, gene flow is mainly the result of human activities. Hence, to better manage these pests in agricultural fields, these two parameters should be evaluated in non-disturbed wild populations. The cyst nematode Heterodera schachtii is growing both on cultivated beet, in the fields, and on its wild relative, the sea beet. To characterize effective sizes and levels of gene flow in the wild, we assessed the temporal variation of allele frequencies at microsatellite loci from two successive samples taken one year apart on individual plants from different beaches. According to the environmental conditions of the studied areas, the number of generations produced by Heterodera schachtii between the two samplings was estimated as ranging from 4 to 10. Patterns of genetic diversity observed were incompatible with the occurrence of efficient gene flow, even between neighboring host plants, which resulted in low effective population sizes with respect to the actual number of individuals found in each rhizosphere of host plants. These low effective population sizes and the inability of the parasite to actively disperse over large distances suggested very limited possibilities to overcome resistances, provided that the passive transport of cysts by agricultural machinery, and by spreading sludge processing from sugar factories, are themselves limited

On the application of NLP techniques to French geological descriptions

International audienceGeological descriptions are written in natural language by different geologists during the acquisition process, without any constraints on the format or the content of the descriptions As a result, the records are highly heterogeneous, ranging from brut observations to high level interpretations and all the nuances in between. This heterogeneity imposes manual reprocessing of the data by experts to avoid mistakes occurring in downstream applications. Instead, we try to automate this process via Natural Language Processing (NLP) technique

Sensitivity to pH and ability to modify ambient pH of the take-all fungus Gaeumannomyces graminis var. tritici

International audiencepH is one of the major ambient factors affecting life history traits of soilborne phytopathogenic fungi. The diversity of phenotypic responses to pH changes has not been extensively explored within fungal populations. To investigate this question, the ability of 82 strains of a worldwide collection of the take-all agent Gaeumannomyces graminis var. tritici (Ggt) to grow in controlled pH conditions, reflecting their pH sensitivity, was measured. Of these 82 strains, 37 belonged to the G1 type and 45 to the G2 type, the two main genetic groups identified in Ggt populations. The experiments were conducted in Petri dishes on Fahraeus solid media buffered at pH 46, 60 or 70 with citrate-disodium phosphate solutions. The 82 strains exhibited a wide range of hyphal growth rates at the three pH levels. Ten statistically different pH profiles were described. The G2 strains grew significantly better than the G1 on the slightly acidic (pH 60) and the neutral (pH 70) buffered media. The ability of three strains to change ambient pH was also measured on unbuffered Fahraeus solid media initially adjusted to pH 56 or 80. All three strains were able to alkalinize the acidic medium. However, important variations between strains in the intensity, range and persistence of this alkalinization were measured. These results provide the first evidence of intraspecific variability in pH sensitivity within soilborne fungal species

Variabilité phénotypique de sensibilité et d’adaptation aux variations de pH des populations de Gaeumannomyces graminis var. tritici, champignon tellurique parasite des racines du blé.

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Variabilité du déterminisme génétique de la réponse au pH chez un champignon pathogène du blé, Gaeumannomyces graminis var. tritici

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Modelling site response at regional scale for the 2020 European Seismic Risk Model (ESRM20)

International audienceQuantitative estimation of seismic risk over a region requires both an underlying probabilistic seismic hazard model and a means to characterise shallow site response over a large scale. The 2020 European Seismic Risk Model (ESRM20) builds on the 2020 European Seismic Hazard Model (ESHM20), requiring additional information to firstly parameterise the local site condition across all of Europe, and subsequently determine its influence on the prediction of seismic ground motion. Initially, a harmonised digital geological database for Europe is compiled, alongside a model of topographic/bathymetric elevation and a database of 30 m averaged shearwave velocity measurements ( $$V_{S30}$$ V S 30 ), in order to produce separate 30 arc-second maps of inferred $$V_{S30}$$ V S 30 based on topography and on geology. We then capitalise on a large database of seismic recording stations in Europe for which site-to-site ground motion residuals ( $$\delta S2S_{S}$$ δ S 2 S S ) have been determined with respect to the shallow crustal ground motion model used in the ESHM20. These residuals allow us to incorporate site amplification functions into the European GMM calibrated upon either observed or inferred $$V_{S30}$$ V S 30 , or on the European geology and topography models. We present the resulting pan-European seismic site amplification model and assess its impact on seismic hazard and risk compared against other approaches. The new site amplification model fulfils the requirements of the ESRM20 and, providing uncertainty is fully propagated, yields estimates of seismic hazard and risk at a large space scale that may be comparable to other methods often applied at local/urban scale where better-constrained site information is available