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[hal-05652738] Spatio-temporal field, landscape and meteorological datasets describing bruchid beetle populations, grain damage and parasitism in faba bean and lentil fields in France
This dataset provides a multi-scale and multi-year characterization of population, grain damage and larval parasitism of bruchid beetle populations (Coleoptera: Chrysomelidae: Bruchinae) populations, i.e. Bruchus rufimanus Boheman, 1833 and Bruchus signaticornis Gyllenhal, 1833. This dataset covers 45 faba bean (Vicia faba Linnaeus, 1753) and 60 lentil (Lens culinaris Medikus, 1787) fields across four major production regions in France. Data were collected over three consecutive growing seasons (2019-2020 to 2021-2022) across three phenological crop stages (vegetative, flowering, and young pods) and at five distances from field edge to capture spatio-temporal dynamics. Datasets include bruchid counts, grain damage as well as parasitism rates by micro-hymenoptera (mainly Triaspis cf.<p>thoracica Curtis, 1860). Field observations are integrated with environmental variables, including GISbased landscape metrics (land use, semi-natural habitats, and hedgerow length) calculated at 500, 1000, and 2000 m buffer radii from field observation plots. Additionally, daily meteorological data from the SAFRAN platform (https://agroclim.inrae.fr/siclima/) at a resolution of 8-km grid and then aggregated per crop stage, covering temperature thresholds, precipitation, and wind speed.Agricultural management information, such as crop sowing dates, varieties, tillage and pest management, is also provided for each of the 105 fields. This integrated dataset allows for crossdisciplinary reuse in agronomy, ecology, and entomology to explore pest-enemy interactions, edge effects, and the influence of landscape and climate on crop-pest dynamics.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Cayetano Herrera) 12 Jun 2026
https://hal.inrae.fr/hal-05652738v2
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[hal-05353058] Digital droplet PCR quantification and field-scale spatial distribution of <i>Plasmopara viticola</i> oospores in vineyard soil
Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases affecting grapevine worldwide. Primary inoculum (i.e., oospores) plays a decisive role in downy mildew epidemics, but we still know very little about its abundance in vineyard soil. This study presents a novel molecular method for quantifying P. viticola oospore concentration in vineyard soil using digital droplet PCR (ddPCR). The development of this method enabled the characterization of both the abundance and spatial distribution of oospores in a vineyard at the onset of the growing season. Following a regular grid, a total of 198 soil samples (0-15 cm horizon) were collected in March 2022 in grapevine rows in a 0.22 ha vineyard planted with cv. Merlot and conducted according to French organic viticulture specifications. Additional samples were collected from the same field within five nested sampling plots with three distance levels, including samples collected in the inter-rows. Using ddPCR, we found P. viticola DNA in all soil samples except one, and we estimated that oospore concentration ranged from 0 to 1,858 oospores per gram of soil (303 ± 308 on average). The distribution of oospores at field scale was not random but characterized by 15-m diameter patches of concentrically increasing oospore concentration. Oospores accumulated five times more below the vine stocks than in the inter-row. Using a leaf disc bioassay, we found that soil infectious potential significantly increased with oospore concentration assessed by ddPCR. However, the low coefficient of determination of the relationship indicated that DNA-based oospore quantification lacked clear epidemiologi cal significance. Both ddPCR and bioassay methods are valuable tools that could be used to assess reservoirs of P. viticola primary inoculum across different agroclimatic contexts, thereby bringing greater genericity. Further methodological improvement will also help refine the accuracy of DNA-based assessment of primary inoculum reservoir and improve our understanding of the relationship between primary inoculum reservoir and epidemic dynamics. Ultimately, these data will be essential for improving epidemic risk models and evaluating new preventive disease management strategies targeting the primary inoculum.<p>IMPORTANCE Grapevine downy mildew caused by the oomycete Plasmopara viticola affects leaves and bunches and leads to important economic losses for viticulturists. Recently, evidence has accumulated that soilborne primary inoculum (i.e., oospores in the soil) importantly contributes to disease progress. The significance of our work is in presenting a direct and sensitive method for assessing soil oospore concentration, as well as quantitative and spatially explicit data on downy mildew primary inoculum. This opens the way to new research, the evaluation of new disease control strategies based on primary inoculum management and the improvement of epidemic risk models, which will potentially contribute to lower fungicide use in viticulture in fine.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Poeydebat) 28 Jan 2026
https://hal.inrae.fr/hal-05353058v2
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[hal-03850506] Neighbourhood effect of weeds on wheat root endospheric mycobiota
1. Micro-organisms associated with plants provide essential functions to their hosts, and therefore affect ecosystem productivity. Agricultural intensification has modified microbial diversity in the soil reservoir and may affect plant–microbial recruitment. Weeds develop spontaneously in crop fields, and could influence micro-organisms associated with crop plants through a neighbourhood effect. We explore the effect of weed species on crop plant microbiota as potentially auxiliary plants that affect agricultural productivity. 2. We combined field and controlled laboratory studies to analyse the neighbourhood effect of weeds on wheat root endospheric mycobiota (i.e. fungi within roots) and growth. First, we analysed the effect of weed species diversity and identity recorded in the neighbourhood of individual wheat plants on soil and wheat root mycobiota in the field. Second, we used a plant-matrix design in laboratory conditions to test the effect of weed identity (nine weed treatments) and their ability to transmit root mycobiota to wheat roots, and the resulting impact on wheat growth. 3. In contrast to soil mycobiota, we demonstrated that wheat root endospheric mycobiota was influenced by the diversity and identity of weeds developing in their 1 m2 neighbourhood. Wheat root endospheric microbiota strongly differs in terms of richness and composition depending on the neighbouring weed plant species. Weed species transmitted from 13% to 74% of their root microbiota to wheat roots depending on weed identity in controlled conditions. 4. Synthesis. Weed neighbours modified wheat plant performance, possibly as a result of competitive interactions and changes in microbiota. Our findings suggest that crop root mycobiota was variable and was modulated by their weed neighbourhood. Synergistic effects between mycobiota of crops and weeds could therefore contribute to soil biodiversity and sustainable agriculture.
ano.nymous@ccsd.cnrs.fr.invalid (Jie Hu) 31 May 2023
https://hal.inrae.fr/hal-03850506v1
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[hal-05299472] Altered Behavioural Response of Whitefly (Bemisia tabaci) on Tomato Associated with Biocontrol Plants
The whitefly, Bemisia tabaci , is a significant pest in tomato production, causing extensive damage and economic losses. In pursuing sustainable pest management strategies, this study investigates the deterrent effects of Tagetes species ( T. erecta , T. patula , and T. minuta ) and Crotalaria juncea on B. tabaci settlement and oviposition on tomato plants. Two free dual-choice experimental setups were conducted in a climate-controlled chamber. The study confirmed the efficacy of the experimental setup, with similar B. tabaci dispersion and oviposition on the sides with tomato plants alone. When Tagetes or C. juncea was introduced, a significant reduction in B. tabaci settlement and oviposition was observed compared to the tomato control side. To identify the modes of action of the companion plants on B. tabaci , a follow-up experiment, modifying the spatial arrangement of the plants, was set up to discriminate between physical barrier and chemical repellent effects. The findings suggest a potential crossing between repellence and barrier effects for Tagetes species when C. juncea acted as a sinkhole, trapping the whiteflies. A DHS-ATD-GC-MS analysis revealed that the repellent effect seems more associated with the composition than the intensity of the blend. Some already known repellent volatile compounds of Tagetes , such as limonene, were identified, but the major ketone compounds must also be tested. This study demonstrates the effectiveness of Tagetes and Crotalaria species as biocontrol plants in pest management for tomato production. These plants reduce pest pressure and support sustainable agriculture, offering an alternative to chemical pesticides. Further research should investigate mechanisms, field applications, and broader agroecological benefits.
ano.nymous@ccsd.cnrs.fr.invalid (Cliven Njekete) 27 Jul 2026
https://hal.science/hal-05299472v1
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[hal-05651321] A Modeling Approach to Separate Within-Leaf Pathogen Growth from Whole-Plant Pathogen Dispersal – A Case Study on Pea Fungal Diseases
Describing and predicting epidemic progress is critical for effective reduction of crop losses due to infectious diseases. Disease progression is commonly characterized using quantitative or semi-quantitative indicators of severity, influenced by both pathogen growth at the organ scale and its spread at the plant scale. Although these two processes cannot be disentangled from raw data alone, we developed a mechanistic model that, for the first time, distinguishes disease growth within organs from dispersal between organs. We fitted this model to a set of experimental data on the severity of foliar anthracnose and Ascochyta blight on four susceptible pea cultivars (Flambo, Hamino, Smiley, and Spencer) at five time points in pure stand plots or in plots intercropped with wheat under natural infection conditions. Disease spread and growth over thermal time (degree days) and space (leaf levels) was modeled by a two-variable logistic function, derived from an approximation of the traveling wave Fisher–KPP model solution. Results showed that the apparent diffusion speed of the disease varied across cultivars, years, and cropping systems and was consistently reduced under intercropping. By interpreting model parameters biologically, we identified apparent diffusion as a novel quantitative trait to characterize pathogen strategies and epidemic speed. This new metric offers plant pathologists and breeders a useful tool to better describe within-plant disease progression across environments and genotypes.
ano.nymous@ccsd.cnrs.fr.invalid (Manu Affichard) 10 Jun 2026
https://hal.science/hal-05651321v1
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[hal-04478362] Évolutions réglementaires et adaptations en grandes cultures
L’utilisation de mélanges, qu’ils soient de variétés ou d’espèces, pose des questions en termes de réglementation, mais aussi de sélection, d’évaluation ou encore de commercialisation.
ano.nymous@ccsd.cnrs.fr.invalid (Virginie Bertoux) 26 Feb 2024
https://hal.science/hal-04478362v1
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[hal-05297196] Deciphering microbial interactions protecting grapevine against downy mildew: Integrating field studies and synthetic community approaches
Grapevine hosts numerous microorganisms that impact its health and growth. Among the key pathogens are Plasmopara viticola (downy mildew) and Erysiphe necator (powdery mildew). When these pathogens colonize grapevine leaves, they encounter the resident microbiome, which can act as a barrier to their growth through various ecological interactions. Additional interactions may occur in the soil and litter but these have been largely overlooked. A current challenge is to identify microbiome members that naturally regulate mildews and find management practices that support these natural antagonists. To address this, we analyzed leaf and soil microbiomes in vineyard plots with long-term epidemiological records. We compared microbial community compositions between plots with contrasting disease susceptibilities and between symptomatic and asymptomatic tissues. Using differential abundance analyses, Random Forest algorithms, and network learning methods, we identified potential antagonists or facilitators. Microbial taxa of interest for downy mildew were found in the topsoil, which serves as both a microbial reservoir and the overwintering site for pathogen oospores, and in the phyllosphere, where pathogen zoospores enter leaves. The leaf endosphere contained very few taxa of interest. The diversity of microbial communities was not consistently related to disease susceptibility, suggesting that susceptibility is more related to the abundance of specific microbial taxa. Several taxa were integrated into Synthetic Microbial Communities (SynComs) and tested against downy mildew in vitro and in the field, aiming to develop microbial biocontrol of grapevine diseases and move towards pesticide-free viticulture.
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297196v1
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[hal-05297768] Identifier des consortiums microbiens qui interfèrent avec les agents pathogènes de la vigne
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 19 Mar 2026
https://hal.science/hal-05297768v1
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[hal-05297773] Identifying microbial consortia that interfere with grapevine pathogens
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297773v1
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[hal-05687891] Eliciting beliefs when the distribution matters: a horse race of elicitation interfaces
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687891v1
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[hal-05687897] On the external validity of risk attitudes
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687897v1
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[hal-05687889] Eliciting beliefs when the distribution matters: a horse race of elicitation interfaces
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687889v1
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[hal-05684099] Livret de ressources BE-CREATIVE : fiches "conception", méthodes et applications
Ce livret a été pensé pour le consortium du projet BE-CREATIVE en 2023 pour partager un certain nombre de méthodes de conception mobilisables dans les territoires cas d’étude de ce projet. L’acception que nous avons retenue pour le terme de « conception » est large, avec certaines méthodes relevant de la conception à proprement parler (génération de solutions), et d’autres méthodes portant sur l’apport de connaissances pour la conception (ex. Fiche Traque aux innovations), ou pouvant être mobilisées à la fois pour le diagnostic et en aide à la conception (ex. Fiche cartes mentales). Notre objectif était d’illustrer plusieurs méthodes de conception via des fiches synthétiques permettant de saisir rapidement leur contenu et leurs usages. Notre objectif n’est pas d’orienter vers une méthode spécifique ni de limiter le choix des méthodes mais bien de mettre à disposition la description d’une variété de méthodes pour ouvrir et enrichir la réflexion sur les méthodes qui seront mobilisées localement. Ce recensement n’est pas exhaustif. Il a été orienté par les connaissances de ces méthodes par les porteuses de ce travail (L. Prost, L. Hossard), en veillant à décrire des méthodes à la fois très utilisées (ex. Scénarisation), en développement fort (ex. Jeux sérieux), et plus récentes/moins utilisées dans notre communauté INRAE (ex. Méthodes hors agronomie – Ecoidéation ; portées par des collègues travaillant au Sud, CIRAD – DATE – et Wageningen – DEED). Nous avons réalisé deux types de fiches : - Les fiches méthodes : présentent des méthodes plus ou moins connues en agronomie permettant de faire de la conception. Certaines correspondent à des familles de méthodes, i.e. il existe une variété d’approches se revendiquant de cette méthode (ex. Fiches cartes mentales, ateliers de conception). D’autres sont plus spécifiques, élémentaires, avec un déroulé plus « normé » (ex. Fiches méthodes DISCS, DATE, RIO/RID, DEED). Les fiches visent à donner les éléments clés de la méthode. Toutes sont organisées de la même manière (A noter que certaines présentent aussi une section « application »). Ces fiches présentent : (1) l’objectif de la méthode et son rôle pour la conception, en particulier le type d’objet conçu ; (2) le cadre théorique sur lequel s’appuie la méthode ; (3) les étapes de la méthode (parfois spécifiées pour plusieurs méthodes, en cas de « méta-méthode ») ; (4) le(s) type(s) de sortie produite(s) par la méthode ; (5) les principaux avantages et inconvénients de la méthode ; (6) l’intérêt de la méthode pour Be-Creative ; (7) les compétences nécessaires à la mise en œuvre de la méthode ; (8) les besoins humains (en indiquant le pas de temps) ; (9) le contact « spécialiste » de la méthode et son contact (idéalement participant de Be-Creative) ; (10) les références clés associées à la méthode et à quelques applications. - Les fiches application : illustrent certaines méthodes ou souvent combinaison de méthodes. Comme pour les fiches méthodes, l’exhaustivité n’est pas visée. Nous avons cherché à illustrer via des thèses ayant mobilisé l’échelle territoire ou bassin versant, en mettant en particulier en lumières les étapes clés des démarches et leurs sorties principales. Ces fiches sont synthétiques (environ 3 pages) et organisées de la manière suivante : (1) Objectif de l’étude (basé sur la problématique de la thèse) ; (2) les étapes de l’étude, (3) les parties prenantes mobilisées et leur rôle ; (4) le modèle de simulation, (5) les échelles/niveaux mobilisés ; (6) les principaux résultats ; (7) les références (principalement issues de la thèse).
ano.nymous@ccsd.cnrs.fr.invalid (Laure Hossard) 07 Jul 2026
https://hal.inrae.fr/hal-05684099v1
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[hal-05698513] Réduire les pesticides : quelles conséquences économiques pour les filières agro‑alimentaires ?
Taxe sur les pesticides, diffusion des pratiques agroécologiques, interdiction d’importer des produits cultivés avec des pesticides non-utilisés en France… Les pistes pour permettre une nette baisse de l’utilisation des pesticides sont nombreuses, mais toutes n’ont pas les mêmes effets attendus sur les rendements et les revenus des agriculteurs.
ano.nymous@ccsd.cnrs.fr.invalid (Julie Subervie) 20 Jul 2026
https://hal.inrae.fr/hal-05698513v1
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[hal-05687885] Eliciting beliefs when the distribution matters: a horse race of elicitation interfaces
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 09 Jul 2026
https://hal.inrae.fr/hal-05687885v1
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[hal-05221706] Insights Into the Role of Lysine Acetylation of Non‐Histone Proteins in Plant Immunity
Plant immunity is regulated by numerous transcriptional and posttranslational mechanisms. Among these, lysine acetylation, which is controlled by lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), has been extensively studied, particularly in the context of epigenetic regulation through histone acetylation. However, advances in proteomics have revealed that non-histone proteins also undergo lysine acetylation, prompting increasing efforts to elucidate the underlying mechanisms and functions of this posttranslational modifications. This review provides a comprehensive analysis of acetyl-lysine proteome (acetylome) studies during plant interaction with pathogens (including fungi, bacteria and viruses). By highlighting the significance of lysine acetylation in non-histone proteins, these studies offer valuable insights into potential new targets for lysine acetylation in plant immunity. We further examine the roles of plant KATs and KDACs, as well as pathogen-derived KATs, emphasizing the different types of lysine acetylation in non-histone proteins. In particular, we explore how bacterial effectors, which mimic KAT activity, acetylate lysine residues in non-histone proteins to modulate plant immunity. Additionally, we discuss on emerging molecular mechanisms involving plant KATs and KDACs that finely regulate immune responses, particularly within the jasmonic acid signalling pathway. These findings open new perspectives for future research on this posttranslational regulation within the context of plant immunity.<p>This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Jérémy Villette) 25 Aug 2025
https://hal.science/hal-05221706v1
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[hal-04645630] Broad-Spectrum Efficacy and Modes of Action of Two Bacillus Strains against Grapevine Black Rot and Downy Mildew
Black rot (Guignardia bidwellii) and downy mildew (Plasmopara viticola) are two major grapevine diseases against which the development of efficient biocontrol solutions is required in a context of sustainable viticulture. This study aimed at evaluating and comparing the efficacy and modes of action of bacterial culture supernatants from Bacillus velezensis Buz14 and B. ginsengihumi S38. Both biocontrol agents (BCA) were previously demonstrated as highly effective against Botrytis cinerea in grapevines. In semi-controlled conditions, both supernatants provided significant protection against black rot and downy mildew. They exhibited antibiosis against the pathogens by significantly decreasing G. bidwellii mycelial growth, but also the release and motility of P. viticola zoospores. They also significantly induced grapevine defences, as stilbene production. The LB medium, used for the bacterial cultures, also showed partial effects against both pathogens and induced plant defences. This is discussed in terms of choice of experimental controls when studying the biological activity of BCA supernatants. Thus, we identified two bacterial culture supernatants as new potential biocontrol products exhibiting multi-spectrum antagonist activity against different grapevine key pathogens and having a dual mode of action.
ano.nymous@ccsd.cnrs.fr.invalid (Robin Raveau) 11 Jul 2024
https://hal.inrae.fr/hal-04645630v1
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[hal-04728156] Préconiser et garantir : essai d'un protocole de traitement assurable pour la réduction des pesticides en viticulture
Une importante incertitude entoure l'état des menaces sanitaires en temps réel sur les productions végétales. Selon le rapport entre les coûts directs des traitements phytosanitaires et ceux associés aux pertes de rendement, une stratégie de minimisation des risques peut inclure des traitements inutiles, mais non connus comme tels au moment de la décision, entraînant des nuisances sanitaires et environnementales. Comment déterminer la part réelle de ces traitements inutiles, et soutenir la prise de risque économique directe de leur suppression ? Cet article consacré à la production viticole française, connue pour sa forte utilisation de fongicides, décrit l'expérimentation d'un protocole de traitement assurable sur quatre années, ayant permis une baisse des fongicides de 30 à 55 % entre 2019 et 2022, associé à un système incitatif de versement d'indemnités en cas de pertes, complétant le système actuel de couverture des risques climatiques.
ano.nymous@ccsd.cnrs.fr.invalid (Marc Raynal) 09 Oct 2024
https://hal.inrae.fr/hal-04728156v1
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[hal-05523426] Out-of-year parcel identification using adversarial domain adaptation and multi-temporal satellite imagery to enhance vineyard health monitoring
<div><p>Accurate monitoring of vineyard parcel status is essential for precision viticulture and phytosanitary risk management, particularly for detecting abandoned parcels that may act as disease reservoirs for pathogens such as Flavescence dorée. Conventional monitoring methods are limited by restricted spatial coverage and low temporal frequency, making satellite remote sensing a key alternative for large-scale vineyard monitoring. This study addresses the challenging task of out-of-year vineyard parcel classification, which requires models to generalize across years with varying environmental and climatic conditions.</p><p>We propose a deep learning framework based on conditional adversarial learning to address temporal domain adaptation in multi-year satellite data. The approach relies on freely available Sentinel-1 (radar) and Sentinel-2 (optical) imagery. The framework is evaluated through a real-world case study covering the Graves and Sauternes vineyards in western France. The dataset includes ground truth observations spanning five consecutive years (2020-2024), provided by the GDON du Sauternais et des Graves. Results</p><p>show that the proposed method outperforms standard approaches in handling temporal domain shifts, with weighted F1-score improvements exceeding 5 percentage points overall and more than 10 percentage points for minority class detection, despite class imbalance and interannual environmental variability.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Anna Roussel) 23 Feb 2026
https://hal.science/hal-05523426v1
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[hal-05697915] When machine learning extrapolates in space: How local data shape spatial transferability
Reliable spatial prediction requires assessing model behaviour under extrapolation, a setting in which standard validation schemes and performance metrics may be misleading due to spatial autocorrelation and limited environmental support. We study how validation design, environmental novelty, and data support jointly shape predictive performance in spatial risk modelling. Using plant health surveillance data on Xylella fastidiosa in France (2015-2023), we analyse a high-dimensional spatial prediction problem combining climatic, soil, and land-use predictors. We propose a spatially informed modelling framework integrating ensemble-based feature selection under environmental block cross-validation, a spatially weighted variant of XGBoost based on predictor-specific smoothing of spatially structured predictors, and explicit diagnostics of prediction support through the Area of Applicability, and compare it to a Bayesian hierarchical spatial logistic regression benchmark. Motivated by the east-west spread of Xylella fastidiosa, we introduce a spatial transfer evaluation scheme that assesses predictive performance in previously unobserved regions under progressive incorporation of local data. This scheme reveals a non-linear transition from extrapolative to interpolative prediction regimes governed by expansion of the applicability domain. Resulting gains in discrimination and calibration dominate over the more limited stabilizing effect of spatial smoothing near the extrapolation boundary. These results emphasize the need to interpret spatial predictions conditionally on their domain of applicability and highlight the role of validation and support diagnostics in spatial statistical modelling.
ano.nymous@ccsd.cnrs.fr.invalid (Camille Portes) 20 Jul 2026
https://hal.inrae.fr/hal-05697915v1
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[hal-04909885] Interspecies diversity in morphological responses of a panel of crop and weed species to water stress
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Quentin Cournault) 26 Feb 2025
https://hal.inrae.fr/hal-04909885v1
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[hal-05620798] Transcriptomic data and editing rate quantification of apple knock-out transgenic lines for a family of 17 amaranthin-like lectins
Apple amaranthin-like lectins (Malus domestica agglutinins; MdAGGs) are soluble proteins whose encoding genes are strongly upregulated by plant resistance inducers, such as acibenzolar-S-methyl (ASM), which provides broad-spectrum protection against apple pathogens, suggesting a potential role in plant defense. Here, three transgenic 'Gala' lines generated via CRISPR-Cas9-mediated editing of the 17 MdAGG genes are characterized. We report editing rates and RNA-sequencing-based quantification of transcript levels for each edited MdAGG following ASM treatment. Furthermore, the whole transcriptome of each transgenic line was compared to the wild type genotype to identify differentially expressed genes after elicitation. These datasets provide (1) insights into the variation in editing outcomes among MdAGG genes across transgenic lines and (2) a basis for assessing the transcriptomic consequences of editing an entire gene family within a plant genome
ano.nymous@ccsd.cnrs.fr.invalid (Axelle Frantz) 12 May 2026
https://hal.science/hal-05620798v1
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[hal-05549228] Inducible MdAGG lectins in apple immunity toward fire blight: CRISPR/Cas9 validation and their potential for intragenesis approaches
Fire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of genes effectively involved in resistance to E. amylovora have been identified. Seeking new resistance candidates, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as Malus domestica agglutinins (MdAGGs). When loss-offunction editions were introduced into MdAGG genes, the plant's ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora.
ano.nymous@ccsd.cnrs.fr.invalid (Antoine Bodelot) 12 Mar 2026
https://hal.inrae.fr/hal-05549228v1
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[hal-05690913] Biocontrol of grapevine downy mildew: A Synthetic Microbial Community (SynCom) approach
Culturomic approaches, involving the use of a range of different culture conditions coupled with a high-throughput method of identification, are recommended to isolate and identify microorganisms in environmental samples. In the case of plant samples, a number of studies have shown that microorganism cultivability can be increased by using plant-based culture media rather than conventional media that contain chemically synthesized or animalbased extracts. Being able to access this microbial biodiversity is crucial to the development of microbial biocontrol for plant diseases. Particularly in vineyards, where the majority of fungicide treatments target two major pathogens, the oomycete Plasmopara viticola that causes downy mildew and the fungus Erysiphe necator that causes powdery mildew, the development of new microbial biocontrol products is expected to reduce fungicide use. Tapping into the existing reservoir of naturally occurring disease biocontrol agents and growth-promoting microorganisms associated with grapevines is the first step to formulate effective biocontrol products and move towards more sustainable viticulture.<p>This study aimed to use a culturomic approach to build a collection of grapevine foliar microorganisms which can subsequently be used to assemble Synthetic Microbial Communities (SynComs) for biocontrol of downy mildew. Alongside three conventional culture media, we developed a grapevine leaf-based culture medium to cultivate epiphytic and endophytic bacteria, yeast and filamentous fungi. Overall, we isolated 1090 microorganisms, including 543 bacteria, 243 yeast/yeast-like fungi and 304 filamentous fungi. Using MALDI-TOF MS and Sanger sequencing, we were able to identify 88 % of the isolates with 91 total genera identified across the 4 culture media used. Using the grapevine leaf-based culture medium enabled the cultivation of 4 genera of bacteria, 1 yeast genus and 12 genera of filamentous fungi that were not seen on the other media. We proceeded to build a SynCom of 42 isolates, selecting candidates from the collection that were either known to be representative of the natural grapevine leaf microbiota or to have biocontrol activity against downy mildew or other plant diseases. In vitro confrontation tests on leaf discs revealed that the SynCom significantly reduced downy mildew symptoms. Over a hundred subsets of the whole SynCom were then tested against Plasmopara viticola to test hypotheses on the effect of community diversity and composition on leaf colonization as well as resistance to invasion by the pathogen. These findings could be useful in informing the design of eventual commercial multi-strain biocontrol products.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Aarti D Jaswa) 13 Jul 2026
https://hal.science/hal-05690913v1
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[tel-05113060] De la génomique des éléments transposables à la génétique quantitative des interactions sociales entre plantes cultivées : contributions et perspectives
Dans la première partie de cette HdR, je décris mon parcours en explicitant les éléments qui m’ont permis de développer mon programme de recherche actuel. En thèse de bioinformatique, je me suis intéressé à la quantification de l’abondance et de la diversité des éléments transposables en annotant des génomes séquencés. En post-doctorat de génétique humaine, j’ai étudié la régulation génétique de l’expression des gènes dans plusieurs tissus avec un modèle statistique multivarié. J’ai ensuite été recruté à INRAE pour mener des recherches sur l’architecture génétique de caractères d’intérêt chez la vigne et sur la prédiction génomique. A l’occasion d’une mobilité géographique, ma thématique a évolué vers la diversification intra-parcelle comme levier pour la transition agroécologique, sur laquelle je souhaite continuer à encadrer des doctorants. Dans le cas du blé, pris comme principale espèce d’étude, les variétés actuelles ont été sélectionnées en monoculture, mais elles sont plastiques lorsqu’elles sont co-cultivées dans des mélanges variétaux ou avec une légumineuse comme le pois. Je cherche à comprendre les bases génétiques de cette plasticité due aux interactions sociales entre plantes. En mobilisant de l’expérimentation au champ avec du phénotypage haut-débit, ainsi que de la modélisation, mes recherches visent à quantifier les (co)variances génétiques (i) du rendement en fin de cycle et (ii) des processus de production et d’allocation de biomasse au cours du cycle. Je propose aussi de coupler ces deux approches dans une perspective évolutive pour évaluer la capacité des schémas de sélection en mélange à explorer efficacement des paysages adaptatifs réalistes.
ano.nymous@ccsd.cnrs.fr.invalid (Timothée Flutre) 14 Jun 2025
https://hal.inrae.fr/tel-05113060v1
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[hal-03831436] The characterization of pathotypes in grapevine downy mildew provides insights into the breakdown of Rpv3, Rpv10 and Rpv12 factors in grapevines
We describe a standard method for characterizing the virulence profile of Plasmopara viticola, the causal agent of grapevine downy mildew. We used 33 European strains to inoculate six grapevine varieties carrying the principal factors for resistance to downy mildew (Rpv1; Rpv3.1; Rpv3.2; Rpv5, Rpv6; Rpv10 and Rpv12) and the susceptible Vitis vinifera cv. Chardonnay. For each interaction, we characterized the level of sporulation by image analysis and the intensity of the grapevine hypersensitive response by visual score. We propose a definition for the breakdown of grapevine quantitative resistances combining these two traits. Among the 33 strains analyzed, 29 are virulent on at least one resistance factor. We identified five different pathotypes across the 33 strains analyzed: two pathotypes overcoming a single resistance factor (vir3.1 and vir3.2) and three complex pathotypes overcoming multiple resistance factors (vir3.1-3.2; vir3.2-12; vir3.1-3.2-10). Our findings confirm the widespread occurrence of P. viticola strains overcoming the Rpv3 haplotypes (29 strains). We also detected the first breakdown of resistance to the Rpv10 by a strain from Germany and the breakdown of Rpv12 factors by a strain in Hungary. The pathotyping method proposed here and the associated differential host range lay the groundwork for the early detection of resistance breakdown in grapevines. This approach will also facilitate the monitoring of the evolution of P. viticola populations at large spatial scales. This is an essential step forward to promoting durable management of the resistant grapevine varieties currently available.
ano.nymous@ccsd.cnrs.fr.invalid (Manon Paineau) 10 Dec 2022
https://hal.science/hal-03831436v1
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[hal-05246134] Toward a molecular understanding of plant-plant interactions for agroecological control of fungal infections
Plants interact with neighboring plants through specialized metabolites released into the rhizosphere. These metabolites, known as allelochemicals, often trigger negative effects on surrounding plants, a phenomenon referred to as allelopathy. However, positive effects of these compounds are frequently observed but understudied. While the molecular mechanisms underlying allelopathy are well-documented, the molecular processes driving beneficial plant-plant interactions remain poorly understood. Our research presents unpublished data demonstrating how a major class of maize root-exuded allelochemicals reduces disease severity in neighboring rice plants through a chromatin-based regulatory mechanism in rice roots. This discovery sheds light on positive plant interactions at a molecular level. In addition to these findings, positive interactions in intraspecific plant mixtures, particularly in crops like hexaploid wheat, are common, yet the molecular mechanisms behind them are largely unknown. Using a multidisciplinary approach that integrates forward genetics, metabolomics, transcriptomics, and reverse genetics, we aim to identify the genes and molecular pathways that govern beneficial plant-plant interactions. Specifically, we focus on mechanisms that reduce disease severity caused by key pathogens in wheat. Our long-term goal is to understand how plants recognize and respond to their intraspecific neighbors, with the potential to develop novel biosolutions and optimize crop mixtures for agroecological farming systems.
ano.nymous@ccsd.cnrs.fr.invalid (Louis-Valentin Méteignier) 30 Sep 2025
https://hal.science/hal-05246134v1
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[hal-04948208] Deep-learning-ready RGB-depth images of seedling development
In the era of machine learning-driven plant imaging, the production of annotated datasets is a very important contribution. In this data paper, a unique annotated dataset of seedling emergence kinetics is proposed. It is composed of almost 70,000 RGB-depth frames and more than 700,000 plant annotations. The dataset is shown valuable for training deep learning models and performing high-throughput phenotyping by imaging. The ability of such models to generalize to several species and outperform the state-of-the-art owing to the delivered dataset is demonstrated. We also discuss how this dataset raises new questions in plant phenotyping.
ano.nymous@ccsd.cnrs.fr.invalid (Félix Mercier) 14 Feb 2025
https://hal.science/hal-04948208v1
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[hal-05674919] Conservation auctions: An online double constraint reverse auction experiment
Conservation auctions are designed to allocate payments for environmental services to voluntary farmers. The auctioneer may announce either the maximum number of contracts (target-constrained auction) or, more commonly, the total budget available (budget-constrained auction). Building on previous work that compared these two formats, we introduce a new double-constraint auction, where both constraints—set at the same levels as in the benchmarks—are simultaneously disclosed to participants. Using the same experimental methodology, we assess performance consistent with a generic policy objective: maximizing environmental benefits while minimizing expenditures. On average, the double-constraint auction outperforms both target- and budget-constrained formats.
ano.nymous@ccsd.cnrs.fr.invalid (Adrien Coiffard) 30 Jun 2026
https://hal.science/hal-05674919v1
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[hal-05673287] Challenges in LAMP-based detection of Fusarium spp. responsible for dry rot in garlic
Fusarium dry rot disease (FDR) is an emerging disease worldwide mainly caused by Fusarium proliferatum (Fp) but also by F. oxysporum (Fox). It renders garlic cloves unfit for consumption. Fp and Fox are often present in cloves as an endophyte making it difficult to evaluate garlic health status and to forecast symptoms appearance. To date, there is no simple, rapid test for the detection of Fp and Fox that can be used in the field and help growers to improve garlic production, especially through the management of asymptomatic cloves. This study assesses the challenge of detecting Fp (the main causal agent of FDR) directly on garlic cloves, with Loop mediated isothermal technology (LAMP), and results visualized using turbidity or Phenol-red. We used primers originally designed for Fp strains of maize, tested them on garlic tissues with DNA and mycelium, with and without a prior DNA isolation step. The LAMP assay combined with a prior DNA isolation step using FTA Card, produced the best results. These results obtained from the previously inoculated garlic were consistent with the observed symptoms on garlic and mycelium growth on agar. Sensitivity was variable among strains, ranging from 1 to 50 μg μL -1 per LAMP for mycelium. The LAMP assay was not entirely specific to Fp as several Fox strains were also amplified. Overall, this study shows that a simple FTA Card DNA extraction step is useful for the field detection of Fusarium spp. strains responsible of FDR on garlic. Methods to improve the specificity of the developed LAMP assay to detect only Fp strains are discussed.
ano.nymous@ccsd.cnrs.fr.invalid (Caroline Guilbaud) 29 Jun 2026
https://hal.inrae.fr/hal-05673287v1
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[hal-05249700] Genome-wide association study of frost tolerance in Vicia faba reveals syntenic loci in cool-season legumes and highlights relevant candidate genes
Abstract Cool-season grain legumes are mostly grown over spring and summer due to poor frost tolerance. However, fall-sown varieties often provide higher yields, earlier harvests and avoid late-season drought and heat. Understanding the genetic determinism and molecular basis of frost tolerance is therefore crucial for developing high-performing winter varieties. This study aimed to (1) investigate the genetic architecture of frost tolerance in Vicia faba L. using 247 accessions phenotyped under four field environments, and (2) explore the conservation of frost tolerance loci in cool-season legumes using the OrthoLegKB translational research database. A genome-wide association study identified nineteen V. faba genomic regions with a high density of markers significantly associated with frost tolerance, on all chromosomes. Mapping of frost tolerance QTL from V. faba and related species obtained from the literature onto their respective reference genomes and their integration into OrthoLegKB revealed synteny of major QTL across V. faba , Pisum sativum , and/or Medicago truncatula , particularly near clusters of CBF/DREB1 genes. Frost tolerance QTL at the P. sativum Le locus, which controls internode length, were also syntenic with a frost tolerance QTL in V. faba . Synteny between frost tolerance QTL and those controlling phenology and physiology was found at other loci, suggesting pleiotropy. Finally, expression data from P. sativum and C. arietinum accessions grown under low temperature were considered as information source to highlight potential candidate genes underlying the conserved QTL. Overall, these results provide a valuable resource for understanding and improving frost tolerance in V. faba and other cool-season legumes, including orphan crops by knowledge transfer. The use of OrthoLegKB to explore the genetic and molecular determinism of target traits across species is worth generalising.
ano.nymous@ccsd.cnrs.fr.invalid (Baptiste Imbert) 11 Sep 2025
https://hal.inrae.fr/hal-05249700v1
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[hal-04650172] Integrative genetics and genomics for multi-pest resistance in grain legumes
Grain legumes are major key players of the agro-ecological and food transitions due to their nitrogen-fixing and diversifying qualities in cropping systems and their protein-rich seeds. However, grain legumes are susceptible to multiple diseases and pests, generating high crop yield instabilities. Aphanomyces root rot, Ascochyta blight, and seed weevils have been the most damaging and studied stresses in France over the past 20 years. Other pests, including weeds, aphids and sitona, are currently becoming problematic for grain legumes in the light of new regulations on pesticide use. Breeding varieties for multi-pest resistance is a major challenge for grain legume development. A major objective of the French national SPECIFICS (2021-2027) project is to generate and integrate knowledge on the diversity, genetics, genomics and mechanisms of resistance to multiple pests and protective traits in grain legumes. A Grin-Global database is deployed to manage the pea and faba bean INRAE genetic resources. Automated or manual phenotyping of exome sequenced pea or faba bean collections is performed for seedling emergence, response to water deficit, plant root and nodule architecture and aphid resistance. A NoSQL graph database is developed to integrate QTL, RNASeq and gene annotation data in five legume species. The data base will connect data obtained in the project or previously for resistance to diseases and pests (A. euteiches, D. pinodes, Bruchus spp., A. pisum and A. fabae), seedling establishment and pest or disease-related root/aerial architectural traits to identify putative pleiotropic or syntenic genes. Pea mutant lines in susceptibility genes conserved from other plant species and speed breeding introgression lines are produced to identify and combine genes and loci for multi-pest resistance. Results will provide new knowledge and tools to accelerate breeding of grain legume varieties for pesticide-free cropping systems.
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Laure Pilet-Nayel) 16 Jul 2024
https://hal.inrae.fr/hal-04650172v1
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[hal-04457516] SeptoSympto: a precise image analysis of Septoria tritici blotch disease symptoms using deep learning methods on scanned images
Background Investigations on plant-pathogen interactions require quantitative, accurate, and rapid phenotyping of crop diseases. However, visual assessment of disease symptoms is preferred over available numerical tools due to transferability challenges. These assessments are laborious, time-consuming, require expertise, and are rater dependent. More recently, deep learning has produced interesting results for evaluating plant diseases. Nevertheless, it has yet to be used to quantify the severity of Septoria tritici blotch (STB) caused by Zymoseptoria tritici —a frequently occurring and damaging disease on wheat crops. Results We developed an image analysis script in Python, called SeptoSympto. This script uses deep learning models based on the U-Net and YOLO architectures to quantify necrosis and pycnidia on detached, flattened and scanned leaves of wheat seedlings. Datasets of different sizes (containing 50, 100, 200, and 300 leaves) were annotated to train Convolutional Neural Networks models. Five different datasets were tested to develop a robust tool for the accurate analysis of STB symptoms and facilitate its transferability. The results show that (i) the amount of annotated data does not influence the performances of models, (ii) the outputs of SeptoSympto are highly correlated with those of the experts, with a similar magnitude to the correlations between experts, and (iii) the accuracy of SeptoSympto allows precise and rapid quantification of necrosis and pycnidia on both durum and bread wheat leaves inoculated with different strains of the pathogen, scanned with different scanners and grown under different conditions. Conclusions SeptoSympto takes the same amount of time as a visual assessment to evaluate STB symptoms. However, unlike visual assessments, it allows for data to be stored and evaluated by experts and non-experts in a more accurate and unbiased manner. The methods used in SeptoSympto make it a transferable, highly accurate, computationally inexpensive, easy-to-use, and adaptable tool. This study demonstrates the potential of using deep learning to assess complex plant disease symptoms such as STB.
ano.nymous@ccsd.cnrs.fr.invalid (Laura Mathieu) 20 Feb 2024
https://hal.inrae.fr/hal-04457516v1
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[hal-05222729] Early root-root interactions weaken foliar defense responses against Septoria tritici blotch in a durum wheat varietal mixture
The interactions between co-cultivated plant cultivars are increasingly recognized as influencing their susceptibility to pathogens in mixtures. However, the underlying mechanisms remain largely unexplored. Using a model of durum wheat cultivar mixtures where susceptibility to Septoria foliar disease is increased, we combined aerial and root phenotyping with transcriptional analyses and untargeted metabolomics to elucidate the potential signaling cascade driving this modulation of susceptibility. We observed contrasting root architectures between cultivars in mixture. Molecular analysis showed a delayed induction of defense-related genes and metabolites following pathogen inoculation in plants grown in mixture compared to pure stand. The findings suggest that root architecture potentially triggers a competitive response that could delay the induction of defense responses following pathogen inoculation. Altogether, these results point to a possible interplay between root architecture, resource competition, plant metabolism, and defense modulation in shaping plant–pathogen interactions within varietal mixtures.
ano.nymous@ccsd.cnrs.fr.invalid (Laura Mathieu) 18 Feb 2026
https://hal.science/hal-05222729v2
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[hal-05382183] Welcome Pathogens: Transient Heat Dampens Immune Responses to Acibenzolar‐ <i>S</i> ‐Methyl in Apple Plants
Climate change affects plant-pathogen interactions, with disease outcome varying depending on the pathosystem and environmental scenario. In Arabidopsis, a thermo-sensitive module of salicylic acid (SA) signalling makes immunity vulnerable to heat. The potent resistance inducer acibenzolar-S-methyl (ASM), an SA analogue that up-regulates transcription of defence genes, could restore plant protection under heat but not core SA signalling. Here, we investigated how high temperature rewires the ASM-induced responses of the apple immune system. We treated apple plants with ASM under contrasting heatwave scenarios and subsequently exposed them to Erwinia amylovora (the fire blight bacterium) or Venturia inaequalis (the apple scab fungus) while monitoring gene expression. While pre-exposing apple plants to high temperature did not change their susceptibility to pathogens, it drove a loss of ASM-induced protection. Transcriptomic analysis revealed broad dampening of ASM-regulation upon high temperature, for a wide range of biological processes beyond defence. We uncovered thermosensitive 'resistance' and 'susceptibility' marker genes with ASM-responsiveness being critically vulnerable to heat. We concluded that exposure to heatwaves prevents ASM from fully mounting its protective responses in apple, not only lowering defences but also offering more favourable hosting conditions. Our work highlights plant immunity as the joint outcome of resistant and susceptible responses. <div>| Introduction<p>Climate change modifies the many interactions between plants and pathogens. The 'disease triangle' framework posits that successful disease establishment requires a virulent pathogen, a susceptible host plant and favourable environmental conditions (Stevens 1960; Velásquez et al. 2018; Roussin-Léveillée et al. 2024). Changes in temperature, radiation, relative humidity (RH), soil water content and atmospheric CO 2 concentration may all affect the physiology and development of plants and pathogens, either directly or through their mutual interaction. For instance, temperature elevation has profound effects on plants, triggering</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Erwan Chavonet) 25 Nov 2025
https://institut-agro-rennes-angers.hal.science/hal-05382183v1
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[hal-05661572] Sequential area interaction sampling for early plant disease detection
We develop general novel sequential point process models for plant disease surveillance, aiming to accelerate early detection of disease presence in a study domain. The framework adapts to the level of knowledge about the propagation parameters: with full information, it reduces to a sequential hard-core process, whereas under uncertainty it becomes a sequential area-interaction process. By incorporating past observations at each step, the proposed models optimize detection time in an adaptive setting. The dynamics of the proposed sequential point process models are analyzed, compared to alternative sampling strategies through a simulation study, and illustrated in a real surveillance context.
ano.nymous@ccsd.cnrs.fr.invalid (François d'Alayer) 18 Jun 2026
https://hal.inrae.fr/hal-05661572v1
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[hal-04163681] Improving Weed Management Based on the Timing of Emergence Peaks: A Case Study of Problematic Weeds in Northeast USA
We reviewed the timing of the peak rate of emergence for 15 problematic weed species as well as ways to use this knowledge to improve control. Much of the previous literature modeled emergence based on growing-degree-days. For these models, we input average temperature data from several zones of Northeast USA. Within species, model-predicted peak emergence in the warmest and coolest zones differed by an average of 39 days. Also within species, there was some variation between models, likely reflecting different conditions in study locations and population-level differences that will need to be addressed in future modelling efforts. Summarizing both observed and modelled results, emergence typically peaked early-season for barnyardgrass, Canada thistle, common lambsquarters, common ragweed, giant foxtail, large crabgrass, perennial sowthistle, and smooth crabgrass. Emergence typically peaked mid-season for hairy galinsoga, mouseear chickweed, and red sorrel. Emergence typically peaked late-season for annual bluegrass. Several species emerged in a protracted manner, including common chickweed, quackgrass, and redroot pigweed. With this improved knowledge, farmers may target key problematic species of a particular field in several ways. Weed seedling control efforts can be timed at the highest densities or most vulnerable phenological stage. Residual herbicides and suppressive mulches can be timed to maximize effectiveness prior to their breakdown. And if management flexibility allows, crop selection and associated planting dates may be adjusted to improve crop competition or facilitate seedbank depletion through timely bare fallow periods. Such improvements to weed management based on timing of emergence will likely become even more impactful as predictive model reliability continues to improve.
ano.nymous@ccsd.cnrs.fr.invalid (Bryan Brown) 17 Jul 2023
https://hal.inrae.fr/hal-04163681v1
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[hal-05372415] Adapter la densité de semis à la date de semis des couverts pour maximiser la biomasse à destruction : Vesce velue
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ano.nymous@ccsd.cnrs.fr.invalid (Cordeau, S.) 19 Nov 2025
https://hal.inrae.fr/hal-05372415v1
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[hal-05296080] Integrating sheep into vineyards: diversity of farmers' agronomic logics and trajectories
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ano.nymous@ccsd.cnrs.fr.invalid (Elsa Robelot) 03 Oct 2025
https://hal.inrae.fr/hal-05296080v1
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[hal-05100639] Opportunities and Challenges in Combining Optical Sensing and Epidemiological Modelling
Plant diseases impair yield and quality of crops and threaten the health of natural plant communities. Epidemiological models can predict disease and inform management. However, data are scarce, since traditional methods to measure plant diseases are resource intensive and this often limits model performance. Optical sensing offers a methodology to acquire detailed data on plant diseases across various spatial and temporal scales. Key technologies include multispectral, hyperspectral and thermal imaging, and light detection and ranging; the associated sensors can be installed on ground-based platforms, uncrewed aerial vehicles, aeroplanes and satellites. However, despite enormous potential for synergy, optical sensing and epidemiological modelling have rarely been integrated. To address this gap, we first review the state-of-the-art to develop a common language accessible to both research communities. We then explore the opportunities and challenges in combining optical sensing with epidemiological modelling. We discuss how optical sensing can inform epidemiological modelling by improving model selection and parameterisation and providing accurate maps of host plants. Epidemiological modelling can inform optical sensing by boosting measurement accuracy, improving data interpretation and optimising sensor deployment. We consider outstanding challenges in: A) identifying particular diseases; B) data availability, quality and resolution, C) linking optical sensing and epidemiological modelling, and D) emerging diseases. We conclude with recommendations to motivate and shape research and practice in both fields. Among other suggestions, we propose to standardise methods and protocols for optical sensing of plant health and develop open access databases including both optical sensing data and epidemiological models to foster cross-disciplinary work.
ano.nymous@ccsd.cnrs.fr.invalid (Alexey Mikaberidze) 18 Jun 2025
https://hal.science/hal-05100639v1
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[hal-05591524] LifeCLEF 2026 Teaser: AI Challenges for Biodiversity Understanding and Ecosystem Management
AI is increasingly central to understanding and managing biodiversity and ecosystems. Since 2011, the LifeCLEF lab has provided large-scale benchmarks that stimulate progress in multimodal species recognition, ecological prediction, and knowledge extraction. The 2026 edition expands this scope with five complementary challenges spanning visual, acoustic, and textual data: (i) AnimalCLEF: discovery and re-identification of individual animals, (ii) BirdCLEF+: multi-taxonomic species recognition in complex soundscapes, (iii) MarineCLEF: detection of marine species in underwater imagery under positive-unlabeled constraints, (iv) PestCLEF: extraction of information on plant pests from heterogeneous textual sources, (v) PlantCLEF: multi-species plant identification in quadrat images. Together, these challenges address critical dimensions of biodiversity science and ecosystem management, while fostering collaboration between AI researchers, ecologists, and practitioners. This paper provides an overview of the LifeCLEF 2026 lab and its tasks, outlining their motivation, data, and evaluation methodology to guide participants and inform the wider research community.
ano.nymous@ccsd.cnrs.fr.invalid (Alexis Joly) 14 Apr 2026
https://hal.inrae.fr/hal-05591524v1
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[hal-04520388] Equilibrium bids for reverse auctions when the budget is announced - Some preliminary results
We consider a budget-constrained reverse auction: offers are accepted until some predefined budget is exhausted. Payments are discriminatory: bidders receive their own bid as payment when they win the bid. Bidders have a private value for their item which is uniformly distributed between 0 and 1; they are risk-neutral and items are indivisible. For small budget and an arbitrary number of bidders, as well as in the case of two bidders, we find an equilibrium bidding function. When possible, we compare with the equilibrium bidding function of target-constrained reverse auctions.
ano.nymous@ccsd.cnrs.fr.invalid (Alain Jean-Marie) 26 Mar 2024
https://inria.hal.science/hal-04520388v1
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[hal-05249655] Promotion of Translational Research in Plants by the Development of a Knowledge Graph Framework: A case Study on Grain Legumes
With global population growth, climate change and evolving regulations on the use of pesticides herbicides, researchers and breeders must adapt and accelerate crop improvement to meet the challenges ahead. Major crops have benefited from genomic efforts, which have enabled the identification of key genetic drivers that can be rapidly implemented to ensure food security. Thanks to translational research, less studied crops, including some legumes, can benefit from both the wealth of research and, in particular, the knowledge available from closely related crops or species. This requires the correct identification of functional orthologs, the retrieval of available data and knowledge, and the linking of diverse heterogeneous data, which becomes more difficult as the number of species increases. To facilitate this process of translational research, we have developed two pipelines, namely the structural and the functional pipeline, to create a framework for a NoSQL graph database (Neo4j) to integrate and query heterogeneous data from multiple species. The structural pipeline identifies orthologous genes and syntenic chromosomal regions to highlight functional orthologs that serve as bridges between species for knowledge transfer. The functional pipeline integrates published and unpublished biological information, including quantitative trait loci (QTL) and RNA-seq datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. The constructed graph, called Ortho_KB and its instance for legumes OrthoLegKB, can be queried to make quasi-instantaneous use of the included datasets. This platform can be useful, for example, for comparing current knowledge on complex genetic traits, checking the conservation of genes of interest within QTL intervals, crossing information on gene expression profiles or suggesting pleiotropy.
ano.nymous@ccsd.cnrs.fr.invalid (Baptiste Imbert) 11 Sep 2025
https://hal.inrae.fr/hal-05249655v1
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[hal-04145269] A workflow for processing global datasets: application to intercropping
Field experiments are a key source of data and knowledge in agricultural research. An emerging practice is to compile the measurements and results of these experiments (rather than the results of publications, as in meta-analysis) into global datasets. Our aim in the present study was to provide several methodological paths related to the design of global datasets. We considered 37 field experiments as the use case for designing a global dataset and illustrated how tidying and disseminating the data are the first steps towards open science practices. We developed a method to identify complete factorial designs within global datasets using tools from graph theory. We discuss the position of global datasets in the continuum between data and knowledge, compared to other approaches such as meta-analysis. We advocate using global datasets more widely in agricultural research.
ano.nymous@ccsd.cnrs.fr.invalid (Rémi Mahmoud) 27 Mar 2024
https://hal.inrae.fr/hal-04145269v4
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[hal-05627550] Intercropping chickpea with a competitive service plant and mowing the inter-rows controls weeds and ascochyta blight while mitigating interspecific competition
Chickpea (Cicer arietinum L.) is a promising crop for adapting to climate change and reducing the reliance of cropping systems on synthetic N fertilizers. However, its yield is highly variable, mainly due to weed competition and ascochyta blight (Ascochyta rabiei). Hence, this study investigated the effects of intercropping chickpea with a mowed service plant to control both weeds and ascochyta blight, while mitigating competition to minimise yield reductions. In a two-year field experiment in Western France, chickpea was grown as sole crop and intercropped with four single service plants (Egyptian clover, faba bean, oat, and Sudan grass) in alternate rows. These species were chosen for their contrasted traits, allowing to create different levels of interspecific competition. Chickpea’s inter-rows were either mowed at the beginning of flowering or left without mechanical regulation. Introducing oat decreased weed biomass in both years. Under high weed and disease pressures, adding unmowed oat reduced both weed biomass and ascochyta blight severity by 66% and 56% compared to the unmowed sole chickpea, respectively. No differences were found between the sole chickpea and the other intercrops. Unlike the other species, oat had a high biomass production early in the crop cycle, which partly explains its weed-suppression effect. However, adding oat reduced chickpea grain yield in 2023 by 72%, although mowing limited this reduction to 48%. This study highlights that intercropping chickpea with a mowed competitive service plant that generates an aerated canopy, like oat, can help to control both weeds and ascochyta blight, while mitigating interspecific competition.
ano.nymous@ccsd.cnrs.fr.invalid (Margaux Guy) 20 May 2026
https://hal.science/hal-05627550v1
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[hal-04263759] Comparing input interfaces to elicit belief distributions
This paper introduces a new software interface to elicit belief distributions of any shape: Click-and-Drag . The interface was tested against the state of the art in the experimental literature—a text-based interface and multiple sliders—and in the online forecasting industry—a distribution-manipulation interface similar to the one used by the most popular crowd-forecasting website. By means of a pre-registered experiment on Amazon Mechanical Turk, quantitative data on the accuracy of reported beliefs in a series of induced-value scenarios varying by granularity, shape, and time constraints, as well as subjective data on user experience were collected. Click-and-Drag outperformed all other interfaces by accuracy and speed, and was self-reported as being more intuitive and less frustrating, confirming the pre-registered hypothesis. Aside of the pre-registered results, Click-and-Drag generated the least drop-out rate from the task, and scored best in a sentiment analysis of an open-ended general question. Further, the interface was used to collect homegrown predictions on temperature in New York City in 2022 and 2042. Click-and-Drag elicited distributions were smoother with less idiosyncratic spikes. Free and open source, ready to use oTree, Qualtrics and Limesurvey plugins for Click-and-Drag, and all other tested interfaces are available at https://beliefelicitation.github.io/ .
ano.nymous@ccsd.cnrs.fr.invalid (Paolo Crosetto) 11 Oct 2024
https://hal.science/hal-04263759v1
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[hal-05671803] Social Learning to Reduce Pesticides: Evidence from a French Agricultural Extension Programme
Social learning is likely to play a crucial role in disseminating new agricultural technologies and driving the agroecological transition in European countries. We evaluated a French pesticide reduction programme designed to train farmers and promote practices through demonstration days on participating farms. Using pseudo-panel data from surveys conducted before and after the programme’s launch, we found evidence of decreased pesticide use among cohorts linked to farms attending demonstration days. Our analysis, supported by a placebo test and various robustness checks, suggests that peer-sharing in training programmes can scale up effectively at no additional cost.
ano.nymous@ccsd.cnrs.fr.invalid (Rose Deperrois) 27 Jun 2026
https://hal.science/hal-05671803v1
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[hal-05671801] Early Adopters and the Diffusion of Agroecological Knowledge in Peer Groups
Peer-to-peer knowledge diffusion is increasingly recognized as a key mechanism in various economic contexts and may play a crucial role in fostering the adoption of agroecological practices among farmers. However, the conditions for effective peer learning remain poorly understood, particularly regarding the role of the injection point -- the first individual to receive information -- within a peer group. This study examines whether the profile of the injection point affects the diffusion of agroecological knowledge. We conduct a randomized controlled trial (RCT) with roughly 850 voluntary French farmers, randomly assigned to peer groups on a digital communication platform. Over an 18-month period, only one farmer per treated group receives information on agroecology, serving as the injection point for diffusion. Treatment varies according to whether the injection point is an early adopter of agroecology or an ordinary peer. A benchmark group receives direct broadcasting of the information to all members. The experiment began in January 2025 and will run until June 2026, with data collection ongoing.
ano.nymous@ccsd.cnrs.fr.invalid (Rose Deperrois) 27 Jun 2026
https://hal.science/hal-05671801v1
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[hal-04848563] Tailored policies for perennial woody crops are crucial to advance sustainable development
Perennial woody crops, which are crucial to our diets and global economies, have the potential to play a major role in achieving multiple UN Sustainable Development Goals pertaining to biodiversity conservation, socio-economic development and climate change mitigation. However, this potential is hindered by insufficient scientific and policy attention on perennial woody crops, and by the intensification of perennial crop cultivation in the form of monocropping with high external inputs. In this Perspective, we highlight the potential of properly managed and incentivized perennial woody crops to support holistic sustainable development and urge scientists and policymakers to develop an effective agenda to better harness their benefits.
ano.nymous@ccsd.cnrs.fr.invalid (Carlos Martinez-Nuñez) 19 Dec 2024
https://hal.science/hal-04848563v1
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[hal-03834661] Single seed microbiota: assembly and transmission from parent plant to seedling
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 05 Sep 2024
https://hal.inrae.fr/hal-03834661v1
