Services déconcentrés d'appui à la recherche Occitanie-Toulouse

Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and their estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta with spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluated this model for population sizes not accessible to the Wright-Fisher model and illustrated its performance on a dataset of two divergently selected chicken populations.

The imperative of carbon neutrality requires a drastic, rapid, and sustained reduction in fossil energy consumption and greenhouse gas emissions. The Russia-Ukraine war has led to a major energy crisis, whose end does not seem imminent. The sudden and major increase in energy prices resulting from this crisis has major impacts on many sectors of the societies. This is especially true for agriculture, a direct consumer of energy that also has considerable indirect consumption through the manufacture, transport, and distribution of chemical inputs such as fertilizers and pesticides. Taking the example of France, from July 2021 to July 2022, farmers were challenged with price increases as high as 48% and 111% for energy and fertilizers, respectively (Agreste, 2022). At the global scale, in 2018, greenhouse gas emissions from fossil energy consumption in agriculture represented 0.9 Pg CO2 eq. (against 9.3 Pg CO2 eq. due to agriculture, excluding emissions due to this energy consumption) and those emissions have increased by 23% since 2000 (FAO, 2020). This context calls for in-depth transformation of agriculture, which is currently overly dependent on non-renewable energy in high-income economies. While research on the subject continues to grow (Box 1), this large body of work focuses more on assessing the energy consumption of current agricultural systems using multiple metrics (Box 2) than on developing supply- or demand-side alternatives that use less energy. In response to these trends, Ramankutty and Dowlatabadi (2021) suggested pathways to sustainable food systems. However, while their recommendations included energy reduction options on the food consumption side, their focus on farming practices was restricted to improving the energy efficiency of current agricultural systems and missed the necessary redesign of farming and food systems. In this article, we look back to understand how agricultural systems came to progressively depend on non-renewable energy. We then briefly review agricultural practices and systems reducing energy consumption without compromising energy efficiency. Finally, we propose future research avenues to explore pathways for reducing energy consumption without compromising food security and sustainability challenges.

The issues of power and equity are gaining attention in research on ecosystem services (ESs).Stakeholders benefiting from ESs are not necessarily able or authorized to participate in ES management.Thus, we have proposed an analytical framework to identify and qualify stakeholders' roles in relation to ES flows.Building on existing frameworks in the ES literature, we aimed to unravel the different direct and indirect management contributions to ES flows and link them to ES benefits.Direct management targets the functioning of ecosystems, the flows of services, and the benefits received by society, whereas indirect management facilitates, controls, or restricts the activities of direct managers.We applied this framework to the Mariño watershed (Peru) to describe stakeholders' roles using a set of 8 ESs.We have discussed the implications of our findings in terms of equity and power distribution.We conducted faceto-face semistructured interviews with representatives of 52 watershed stakeholders to understand how they managed and benefited from ESs.We used statistical analysis (permutation tests) to detect significant differences in the number of received and managed ESs among stakeholder sectors, i.e., civil society, nongovernmental organizations (NGOs), business, and the public sector, and scales, from local to national levels.Indirect forms of ES management were more frequent than direct ones for all ESs.Water quantity, water quality, and agricultural production were managed by the largest number of stakeholder types.The differences in the number of stakeholder types benefiting from and managing ESs could result from intentional choices, e.g., preferences for local benefits.We also found clear differences in the identity of stakeholders who managed or benefited from ESs. Local stakeholders and the business sector benefited from a higher number of ESs, and public organizations and NGOs were most involved in ES management.More equitable governance of ESs should aim to integrate more diverse stakeholders into decision making.Further empirical research could use our framework to explore the factors determining stakeholders' roles and power distribution.There is a particular need to understand how rights, endowments, and entitlements, as well as spatial configuration, underpin inequities in different social and cultural contexts.

Abstract Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markoiv chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta-with-Spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluate this model for population sizes not accessible to the Wright-Fisher model and illustrate its performance on a dataset of two divergently selected chicken populations.

Long-read sequencing and pangenomics are revolutionizing crop research by providing more complete genome information and revealing crucial structural variations (SVs) linked to important agricultural traits. Building on recent advances in intraspecific pangenome construction, this study addresses the challenge of creating broader, cross-taxon pangenomes, using the Armeniaca taxonomic section as a model. Leveraging a diverse panel of genome assemblies as well as completing it with seven more genome assemblies generated for this study, we constructed a pangenome graph and cataloged the associated genetic variation, identifying approximately 25 million single nucleotide polymorphisms and over 537 000 structural variants. We characterized the diversity of these variants and assessed the extent to which different taxa contribute to overall pangenome expansion. Additionally, we evaluated the performance of low-depth sample mapping to the graph-based reference, highlighting key technical limitations that may affect the quality of downstream analyses. We further identified specific subsets of SVs that exhibit associations with particular classes of transposable elements (TEs). We showed that TEs are a major driver of SV, particularly insertions and deletions, with distinct size and distribution patterns (peaking in the 200- to 400-bp indel bin). They are also nonrandomly positioned in the genome, showing a tight concentration near coding genes, which suggests a role in gene regulation. As a case study illustrating the potential functional relevance of graph-derived SVs, we examined the genomic configuration of the Dormancy-Associated MADS box locus within the Armeniaca pangenome. These findings provide a framework to investigate adaptation in perennial fruit trees of the Armeniaca section.

Pour permettre à la variété d’exercer pleinement son rôle dans la transition agroécologique et lever les verrous identifiés dans cet avis, il faut agir simultanément à plusieurs niveaux afin d’initier une transformation profonde de notre système d’évaluation. Qu’il s’agisse d’introduire de nouvelles espèces, d’associer plusieurs cultures ou de recourir à des variétés populations, la diversification suppose d’abord la mise en place de filières qui les valorisent mais également la disponibilité de variétés adaptées. C’est en ce sens que, si elle n’est pas suffisante, l’évolution du système d’évaluation est en revanche incontournable. Repenser l’évaluation variétale, c’est repenser la manière dont l’ensemble du système agricole et alimentaire conçoit la performance et la résilience. C’est accepter que l’incertitude climatique est devenue la règle, et que la diversité – longtemps perçue comme un bruit – est désormais une ressource stratégique. L’évolution proposée ici n’est pas une remise en cause du système actuel : c’est sa continuité dans un monde transformé. C’est le passage d’un pilotage par la standardisation à un pilotage par la connaissance, la diversité et la coconstruction. L’évaluation variétale doit redevenir ce pour quoi elle a été mise en place : un moteur de l’adaptation des plantes aux besoins et contraintes actuels et futurs, capable d’ouvrir le champ des possibles plutôt que de le refermer, ainsi qu’un accélérateur des transitions indispensables pour faire face à l’urgence (climatique, environnementale et économique ?).

In the 1970s, Pierre Boistard and Jean Dénarié, then researchers at INRA Versailles, formulated an ambitious project: to understand the fundamental genetic mechanisms of interactions between plants and micro-organisms. At a time marked by the first oil crises and the rise of biotechnologies, the symbiotic fixation of atmospheric nitrogen by cereals held out the promise of attracting a great deal of support. Investment in this area of research will have a major scientific impact, renewing the approach to interactions between plants and micro-organisms. If the promise of nitrogen fixation by cereals has not been fulfilled, major applications will emerge. In the 1990s, Jean Dénarié's team at LIPM2 (INRA/CNRS in Toulouse) discovered lipochito-oligosaccharides (LCOs). They demonstrated that these signaling molecules, “called Nodulation Factors (or Nod-LCOs)”, produced by rhizobia trigger the nodulation process in leguminous plants. In the 2010s, the same team demonstrated that certain fungi (arbuscular mycorrhizal fungi and ecto mycorrhizal fungi) also produce LCOs, enabling them to establish symbiotic relationships with plants. Researchers have also observed that LCOs can stimulate root system development.These discoveries have been patented by LIPM's supervisory bodies (CNRS and INRA). Exclusive licenses have been granted to an industrial player who has developed products that are now used in many countries. This industry player has observed that during field trials LCO-based biostimulants increase yields by around 3%. Nod-LCOs are used on 3 million hectares for legumes, while Myc-LCOs are used on 17 million hectares, mainly for corn.

Les ressources phytogénétiques constituent un bien commun essentiel, d’une importance vitale pour l’avenir des systèmes agricoles et alimentaires. Or, depuis la révolution verte, on observe une réduction de la diversité des espèces cultivées, ainsi que de la diversité intraspécifique présente au champ (Pilling et al., 2020a1). Neuf espèces représentent 67 % de la production mondiale (Pilling et al., 2020a) et seulement cinq céréales fournissent 60 % de l’apport énergétique mondial (source FAO, 2019, 2024). L’érosion génétique constitue ainsi une menace majeure pour la durabilité des systèmes agricoles et alimentaires (Pilling et al 2020b2). Dans ce contexte, la conservation et l’utilisation des ressources phytogénétiques sont d’une actualité brûlante.

Sustainability Science in the International Knowledge Economy. Strategic Analysis and Opportunities for INRAE.

Les sciences de la durabilité dans l’économie de la connaissance internationale. Analyse stratégique et opportunités pour INRAE

International audience

International audience

The MoU is a non-binding framework for cooperation between IBISBA partners. It was finalized in 2022 and has been signed by 20 RTOs and

Conseil scientifique de l'Agence de sécurité sanitaire de l'alimentation, de l'environnement et du travail -Anses Avis relatif au rapport du GT « Crédibilité de l'expertise scientifique » issu du Conseil scientifique Au cours des dernières années, parmi les centaines d'avis rendus par l'Anses, quelques-uns ayant notamment trait à des produits réglementés ont suscité controverses et polémiques.Dans ce contexte, le Conseil scientifique de l'Agence a mandaté un groupe de travail (GT) pour analyser la situation et formuler des recommandations visant à renforcer la crédibilité des expertises de l'Agence.Il répond ainsi à l'objectif de réflexion permanente énoncé par l'Agence dans son document de cadrage sur la méthodologie de l'expertise collective à l'Anses (juin 2012) comme à l'objectif de renforcement de l'excellence scientifique, de qualité et d'indépendance de l'expertise (Contrat d'objectif et de performance de l'Anses 2018-2022).Le GT a abordé la question de la crédibilité de l'expertise, c'est-à-dire du degré de confiance dont elle bénéficie, à partir d'une approche de retour d'expérience sur trois études de cas ayant fait l'objet de controverses à des degrés divers (glyphosate, SDHI, néonicotinoïdes) et de l'examen des facteurs qui déterminent la crédibilité de l'expertise par une analyse de la littérature et par une trentaine d'auditions.Les données ont été examinées selon quatre axes : le décalage entre les connaissances scientifiques disponibles et celles utilisées pour les trois expertises, les procédures, le décalage entre les conclusions de l'expertise et les attentes des parties prenantes et enfin, l'impact socio-économique de la mise en œuvre des mesures de gestion des risques. PRINCIPAUX RESULTATS : L'EXPERTISE SCIENTIFIQUE AU CŒUR DE TROIS GRANDES TENSIONSLes résultats de ce travail éclairent trois grandes tensions touchant l'expertise scientifique de manière générale.L'expertise scientifique est soumise à une première tension : d'une part, la nécessité de prendre en compte les connaissances scientifiques les plus avancées et, en même temps, la nécessité de s'appuyer sur des règles claires et partagées par l'ensemble des acteurs concernés, de façon à réaliser une évaluation des risques transparente, robuste et reproductible.Il peut en résulter un décalage entre connaissances scientifiques et résultats de l'expertise, source de controverses publiques.La deuxième tension renvoie d'un côté, à l'urgence de rendre certains avis et, de l'autre, au temps nécessaire pour effectuer une expertise scientifique de qualité.L'urgence peut conduire à adapter aux contraintes temporelles les règles usuelles et codifiées de l'expertise collective (pluralité, capacité d'analyse de l'ensemble des données disponibles, temps pour le travail collectif …).Leurs résultats peuvent être fragiles et de ce fait, faire l'objet de contestations.Une troisième tension traverse l'expertise.Elle induit d'une part la nécessité de séparer l'évaluation et la gestion des risques et, d'autre part, la nécessité de mettre en perspective les résultats de l'évaluation au regard de la faisabilité des mesures de gestion.Cette tension est particulièrement forte dans des situations d'incertitude, où, en application du principe de précaution, il convient de qualifier l'incertitude et le niveau de risque, et de mettre en œuvredes mesures proportionnées.Ceci exige notamment de connaître les impacts socio-économiques des mesures et les alternatives possibles.Un manque de lisibilité des modalités de séparation de l'évaluation et de la gestion et un manque de transparence quant à la traduction des avis en mesures de gestion contribuent à l'érosion de la crédibilité de l'expertise. RECOMMANDATIONSConcernant l'Anses, le Conseil scientifique souligne que les enjeux procéduraux font déjà l'objet d'une attention et d'efforts constants de l'agence (collectifs d'experts réunissant des scientifiques choisis pour leurs compétences, sous condition d'indépendance dans le secteur d'activité considéré).Il en est de même concernant les relations avec la recherche (capacités de recherche propres, financement de programmes soutenant des études destinées à combler des déficits de connaissances, coordination du Partenariat européen pour l'évaluation des risques liés aux substances chimiques (PARC)).Au niveau international, l'agence est très généralement considérée comme l'une des plus avancées sur ces questions.Pour autant, l'Anses est soumise aux tensions de l'expertise.Les enseignements et recommandations issus des trois études de cas analysées par le GT sont particulièrement adaptés aux situations dans lesquelles il existe de fortes incertitudes et/ou des controverses entre experts.Soucieux de limiter les risques de mise en cause de l'expertise, le Conseil scientifique formule quatre groupes de recommandations visant à améliorer les procédures, à mieux éclairer le processus de décision, à intensifier les interactions avec les parties prenantes et à renforcer la séparation de l'évaluation et de la gestion des risques au sein de l'Anses. Anses/FGE/0035 [version h] -PR1/Anses/9La crédibilité de l'expertise scientifique Enjeux et recommandations RAPPORT du groupe de travail du

National audience

International audience

National audience