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[hal-05655335] The Value of Seed Quality Certification in Integrated Supply Chains
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655335v1
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[hal-05655305] Seed mixtures development and their impact on farmers' surplus.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655305v1
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[hal-05655317] The Value and Quality of Private Labels on the Agricultural Seed Mixtures Market. A Mixed Method Approach
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ano.nymous@ccsd.cnrs.fr.invalid (Benaissa Larbi) 12 Jun 2026
https://hal.science/hal-05655317v1
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[hal-05648843] 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.</p><p>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) 08 Jun 2026
https://hal.inrae.fr/hal-05648843v1
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[hal-05261877] Empowering systemic change at a territory scale: a collective learning experiment with stakeholders along the agrifood chain in the Pilat, France
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ano.nymous@ccsd.cnrs.fr.invalid (Anna Hirson-Sagalyn) 15 Sep 2025
https://hal.inrae.fr/hal-05261877v1
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[hal-05564088] Combining wheat with multi-species prairie strips reduces the development of Septoria tritici blotch
Crop diversification, notably through intercropping, is known for regulating disease development in agroecosystems. However, intercropping usually involves two or three species, limiting its potential to enhance ecosystem multifunctionality. This study investigates the impact of “agroprairies”, a cropping system design consisting of alternating narrow strips of wheat and multispecies prairies (∼12 species), on the development of Zymoseptoria tritici, the causal agent of Septoria tritici blotch (STB), a major foliar disease in wheat. Two complementary field experiments were conducted. The first one monitored the incidence and severity of STB under natural epidemic conditions across combinations of four wheat cultivars and four prairie mixtures with contrasted functional traits. The second experiment used above-canopy inoculation on a subset of treatments to assess disease dynamics under high disease pressure, independent of physical barrier effects. Rhizosphere microbiomes were analyzed before inoculation to evaluate enrichment in taxa associated with plant defense and disease suppression. Under natural conditions, STB incidence and severity were reduced by 52% and 41% in two agroprairie types compared to monocrop. Prairie biomass and specific leaf area (SLA) were identified as key factors associated with this reduction. When the disease was inoculated above the canopy, this reduction effect disappeared, highlighting the dominant role of physical barriers in disease regulation. However, one agroprairie treatment still reduced disease progression by 18%, suggesting the involvement of additional regulatory mechanisms. Microbiome analysis revealed shifts in bacterial beta diversity and an enrichment of potentially beneficial taxa in the wheat rhizosphere, although no direct link with disease regulation was established.
ano.nymous@ccsd.cnrs.fr.invalid (Lisa Besson) 31 Mar 2026
https://isara.hal.science/hal-05564088v1
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[hal-04344007] Plant–soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems
Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant–soil and plant–plant interactions, eco‐physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature‐based practices allowing for site‐specific modifications. This new synthetized knowledge should help practitioners to improve the long‐term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.
ano.nymous@ccsd.cnrs.fr.invalid (Sébastien Fontaine) 14 Dec 2023
https://isara.hal.science/hal-04344007v2
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[hal-05458576] Valoriser la production fruitière écologique du Pilat un projet de recherche-action
Ces travaux décrivent les démarches de co-conception d'un territoire de production fruitière, visant à valoriser le caractère écologique de la production fruitière, permettant de bien rémunérer les agriculteurs et de leur offrir des bonnes conditions de travail tout en favorisant les biodiversité et préservant les ressources naturelles et en participant à la sécurité alimentaire des bassins de vie.
ano.nymous@ccsd.cnrs.fr.invalid (Muriel Valantin-Morison) 14 Jan 2026
https://hal.science/hal-05458576v1
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[hal-04583002] Une arboriculture sans produits phytosanitaires de synthèse dans le Pilat, verrouillages et perspectives de transformation
Une production dynamique de pommes qualitatives s’est développée au sein du Parc Naturel Régional du Pilat grâce aux conditions pédoclimatiques favorables et à l'ingéniosité des producteurs locaux, mais également à l'utilisation de produits phytosanitaires de synthèse. Nous avons conduit un diagnostic sociotechnique en enquêtant une diversité d’acteurs de la filière afin d’identifier les processus de verrouillage pouvant expliquer la difficulté des systèmes arboricoles de se passer de produits phytosanitaires de synthèse. Nous avons caractérisé un système sociotechnique organisé autour d’une coopérative agricole commercialisant des pommes à la grande distribution et au marché de gros, ainsi que des dynamiques de niche. Ces éléments, et leurs interconnections, nous permettent d’identifier de possibles trajectoires de transitions sociotechniques vers une arboriculture sans produits phytosanitaires de synthèse.
ano.nymous@ccsd.cnrs.fr.invalid (Anna Hirson-Sagalyn) 22 May 2024
https://hal.inrae.fr/hal-04583002v1
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[hal-05319034] Unveiling the effects of diversified prairies on wheat nutrition, phenology and growth in strip intercropping
<div><p>Crop diversification is a promising strategy to improve agroecosystem sustainability in terms of plant nutrition and production, but it is frequently too restricted to reach its full potential. Insufficient diversity prevents agroecosystems from using nitrogen (N) efficiently enough to maintain enough yield without strongly relying on external inputs that are damaging to the environment. We advocate that combining annual crops like winter wheat with perennial and diversified prairies would be a major step toward enhancing cereal system sustainability, by promoting plant-soil interactions that improve long-term plant nutrition and growth. Yet, managing highly diversified agroecosystems requires a better understanding of complex and dynamic plant-plant interactions that can either boost or hinder crop development. We conducted a field experiment in which we associated four varieties of wheat with four functionally different prairies, in fine scale strips intercropping systems called "agroprairies". We assessed the effects of prairie strips on wheat nutrition, phenology, and growth under two N-fertilization conditions, with a focus on the influence of prairie functional traits.</p><p>The analysis of the interactions between prairie functional trait syndromes, N fertilization, and wheat varieties uncovered key parameters that favor beneficial outcomes. Notably, we showed that plant resource-acquisitive trait syndrome known to shape N release from soil resources and a higher proportion of legumes in prairie strips significantly improved wheat nutrition, earliness, growth and biomass production. Our study reveals an existing avenue for developing cropping systems that incorporate high species richness, with synergistic benefits based on the mobilization of N from the soil and the atmosphere.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Bécu) 17 Oct 2025
https://hal.science/hal-05319034v1
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[hal-05587920] Pesticide-free fields under minimum tillage and flower strips enhance carabid beetles and spiders through increased overwintering and spill over processes
Enhancing generalist arthropod predators in arable farming can contribute to pest control and pesticide use reduction, and be achieved through a diversity of management options at field and farm scales. Most studies however link management options to densities of circulating adults, which gives little insight into potential source-sinks dynamics and the occurrence of ‘source’ habitats enabling overwintering. In this study, we assessed the assemblages of emerging and circulating ground-dwelling carabids and spiders during four months in a continuous mosaic of pesticide-free winter-sown crops under contrasted tillage regimes (minimum vs. conventional tillage) and sown flower strips bordering fields. We detected clear patterns, with high in-field carabid and spider overwintering densities than in adjacent flower strips, which were rarely a preferred overwintering habitat. Our results nevertheless indicate that within both taxa, different species exhibit different responses and source-sink dynamics. Our results also demonstrate the key role of pesticide-free fields under minimum tillage, acting both as a high-quality overwintering site for some dominant carabid species and as a source habitat, as several predator species activity-density responded positively to the increased area of minimum tillage fields in the surroundings. We detected a comparable positive effect of the area of flower strips in the surrounding for some species, suggesting that these linear features could also act as a temporary refuge and source. These findings highlight that sustaining diverse communities of carabid beetles and spiders probably requires adopting several and complementary management options and that in-field farming practice represent a powerful lever to foster natural enemies populations.
ano.nymous@ccsd.cnrs.fr.invalid (Paul Bannwart) 11 Jun 2026
https://hal.inrae.fr/hal-05587920v1
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[hal-05265454] GWASpipe: a Nexflow pipeline for GWAS analyses incorporating quality control
Genome-wide association studies (GWAS) are powerful tools to link genetic variants with phenotypic traits. However, running GWAS involves several complex steps, including VCF preprocessing, quality control, population structure and relatedness correction, and selecting the right statistical models. We developed GWASpipe, an easy-to-use and automated pipeline to make GWAS more accessible, especially for non-expert users. GWASpipe is built with Nextflow[1] and follows nf-core standards. All tools are packaged in Singularity containers, ensuring reproducibility and easy deployment on any computing system. The pipeline includes :Data quality control, Filtering of low-quality variants and individuals, Population structure analysis, Kinship calculation, Association testing using two R packages (MM4LMM[2] et GAPIT[3] )
ano.nymous@ccsd.cnrs.fr.invalid (Sophia Marguerit) 17 Sep 2025
https://hal.inrae.fr/hal-05265454v1
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[hal-04827822] Quantitative assessment and spatial distribution of Plasmopara viticola oospores in vineyard soil
Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. While primary inoculum plays a decisive role in disease epidemics, we still know very little about the abundance and the distribution of oospores, which are the overwintering forms of the pathogen resulting from sexual reproduction. In this study, we used ddPCR to describe the spatial distribution of P. viticola inoculum in a vineyard soil at the onset of the growing season. We found P. viticola oospores in all soil samples except one. The distribution of primary inoculum at the field scale was not random but characterized by 25 m-diameter patches of concentrically increasing oospore concentration. There was a positive coregionalization between soil inoculum and soil moisture spatial distributions, possibly mediated by disease incidence. The results indicated that oospores accumulated 5 times more in the ridge of soil below the vine stocks than in the inter-row. We conducted a leaf disc bioassay to assess soil infectious potential on a subset of samples collected in the field. Soil infectious potential estimated through infected leaf-disc area was positively correlated with our DNA-based quantification of oospores. Overall, the quantitative and spatially explicit survey of primary inoculum reservoir gained from these molecular and biological methods will contribute to the design of management strategies aimed at preventing primary inoculum accumulation in the vineyard from one season to the next.
ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Poeydebat) 09 Dec 2024
https://hal.inrae.fr/hal-04827822v1
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[hal-04967045] Population genomics of the rice landrace Acuce reveals exceptional dynamics of immune receptors
Landraces are important resources for breeding programs. However, the diversity harbored at the genomic level by landraces is yet to be analyzed. Here we sequenced more than 200 individual plants from the long-lasting and durably resistant rice landrace Acuce (Oryza sativa subsp. indica). We found that Acuce exhibits diversity levels as high as 38% of the entire indica sub-species. We pinpoint signatures of selection in favor of polymorphism associated with resistance, but not other agronomic trait genes. Furthermore, we provide evidences that emerging properties upon mixing genomic diversity also increase Acuce's performances.
ano.nymous@ccsd.cnrs.fr.invalid (Stéphane de Mita) 26 Feb 2025
https://hal.science/hal-04967045v1
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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-04455685] Induction of common bean OVATE Family Protein 7 (PvOFP7) promotes resistance to common bacterial blight
Common bacterial blight of bean (CBB) is a devastating seed-transmitted disease caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans on common bean (Phaseolus vulgaris L.). The genes responsible for CBB resistance are largely unknown. moreover, the lack of reproducible and universal transformation protocol limits the study and improvement of genetic traits in common bean. We produced X. phaseoli pv. phaseoli strains expressing artificially-designed Transcription-Activator Like Effectors (dTALEs) to target 14 candidate genes and performed in planta assays in a susceptible common bean genotype to analyse if the transcriptional induction of these genes could confer resistance to CBB. Induction of PvOFP7, PvAP2-ERF71 and PvExpansinA17 resulted in CBB symptom reduction. In particular, PvOFP7 induction led to strong symptom reduction, linked to reduced bacterial growth in planta at early colonisation stages. RNA-Seq analysis revealed up-regulation of cell wall formation and primary metabolism, and major downregulation of Heat Shock Proteins. Our results demonstrate that PvOFP7 is contributes to CBB resistance, and underline the usefulness of dTALEs for highlighting genes of quantitative activity.
ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Gaudin) 13 Feb 2024
https://hal.science/hal-04455685v1
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[hal-05100713] Efficient and heritable gene editing through CRISPR-Cas9 in Pisum sativum
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ano.nymous@ccsd.cnrs.fr.invalid (Chloé Soulard) 06 Jun 2025
https://hal.science/hal-05100713v1
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[hal-05297242] The phyllosphere microbiome: mediator or indicator of plant water stress?
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ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297242v1
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[hal-05297773] Identifying microbial consortia that interfere with grapevine pathogens
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ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297773v1
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[hal-03358998] Functional–Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures
Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
ano.nymous@ccsd.cnrs.fr.invalid (Emmanuelle Blanc) 07 Oct 2021
https://inria.hal.science/hal-03358998v1
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[hal-05485752] Beyond pesticide reduction: Exploring synergies between contrasted territorial scenarios
Pesticide use creates significant environmental, health and socioeconomic challenges and its reduction is hindered by sociotechnical lock-ins. The territorial level, combined with systemic approaches, is promising to overcome these systemic challenges. This research proposes an original methodological approach which, instead of aiming at creating consensus, explores contrasted pesticide reduction scenarios with local stakeholders based on existing initiatives in order to identify pathways for collective action. The study was conducted in the Western Plain of Montpellier, in Southern France, and involved a diversity of stakeholders from the territory and outside of the territory in 5 steps, using the Co-Click’Eau tool and workshops. The scenarios explored the potential of diversification for food production, biodiversity conservation and crop-livestock integration to meet pesticide reduction challenges. In addition to an important pesticide use reduction, each scenario proposed significant land-use and farming practices transformations. The analysis revealed that the approach was able to create spaces for dialogue through the formulation of synergies between these strategies by participants, especially on land-use management, technical levers, linking production to consumers and highlighted complementary contributions of biodiversity and livestock to the territory. Beyond its agronomic dimensions, the process opens the pathway to better coordination with the identification of synergies and tensions between different visions, helping to identify coherent strategies including agricultural production, biodiversity, and food objectives. By doing so, our approach contributes to embedding pesticide reduction into a broader, systemic reconfiguration of agroecosystems and territorial governance.
ano.nymous@ccsd.cnrs.fr.invalid (Myrto Parmantier) 25 Feb 2026
https://hal.science/hal-05485752v1
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[hal-05166191] Comment la diversité végétale peut nous aider à réduire les pesticides
Une récente expertise scientifique collective conduite par l’INRAE et faisant la synthèse de plus de 2000 articles scientifiques internationaux montre qu'intégrer davantage de diversité végétale dans les parcelles et les paysages est une solution pour contrôler les espèces qui causent du tort aux cultures (maladies, mauvaises herbes, insectes herbivores…) et un levier pour sortir des pesticides.
ano.nymous@ccsd.cnrs.fr.invalid (Aude Vialatte) 16 Jul 2025
https://hal.inrae.fr/hal-05166191v1
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[hal-05117262] Crop diversity reduces pesticide use more efficiently with refined diversification strategies
Pesticides assured food security for decades, but have left humanity with degraded soils, polluted water, and biodiversity losses. Enhanced crop diversity contributes to the regulation of insect pests, weeds, and diseases, and is therefore assumed to allow pesticide reduction. At the cropping system scale, pesticide use is affected more by crop species than by the number of crops, because crops have contrasting sensitivities to pests and contrasting pesticide requirements. Here, we disentangled the effects of diversity from the effects of crop species, for 1285 cropping systems in French commercial arable farms, using 28 indicators of functional diversity. A composite diversity metric, combining indicators with the greatest explanatory power, accounted for 8% of the pesticide use variance, much less than the variance due to crop species. The results suggest that reducing agricultural reliance on pesticides through diversification is feasible when different components of diversity—namely, crop species and diversity features—are combined.
ano.nymous@ccsd.cnrs.fr.invalid (Yaoyun Zhang) 17 Jun 2025
https://hal.inrae.fr/hal-05117262v1
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[hal-05526495] Colonization and spatiotemporal distribution of bruchid pests in lentil and faba bean fields
BACKGROUND: Lentils (Lens culinaris Medikus, 1787) and faba beans (Vicia faba Linnaeus, 1753) are important crops in France facing threats from Bruchus spp. We analyzed 59 lentil and 45 faba bean fields across four French regions over three growing seasons (2019-2020 to 2021-2022). We investigated the diversity, colonization patterns and spatiotemporal distribution of bruchids at different crop phenological stages and distances from field edges. RESULTS: Bruchus rufimanus Boheman, 1833 and Bruchus signaticornis Gyllenhal, 1833 were the only species emerging from faba beans (97.8%) and lentils (99.5%), respectively. B. rufimanus colonization was concentrated during pod development, maintaining a balanced male-female ratio throughout. B. signaticornis exhibited a colonization period of ≈1 month, with a gradual increase in female proportion over time. The spatial distribution of bruchids and damage were relatively uniform within fields, indicating strong dispersal capabilities. A significant positive correlation, with a high degree of dispersion, was identified between female abundance and bruchid-damaged grains. CONCLUSION: We confirmed that B. rufimanus and B. signaticornis were the only species damaging faba beans and lentils in France, respectively. The homogeneous spatial distribution suggests a strong dispersal ability of bruchids. The high degree of dispersion in the relationship between female abundance and bruchid-damaged grains highlights the importance of regulatory factors influencing larval and egg survival. These results, together with the presence of B. signaticornis in faba beans, emphasize the need for species-specific, phenology-based and spatially informed integrated pest management strategies, to mitigate the impact of bruchids and reduce reliance on chemical in their control.
ano.nymous@ccsd.cnrs.fr.invalid (Anastasia Chery-Lagrange) 25 Feb 2026
https://hal.inrae.fr/hal-05526495v1
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[hal-05247368] Increasing crop diversity reduces pesticides across diverse production situations
Pesticides have caused significant losses of biodiversity and pose a threat to human health. Crop diversification is proposed as a major solution to achieve the needed pesticide reduction in agriculture, by moderating the pressure of weeds, insect pests, and fungal diseases. According to the pest triangle framework, the impact of a pest outbreak depends on the interactions between crop, pest, and the environment. Diversifying crop sequences in a cropping system could impact the interactions between the three factors and recalibrate the need for pesticides to control pests and avoid yield losses. A previous study found that pesticide use, measured by the Treatment Frequency Index at the cropping system level, is affected both by crop species and crop diversity (assessed in this study through the number of crops), with crop species having a greater impact. However, to our knowledge, no study has quantified the role of the farming environment in the effect of crop diversity on regulating pest pressure, and limiting the need for pesticides. In this study, we used the classification and regression trees method to identify six clusters of production situations with contrasting levels of pesticide use, taking into account the nature of crop species grown. Our results show that production situations, the crop species, and crop diversity, jointly shaped pesticide reliance at the cropping system level. Specifically, production situations explained 5.6% of the variance in total pesticide use. Crop diversification by adding one extra crop reduced total Treatment Frequency Index by 0.10, after filtering out the influences of production situation, and this effect was significant across all pesticide groups, namely herbicides, fungicides, and insecticides. Our findings provide evidence that increasing crop diversity consistently reduces pesticide reliance across diverse production conditions. These insights highlight the potential of crop diversification as an effective and scalable strategy for sustainable pest management.
ano.nymous@ccsd.cnrs.fr.invalid (Yaoyun Zhang) 09 Sep 2025
https://hal.science/hal-05247368v1
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[hal-05325705] Modelling pest control and vector-borne disease spread to explore landscape and agricultural management strategies: the SimBAL agent-based model
1. As the urgency to transition to sustainable agricultural systems grows, tools are required to support stakeholders, including farmers and advisors, in designing agricultural landscapes that strengthen ecosystem services. Landscape management is key to support natural pest control, allowing to reduce pesticide use. But the contextspecific nature of trophic interactions induces that, in practice, it is hardly feasible to test different changes in landscapes that are conducive to pest control and that guarantee it sufficiently to dispense with pesticide use. An alternative is to explore in silico the large-scale deployment of management options to help stakeholders, including policy makers, make choices and gain confidence in landscape management and selecting priorities. 2. We developed a spatially explicit modelling tool which has a general scope, and which is currently developed for the case of aphid dynamics in agricultural landscapes according to spatio-temporal host plant availability and natural enemy predation. The epidemiological consequences on the transmission of beet yellowing virus are considered. The availability of host plants for the aphid depends on farming practices (crop diversity, sowing and spraying dates, implementation of semi-natural features). The aim here is to limit this availability at population level and, in particular, to break the space-time continuities leading to massive colonisation of sugar beet. This logic is reversed for predation by natural enemies, with the aim of fostering resources and shelter continuity to promote their abundance and aphid control potential within the landscape. 3. An analysis of the model behavior, a sensitivity analysis and a calibration of the model were carried out. Sim-BAL outputs are consistent with current knowledge on aphid and infection dynamics. The model is able to represent inter-annual variability in sugar beet infection rates in the fields, and to discriminate landscapes that are suppressive towards aphids. 4. SimBAL was developed with the aim of exploring and comparing landscape scenarios to foster natural pest control, rather than being a precise predictive tool. The model can be used to test landscape scenarios based on the expressed priorities of stakeholders, and therefore favors transparency in decision-making. It is a solid tool for collective action in the management of territorial issues.
ano.nymous@ccsd.cnrs.fr.invalid (Gaëlle van Frank) 13 Feb 2026
https://hal.science/hal-05325705v2
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[hal-05232413] How contracting in the value chain can reduce farmer's exposure to risks and enhance crop diversification ? A case study approach in the crop sector in France
Marketing contracts are widely used to organise the exchanges in minor crop value chains facing uncertainty. In this study, we investigate how this vertical coordination tool can incentivize farmers to adopt grain-legumes in their crop rotations by transferring part the production and market risks to downstream firms. The risk transfer mechanism is analysed using a methodology based on surveys of chain of agents involved in a given value chain. We examine 5 case studies based on the type of legume and the organisation of the value chain. The results show that the payment system, the design of the contracts and the material and immaterial resources reinforced by the relationship between farmers and downstream firms, especially technical knowledge resources, contribute to reduce farmer’s exposure to risks and favour the development of the legume value chain, which is key for the agro-ecological transition.
ano.nymous@ccsd.cnrs.fr.invalid (Auguste Bréavoine) 01 Sep 2025
https://hal.inrae.fr/hal-05232413v1
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[hal-05148951] Reducing risks of crop diversification for the agroecological transition, is contracting in the value chain a part of the solution?
The sustainability transition in the agri-food sector remains understudied (e.g. Vermunt et al., 2020). A key challenge is crop diversification, which implies a shift from a system dependent on a few major species (like cereals) to one based on many species (including legumes such as chickpeas, lentils, etc.), together with a reorganisation of the value chain, which implies the creation of niche markets, often regulated by contracts between farmers and their first buyer (Adjemian et al., 2016). In addition, low investment in this sector in the past led to a lock-in situation with lack of knowledge, higher yield variability and few outlets (Magrini et al., 2016). Such transformation creates uncertainty and new risks, especially for farmers, including production risks, which require technical knowledge and innovation, and market risks, such as fluctuations in quantity, quality and prices. New organisational arrangements in value chains with farmers, such as production contracts --- pre-planting commitments that fix a quantity, price formulas and technical requirements --- could address uncertainty and develop niche innovation in legumes crops (Cholez and Magrini, 2023). However, whether the governance of exchanges through such contracts could also increase farmers’ innovative capacity to adopt more sustainable practices remains an open question. Additionally, looking at the way the agricultural trade with farmers is structured is also important because market arrangements are major structural dimension of tensions and conflicts within value chains. Our study builds on Cholez and Magrini (2023) initial findings, which highlight the role of production contracts in fostering dialogue, trust, knowledge sharing and learning, which are key to mitigating tensions and conflicts (Andersen et al., 2023). We explore how this vertical coordination tool can support a collective risk management strategy in the French legume sector, and reduce tensions and conflicts within value chains. Our hypothesis is that, while production contracts are primarily designed to secure supply for buyers, they also strengthen trust and collective commitment to sustainable practices, because the contractual design could allow for a risk-sharing mechanism that benefits all parties involved in the long run by reducing opportunism. This encourages investment in both material and human resources needed to sustainably change of the production practices on farms and in processing plants. We developed an original analytical framework based on the economic literature on agricultural risks and contracts (e.g. Hardaker et al., 2004; Roussy et al., 2018, Vavra 2008), combined with the literature on transition studies, in particular on the role of niche innovations (e.g. Smith and Raven, 2012). We apply this framework through 5 in-depth case studies of contract chains, based on 21 interviews with commercial directors of processing and collecting companies and with farmers. Our results highlight the potential role of contracts in supporting the agroecological transition. This research is of particular interest to policy makers at various levels, from the European Commission to local agricultural institutions, and could also inspire other sectors facing value chain organisation challenges for sustainability transition.
ano.nymous@ccsd.cnrs.fr.invalid (Auguste Bréavoine) 07 Jul 2025
https://hal.inrae.fr/hal-05148951v1
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[hal-05155592] Differences in growth features between species are driving cereal-legume intercrop yield: A statistical learning approach based on aggregated dataset
Increasing crop diversification is crucial for developing more sustainable agricultural systems, and cereal-legume intercropping is a promising strategy. This study investigates the factors influencing the yield of cereal-legume intercrops using data from six field experiments in southwestern France, where durum wheat was intercropped with either faba bean or pea. We assessed how differences in plant traits (e.g., height or biomass growth rates) between the associated species were related to the intercrop productivity. Additionally, we developed a novel modeling approach, combining machine learning and mixed-effects models, to identify the key drivers of intercrop performance based on variable importance. Our results showed that interspecific differences in plant traits within intercrops, particularly in biomass accumulation rate, maximum leaf area index, and elongation rates, were the most important factors explaining intercrop yield. These traits and their differences mainly suggest that competitive processes shape the outcome of a mixture and highlight the importance of dynamic measurements in agronomic experiments. The relationship between species yield and trait differences was symmetric for both intercropped species. Furthermore, these relationships were scale-dependent, with trends observed at the aggregate level not always consistent at the level of individual experiments. Our study highlights the importance of considering trade-offs when designing intercropping systems for practical applications and demonstrates the value of combining machine learning with ecological knowledge to gain insights into complex agricultural systems from aggregated datasets.
ano.nymous@ccsd.cnrs.fr.invalid (Rémi Mahmoud) 10 Jul 2025
https://hal.science/hal-05155592v1
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[hal-05333556] Operationalizing collective action for crop diversity in-situ management: insights from a decentralized collective design approach
The modernization of agriculture in Northern countries has led to a loss of crop diversity, as well as a loss of knowledge, know-how and rights of farmers regarding on-farm seed breeding. In France, the Réseau Semences Paysannes (RSP) brings together collectives of actors (farmers, bakers, citizens, gardeners) mobilized in a quest to reclaim these aspects. Within the framework of the decentralized participatory breeding program conducted in collaboration with INRAE, farmers have co-constructed knowledge in terms of dynamic management of heterogeneous wheat populations. Yet, as the RSP network grows, these actors face new types of challenges regarding collective action. To address them, we proposed to consider peasant seeds as « common unknowns » rather than « common goods » and we adapted and applied an innovative design approach drawing upon the KCP (Knowledge-Concept-Proposals) method. This approach consisted in implementing, from 2019 to 2021, five decentralized design workshops with local seed breeding collectives. The replication of design workshops in different contexts provided a framework for interaction among RSP members, allowed the sharing of both scientific and experiential knowledge. Noteworthily, it fostered the generation of many proposals for enhancing collective action, and led to the development of operational proposals with a view to implement them in the future. This methodology-oriented paper mainly describes the decentralized design approach implemented, its outputs and outcomes, as well as its interests and limits in the context of crop diversity management. It also analyses how the workshop outputs enriches previous works in the field; in particular how such a participatory design approach leads to produce original operational solutions to respond to challenges identified in the literature.
ano.nymous@ccsd.cnrs.fr.invalid (Elsa T Berthet) 28 Oct 2025
https://hal.science/hal-05333556v1
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[hal-05440369] Learning about best management practices: Theory and experimentation under the umbrella of crop insurance
Decision Support Systems (DSS) with embedded best management practices help reduce pesticide use. However, costly experimentation is necessary to learn about the quality of their data processing and recommendation models. We study farmers’ choices to try such a DSS. Due to order effects, learning can be inefficient and stop after inadequate recommendations, leading to crop losses. Subsidizing crop insurance conditional on DSS use is a cost-effective policy to foster experimentation. A 4-year living lab on-farm experiment involving French wine cooperatives, an insurer, and researchers supports our theoretical results on learning dynamics and provides additional insight into information requirements for subsidized green insurance.
ano.nymous@ccsd.cnrs.fr.invalid (Cécile Aubert) 05 Jan 2026
https://hal.inrae.fr/hal-05440369v1
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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-05637940] Reduced confidence intervals and novel candidate genes for quantitative trait loci associated with apple scab resistance in Malus domestica
Abstract Apple scab, caused by Venturia inaequalis , remains one of the most damaging diseases in apple orchards, driving intensive pesticide use worldwide. Reducing this dependence requires the deployment of durable resistance, ideally through the combination of major resistance genes (R genes) with quantitative trait loci (QTL) that confer partial and potentially complementary protection. Yet, few apple scab QTLs have been functionally validated, and their underlying mechanisms remain largely unresolved. Here, we refined and functionally described, with transcriptomic data, five resistance QTLs in a biparental population of 1,970 individuals derived from the cross ‘TN 10-8’ × ‘Fiesta’. Using 43 newly developed KASP markers, QTL locations were substantially precised through high-resolution genotyping and phenotyping with two V. inaequalis isolates exhibiting contrasting virulence. Four QTL (qT1, qF11, qF17, qT13) were validated, while qF3 was not confirmed. Transcriptomic data comparison revealed the expression of candidate genes within the narrowed intervals, including receptor-like proteins in qT1, and RNAi- and signaling-related genes in qF11 and qF17, suggesting a diversified and complementary defense network. These findings refine the genetic architecture of apple scab resistance and suppose the existence of shared molecular pathways between major R gene, such as the well-described Rvi6 gene, and quantitative resistance, with for instance the QTL qT1. The identified loci and markers provide robust tools for marker-assisted and genomic breeding aimed at developing apple cultivars with complementary and potentially durable resistance pathways.
ano.nymous@ccsd.cnrs.fr.invalid (Romane Lapous) 01 Jun 2026
https://hal.inrae.fr/hal-05637940v1
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[hal-05633888] Untargeted metabolomic dataset of leaves from twenty-four accessions of wild and cultivated tomato plants
Tomato (Solanum lycopersicum var. lycopersicum), one of the most important crops worldwide, has a complex domestication history that began in Latin America, region hosting also fourteen wild relative species and subspecies. Domestication and subsequent breeding efforts have led to the development of the modern cultivated tomato, prized for its agronomic performance and economic value. However, this process also resulted in a substantial erosion of genetic and metabolic diversity, potentially limiting the plant’s adaptive capacity and resilience to environmental stresses. Previous comparative studies between domesticated tomato cultivars and wild relative species have underscored the evolutionary shifts in various plant traits associated with biotic stress. Yet, most of these studies relied on a limited number of wild accessions, reflecting a general tendency to underestimate their genetic and metabolic diversity. In this study, we sought to characterize both intra- and inter-specific metabolic diversity in tomato and its wild relatives. Using Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS) analysis, we profiled the chemical composition of hydro-methanolic leaf extracts from twenty-four accessions representing five Solanum species and subspecies, each with distinct natural histories and domestication levels. This dataset provides a comprehensive overview of leaf metabolic diversity across cultivated and wild tomato species, offering insights into the evolutionary and ecological forces shaping specialized metabolism within the tomato clade. It is available at https://doi.org/10.57745/QM0BOR.
ano.nymous@ccsd.cnrs.fr.invalid (Komla Exonam Amegan) 27 May 2026
https://hal.science/hal-05633888v1
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[hal-05297755] BCMicrobiome (2018-22) - Learning microbial networks from metabarcoding data: application to biological control
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297755v1
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[hal-05300079] Analyser, modéliser et piloter le microbiote pour renforcer la santé de la vigne
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05300079v1
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[hal-05297752] Microbiote végétal: état de l’art et défis pour une agriculture durable
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Corinne Vacher) 20 Mar 2026
https://hal.science/hal-05297752v1
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[hal-05069777] Arbuscular mycorrhizal fungi as biomarkers of vineyard yield in Champagne
Grapevines are colonized by a multitude of microorganisms (fungi, bacteria, oomycetes), mainly through roots in contact with the soil microbial reservoir. Some microorganisms cause disease and others have positive or negative effects on the plant (protection against pathogens, resistance to abiotic stress, improved nutrition). In addition to their functional roles, microorganisms respond rapidly to environmental changes (climate, cultivation practices), which could make them candidate biomarkers of the performance of the viticultural ecosystem. The aim of this study is (i) to test whether a positive relationship exists between microbial diversity and vineyard yield, (ii) to identify potential microorganisms that are biomarkers of high and stable yields over time, and (iii) to test whether arbuscular mycorrhizal fungi (AMF) are over-represented among these biomarkers. Vine plots with long-term contrasted yields were selected in Champagne based on multi-year records of yield. We sampled the vine roots and characterized the microbiota using metabarcoding approaches targeting bacterial and fungal communities. Our analyses revealed no relationship between microbial taxonomic diversity and grape yield. Using differential abundance analyses and supervised machine learning algorithms, we identified microbial biomarkers of high versus low yield in the root compartment. We identified 58 fungal and oomycete biomarkers, among which there were several AMFs. These AMFs were all biomarkers of high-yielding plots, suggesting a direct role in vine growth and productivity. These microbial biomarkers of stable and high yields will enable the development of diagnostic programs for the functioning of viticultural ecosystems.
ano.nymous@ccsd.cnrs.fr.invalid (Lucile Pellan) 23 Mar 2026
https://hal.science/hal-05069777v1
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[hal-05641963] Sécuriser le changement de pratiques : expérimentation d'une '"assurance verte" en France
Sécuriser le changement de pratiques : expérimentation d'une '"assurance verte" en France.
ano.nymous@ccsd.cnrs.fr.invalid (Yann Raineau) 02 Jun 2026
https://hal.inrae.fr/hal-05641963v1
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[hal-03777604] Pest detection by inversion of a pheromone dispersion model
One third of the annual world's crop production is directly or indirectly damaged by insects. Early detection of invasive insect pests is key for optimal treatment before infestation. Existing detection devices are based on pheromone traps: attracting pheromones are released to lure insects into the traps, with the number of captures indicating the population levels. Promising new sensors are now available to directly detect pheromones produced by the pests themselves and dispersed in the environment. Tracing the source of pheromone emission would allow locating the pest's habitat and performing pesticide-free elimination treatments, in a precision agriculture context. We formalized a 3D diffusion-convection model of pheromone concentration dispersion in the environment that include vegetation-dependant pheromone settling coefficients, in agreement with existing chemical transport models [1]. This model is converted into a 2D reaction-diffusion-convection model after integration. A sensitivity analysis of this direct dispersion (forward) model is performed. An inverse (backward) model is then derived to identify the sources of pheromone emission from signals produced by sensors spatially positioned in the landscape. A priori biological knowledge on pest behaviour (favourite habitat, insect clustering for reproduction...) is introduced to constrain the inverse problem towards biologically relevant solutions. The accuracy of the inverse solution is assessed on simulated noisy data. This work was carried out with the financial support of the French Research Agency (ANR), Pherosensor project (https://pherosensor.inrae.fr/).
ano.nymous@ccsd.cnrs.fr.invalid (Thibault Malou) 14 Sep 2022
https://hal.science/hal-03777604v1
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[hal-04572831] Biology-Informed inverse problems for insect pests detection using pheromone sensors
Most insects have the ability to modify the odor landscape in order to communicate with their conspecies during key phases of their life cycle such as reproduction. They release pheromones in their nearby environment, volatile compounds that are detected by insects of the same species with exceptional specificity and sensitivity. Efficient pheromone detection is then an interesting lever for insect pest management in a precision agroecological culture context. A precise and early detection of pests using pheromone sensors offers a strategy for pest management before infestation. In this paper, we develop a biology-informed inverse problem framework that leverages temporal signals from a pheromone sensor network to build insect presence maps. Prior biological knowledge is introduced in the inverse problem by the mean of a specific penalty, using population dynamics PDE residuals. We benchmark the biological-informed penalty with other regularization terms such as Tikhonov, LASSO or composite penalties in a simplified toy model. We use classical comparison criteria, such as target reconstruction error, or Jaccard distance on pest presence-absence. But we also use more task-specific criteria such as the number of informative sensors during inference. Finally, the inverse problem is solved in a realistic context of pest infestation in an agricultural landscape by the fall armyworm (Spodoptera frugiperda).
ano.nymous@ccsd.cnrs.fr.invalid (Thibault Malou) 28 Jan 2025
https://hal.inrae.fr/hal-04572831v3
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[hal-05485748] Potential of local collective action to reduce pesticide use in a French Mediterranean landscape
Pesticide use in agriculture has significant negative impacts on human health, ecosystems, and natural resources. The failure to meet targets for pesticide reduction at the farm level underscores the need for a systemic, holistic approach that considers the diversity of actors and the complexity of the farming systems involved. The landscape level provides a relevant framework for addressing the reduction of pesticide use and impacts. In this study, we analyzed 19 initiatives aimed to reduce pesticide use or its impacts in agriculture in a Mediterranean peri-urban plain in southern France. Drawing on insights from landscape agronomy and research on collective action, we developed a novel conceptual framework to capture and analyze the diversity and complementarity of local dynamics of pesticide reduction. Through interviews, workshops, and farm surveys, we examined the factors driving the emergence of these initiatives and assessed their anticipated impacts on farming practices, landscape patterns, and natural resources at the landscape level. The results revealed that these initiatives were led by diverse, and sometimes conflicting, strategies to reduce pesticide use that focused mainly on optimizing pesticide use in dominant agricultural systems, alongside farm reconfiguration and biodiversity integration strategies. This study advances current knowledge by providing actionable insights to improve collective action at the landscape level, such as spaces for synergies for landscape-level coordination and identified barriers to this coordination. Our findings emphasize the importance of embracing complexity when designing and implementing pesticide-reduction strategies.
ano.nymous@ccsd.cnrs.fr.invalid (Myrto Parmantier) 25 Feb 2026
https://hal.science/hal-05485748v1
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[hal-04481765] Pest detection from a biology-informed inverse problem and pheromone sensors
One third of the annual world's crop production is directly or indirectly damaged by insects. Early detection of invasive insect pests is key for optimal treatment before infestation. Existing detection devices are based on pheromone traps: attracting pheromones are released to lure insects into the traps, with the number of captures indicating the population levels. Promising new sensors are on development to directly detect heromones produced by the pests themselves and dispersed in the environment. Inferring the pheromone emission would allow locating the pest's habitat, before infestation. This early detection enables to perform pesticide-free elimination treatments, in a precision agriculture framework. In order to identify the sources of pheromone emission from signals produced by sensors spatially positioned in the landscape, the inference of the pheromone emission (inverse problem) is performed. Classical inference is conducted by combining the data and the so-called direct model [1]. In the present case, this entails combining the data from the pheromone sensors and the pheromone concentration dispersion that is a 2D reaction-diffusion-convection model [2]. In the proposed method, the inference involves not only the coupling of the pheromone dispersion model with the pheromone sensors data but also incorporates a priori biological knowledge on pest behaviour (favourite habitat, insect clustering for reproduction, population dynamic behaviour...). This information is introduced to constrain the inverse problem towards biologically relevant solutions. Different biology-informed constraints are tested, and the accuracy of the solutions of the inverse problems is assessed on simulated noisy data. [1] Bocquet, M. (2014). Introduction to the Principles and Methods of Data Assimilation in the Geosciences. Lectures note. [2] Stockie, J.M. (2011). The Mathematics of Atmospheric Dispersion Modeling. SIAM Review.
ano.nymous@ccsd.cnrs.fr.invalid (Thibault Malou) 28 Feb 2024
https://hal.science/hal-04481765v1
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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
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[hal-04982331] Biology-Informed inverse problems for insect pests detection using pheromone sensors
Most insects have the ability to modify the odor landscape in order to communicate with their conspecies during key phases of their life cycle such as reproduction. They release pheromones in their nearby environment, volatile compounds that are detected by insects of the same species with exceptional specificity and sensitivity. Efficient pheromone detection is then an interesting lever for insect pest management in a precision agroecological culture context. A precise and early detection of pests using pheromone sensors offers a strategy for pest management before infestation. In this paper, we develop a biology-informed inverse problem framework that leverages temporal signals from a pheromone sensor network to build insect presence maps. Prior biological knowledge is introduced in the inverse problem by the mean of a specific penalty, using population dynamics PDE residuals. We benchmark the biological-informed penalty with other regularization terms such as Tikhonov, LASSO or composite penalties in a simplified toy model. We use classical comparison criteria, such as target reconstruction error, or Jaccard distance on pest presence-absence. But we also use more task-specific criteria such as the number of informative sensors during inference. Finally, the inverse problem is solved in a realistic context of pest infestation in an agricultural landscape by the fall armyworm (Spodoptera frugiperda).
ano.nymous@ccsd.cnrs.fr.invalid (Thibault Malou) 07 Mar 2025
https://hal.science/hal-04982331v1
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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-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-03722473] Évaluer, détecter, protéger : des pistes à explorer pour lutter contre la fusariose de l’ail
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Christel Leyronas) 13 Jul 2022
https://hal.inrae.fr/hal-03722473v1
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[hal-03910768] Water limitation affects weed competitive ability for light. A demonstration using a model‐based approach combined with an automated watering platform
Climate change is driving the need to investigate responses to water limitation of morphological traits involved in competition for light, the main resource for which crops and weeds compete in conventional temperature and tropical cropping systems, to better understand field crop-weed dynamics. Our objective was to develop an innovative approach to quantify weed species responses to water limitation, using three species. This approach combined (1) key morphological traits involved in competition for light (taken from a mechanistic crop-weed model) as criteria to analyse responses to water limitation and (2) a pot/greenhouse platform allowing automated precision-watering and daily quantification of soil water availability in each pot. For all species and growth stages, increased plant height per unit of aboveground biomass and production of smaller/thicker leaves were the most noteable responses. Plants with a strong increase in plant height per unit of aboveground biomass in response to water limitation maintained high levels of specific leaf area, even at low soil water availability. Increases in biomass allocation to roots (vs. aboveground parts) and leaves (vs. stems and reproductive organs) were also observed, but not for all species and growth stages. Overall, these effects of water limitation on morphological traits indicate strong interactions between competition for light and water.
ano.nymous@ccsd.cnrs.fr.invalid (Delphine Moreau) 14 Jun 2023
https://hal.inrae.fr/hal-03910768v1
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[hal-05448202] Towards a global vision of wheat virome in France
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ano.nymous@ccsd.cnrs.fr.invalid (Armelle Marais) 08 Jan 2026
https://hal.science/hal-05448202v1
