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Selection for growth or carcass yield before final sexual maturation will not impact egg production in rainbow trout Oncorhynchus mykiss
No full textInternational audienceThe rainbow trout is the most widely farmed freshwater species in Europe. Early research on the genetic basis of egg production began in the 1970s, but with several generations of selective breeding now established—mainly focused on body weight—understanding the genetic relationships between growth and spawning performance has become necessary. This study investigated a commercial line of rainbow trout, monitoring about 1600 females from 656 families, from portion size (355 g) to maturity (2600 g), to assess egg production traits at first spawn (total spawn weight and egg number, mean egg weight, relative fecundity, and gonado-somatic index). Thermal growth coefficients (TGCs) were calculated across six periods until spawning. Fillet fat content was measured, and carcass yield was predicted non-invasively through ultrasound tomography. Heritabilities and genetic correlations between growth, carcass quality and spawning traits were estimated using linear animal models. Genetic correlations between body weight at different ages and spawning traits were either nonsignificant or positive (0.05 to 0.70). Comparable trends were observed for TGCs (-0.20 to 0.63) and carcass yield at 16 months (-0.03 to 0.24). In contrast, predicted carcass yield at 20 months showed negative genetic correlations with spawning traits (-0.16 to -0.47). These findings indicate that selection for growth up to 20 months should not adversely affect and may improve spawning performance. However, improving carcass yield after 20 months may compromise egg production. Monitoring spawning performance in selective breeding programs is advised to anticipate shifts in genetic correlations and to optimize selection strategies all along the life cycle
A Cattle Pangenome Approach Reveals Novel Non-Reference Unique Insertions and Their Impact on Economic Traits
No full textInternational audienceThe current cattle reference genome assembly, which is derived from a singleHereford cow, does not encompass the entire range of genetic variationspresent within the species. Several megabases of sequences are still missingand these can contain genomic regions potentially associated with keyphenotypes.Structural variations (SVs ≥ 50 nucleotides) are difficult to detect using onlystandard approaches of either short or long-read sequence mapping to thecurrent bovine genome assembly. To overcome this, recent advances insequencing technologies to produce high-quality long-read sequencescombined with the development of pipelines and tools for sequence analysispave the way for the use of pangenomics in cattle. Those approaches providethorough comprehension of the extent of genetic diversity among cattlebreeds.In this study, we constructed a cattle pangenome graph using 16 high-qualityhaplotype-resolved genome assemblies originating from 9 French cattlebreeds, encompassing both major dairy and beef populations as well asregional breeds, and including the Yak (Bos grunniens) as a close species. Acombination of complementary methods led to the detection andcharacterization of 101,219 structural variations. Of these, 33,634 structuralvariants were classified as non-reference unique insertions (NRUIs), addingseveral megabases of new genomic sequences that are not present in thecurrent Hereford reference genome.These NRUIs were subsequently genotyped (presence/absence) in a largemulti-breed genotyped cattle population. With these NRUI data, all sampleswere clustered in distinct groups corresponding to the breed of origin. Thisresult is of particular interest as the NRUIs were able to provide a cleardescription of the breed structure.Our findings underscore the importance of pangenome-based approaches touncover the full spectrum of genomic variations and establish a potential linkwith cattle key phenotypes
Prediction of source nutrients for microorganisms using metabolic networks
No full textMetagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes remains a major challenge, despite advances in high-throughput culturomic methods. The quantity of simultaneous experimental variables is constrained by time and resources, but the list can be reduced using computational biology. Given an annotated genome, metabolic modelling can be used to predict source nutrients required for the growth of a microbe, which acts as an initial screen to inform culture and isolation experiments. This chapter provides an overview of metabolic networks and modelling and how they can be used to predict the nutrient requirements of a microorganism, followed by a sample protocol using a toy metabolic network, which is then expanded to a genome-scale metabolic network application. These methods can be applied to any metabolic network of interest--which in turn can be created from any genome of interest--and are a starting point for experimental validation of source nutrients required for microorganisms that remain uncultivated to date
Microclimate walk for outdoor thermal comfort assessment of four old and new urban configurations in a mediterranean climate
No full textInternational audienc
Beliefs about EU 2030 climate commitments across public, expert, and policy audiences
No full textInternational audienceThe European Union (EU) has adopted ambitious climate policies to reduce greenhouse gas emissions by 55% by 2030. While technical, economic, and political feasibility have been widely analyzed, far less is known about a critical enabling factor: whether key societal actors perceive these targets as credible and achievable. In this study, we elicit probabilistic beliefs about future EU emission reductions from a sample of citizens designed to be representative across 12 EU member states and compare them with the expectations of climate policymakers and experts. Our findings reveal that all three groups anticipate substantial progress compared to current levels. At the same time, citizens are more skeptical about achieving the target and substantially more uncertain than elites, expecting, on average, a 43% reduction by 2030 compared to the EU’s 55% reference. Moreover, we identify a notable misalignment: elites tend to systematically underestimate public skepticism. This gap underscores the need to improve policy communication, directly address citizens’ concerns, and foster a shared understanding to enhance the perceived credibility and political sustainability of the EU’s climate goals
Diverses voies d'émergence menant à la résistance multidrogue chez les champignons phytopathogènes : le cas de Zymoseptoria tritici
No full textHuman activities promote the rapid adaptation of certain organisms, notably crop pests and pathogens. Active ingredients (AIs), particularly antibiotics and pesticides, have been widely deployed over the 20th and 21st centuries as powerful control tools, favoring the emergence of resistance in target populations. As the renewal of the therapeutic arsenal slows and resistance becomes widespread, it is increasingly urgent to adopt a “One Health” approach to preserve the efficacy of our pharmacopeia, a cornerstone of public health and food security. In this context, we studied the evolution of fungicide resistance in the model fungus Zymoseptoria tritici, the causal agent of septoria leaf blotch in wheat. In particular, we focused on multidrug resistance (MDR), a broad-spectrum generalist resistance phenotype. Associated with moderate resistance factors, its impact on treatment efficacy in agriculture is often underestimated. However, due to its generalist nature, MDR is likely to compromise the effectiveness of resistance management strategies and future AIs. This thesis aims to explore the mechanisms and genomic determinants of MDR in Z. tritici, as a basis for a better understanding of this phenotype. Detected in the field in Europe since 2009, MDR in Z. tritici has been primarily associated with overexpression of the efflux transporter gene Mfs1, driven by transposable element (TE) insertions in its promoter (PMFS1), leading to increased, non-specific efflux of AIs. Recent field monitoring data, however, indicate a quantitative increase in resistance factors, suggesting the contribution of additional mechanisms. To identify these mechanisms, we investigated MDR mutants obtained through experimental evolution under different fungicide selection pressures. Efflux assays revealed contrasting mechanisms depending on the mutant, involving increased efflux or not. Among candidate genes identified by whole-genome resequencing, we identified a gain-of-function C740Y mutation in an AtrR-like transcription factor, which we experimentally validated as contributing to MDR. Furthermore, cases of aneuploidy associated with specific resistance profiles were identified, suggesting that genomic plasticity contributes to adaptive dynamics leading to MDR selection in vitro. We also explored MDR mechanisms in natural strains by analyzing 374 European isolates (2020–2021). Sequencing of PMFS1 revealed TE insertion polymorphism more diverse than previously described, partially associated with the MDR phenotype. Quantification of terbinafine resistance (a phenotypic marker of MDR) in these isolates and their progeny from sexual crosses highlighted the quantitative nature of this trait. Its polygenic basis was confirmed through a genome-wide association study (GWAS), revealing candidate genes with diverse putative functions, consistent with the complex determinism of MDR observed in vitro. This work demonstrates that MDR in Z. tritici can emerge through multiple evolutionary trajectories, leading to the selection of diverse mechanisms, including increased efflux dependent or independent of MFS1 overexpression. It highlights the high genomic plasticity of this fungus, which likely facilitates its rapid adaptation to fungicides, as increasingly reported in other pathogenic fungi. Because limiting the selection of these mechanisms represents a major challenge for sustainable disease control, our study underscores the need to better integrate MDR prevention into resistance management strategies in agriculture.Les activités humaines favorisent l’adaptation rapide de certains organismes, notamment des ravageurs des cultures et des agents pathogènes. Puissant outil de contrôle, les substances actives (Active Ingredients, AIs), en particulier antibiotiques et pesticides, ont été largement déployées au cours des XXᵉ et XXIe siècles, favorisant l’émergence de résistances chez les populations cibles. Alors que le renouvellement de l’arsenal thérapeutique ralentit et que le phénomène de résistance se généralise, il devient urgent d’adopter une approche « One Health » pour préserver l’efficacité de notre pharmacopée, pilier de la santé publique et de la sécurité alimentaire. Dans ce contexte, nous étudions l’évolution de la résistance aux fongicides chez le champignon modèle Zymoseptoria tritici, agent de la septoriose du blé. En particulier, nous nous intéressons à la résistance multidrogue (MDR), un phénotype généraliste à large spectre associé à des facteurs de résistance modérés et dont l’impact sur l’efficacité des traitements en agriculture est souvent négligé. Cependant, par son caractère généraliste, la MDR est susceptible de compromettre l’efficacité des stratégies de gestion de résistance, et des AIs futurs. Ce travail de thèse présente une exploration des mécanismes et déterminants génomiques de la MDR chez Z. tritici, vers une meilleure compréhension de ce phénotype. Détectée depuis 2009 au champ en Europe, la MDR chez Z. tritici est principalement associée à la surexpression du gène codant le transporter Mfs1, liée à l’insertion d’éléments transposables (TE) dans son promoteur (PMFS1), qui mène à un efflux accru non sélectif d’AIs. Toutefois, des données récentes de surveillance indiquent une augmentation quantitative des facteurs de résistance au champ, suggérant la contribution de mécanismes additionnels. Pour identifier ces mécanismes, nous avons étudié des mutants MDR obtenus par évolution expérimentale sous différentes pressions de sélection fongicide. Des tests d’efflux réalisés indiquent des mécanismes contrastés en fonction des mutants, impliquant ou non de l’efflux accru. Parmi les gènes candidats identifiés par reséquençage des génomes, nous avons expérimentalement validé le rôle dans la MDR de la mutation gain de fonction C740Y dans un facteur de transcription de type AtrR. Par ailleurs, des cas d’aneuploïdies associés à des profils de résistance spécifiques ont été identifiés, suggérant que la plasticité génomique participe aux dynamiques adaptatives menant à la sélection de mécanismes de MDR in vitro. Nous avons également exploré les mécanismes de MDR en jeu chez les souches naturelles, en analysant 374 isolats européens (2020-2021). Le séquençage de PMFS1 a permis d’identifier un polymorphisme d’insertion de TE plus divers que décrit précédemment dans ce promoteur, partiellement associé au phénotype MDR. La quantification de l’intensité de la résistance à la terbinafine (marqueur phénotypique de la MDR) de ces isolats et de descendants issus de croisements sexués a mis en évidence la nature quantitative de ce trait. Son caractère polygénique a été confirmé à travers une étude d’association pangénomique (GWAS), révélant des gènes candidats aux fonctions putatives variées, en accord avec un déterminisme complexe observé in vitro. Ce travail montre que la MDR chez Z. tritici peut émerger de multiples trajectoires évolutives et la sélection de mécanismes divers, incluant un efflux accru dépendant ou non de la surexpression de MFS1. Il met en lumière une grande plasticité génomique de ce champignon, susceptible de favoriser son adaptation rapide aux fongicides, comme documenté chez un nombre croissant d’autres champignons pathogènes. Parce que limiter la sélection de ces mécanismes représente un enjeu majeur pour un contrôle durable des maladies fongiques, cette étude souligne la nécessité de mieux intégrer la prévention de la MDR dans les stratégies de gestion de la résistance en agriculture
Arboviroses en France hexagonale :une menace émergente à l’interface hommeanimal vecteur
No full textInternational audienc
Emerging remote sensing techniques for hydrological applications
No full textInternational audienceIn light of the rapid advancements in hydrological science research facilitated by cutting-edge remote sensing technologies, such as synthetic aperture radar (SAR), hyperspectral imaging, and Light Detection and Ranging (LiDAR), we have curated a special issue in Remote Sensing of Environment entitled "Emerging remote sensing techniques for hydrological applications", spanning from October 2022 to April 2024. This special issue comprises 31 publications that highlight methodologies leveraging multi-sensor satellite platforms, unmanned aerial vehicles (UAVs), and advanced physical models and machine learning approaches to improve the monitoring and modeling of key hydrological flux and state variables. These remote sensing retrievals (e.g., river discharge and soil moisture) have been applied to various operational hydrological applications such as real-time flood monitoring and drought risk assessment. To provide a systematic overview, we categorize these publications based upon hydrological themes and the number of publications, covering topics such as water body, soil moisture, river discharge, water level, drought, water storage, and other related areas. Finally, we provide an outlook that envisages how the emerging trends (e.g., multi-sensor integration and machine learning-driven approaches) identified from the published studies will evolve and shape future research directions in hydrological remote sensing
The effect of humidity, temperature, and drying duration on microparticle detachment force: insights into capillary-induced deformation at the particle–substrate interface
No full textInternational audienceWe experimentally investigate how drying history influences microparticle-substrate adhesion in hydrophilic systems. By systematically varying air temperature, relative humidity, and drying duration under controlled conditions, we quantify the detachment force of individual microparticles. Air temperature emerges as the dominant factor: higher temperatures and lower humidity enhance adhesion, while prolonged drying generally reduces it, except under combined high-temperature and low-humidity conditions, where strong adhesion persists. Complementary scanning electron microscopy (SEM) results reveal drying-time-dependent changes in the particle-substrate contact size, consistent with capillaryinduced compression of the contact zone followed by partial relaxation. These findings indicate that transient capillary stresses during evaporation deform the particle-substrate interface and leave a lasting imprint on adhesion strength. Overall, the study shows how capillarity, drying dynamics, and contact mechanics couple to regulate adhesion in colloidal systems, offering new insights into particle-substrate interactions in soft matter contexts.</div
Quels leviers d'adaptation de l'agriculture au changement climatique ? Inventaire et analyse des projets de recherche et développement en région Auvergne Rhône Alpes.
No full textClimate forecasts predict a general rise in temperatures and an intensification of droughts, especially in Mediterranean zones moving northward in France. By 2050, the climate of the Auvergne-Rhône-Alpes region is expected to become more Mediterranean, and its agriculture will have to face new meteorological challenges. Moreover, given the globalized system in which this agriculture operates, this is not the only challenge it will encounter, and an agroecological transition is underway to meet these food, health, environmental, economic, and social issues, among others.In this context, the AgriAuRA2050 project aims to design viable production methods and practices to ensure the sustainability of farms and the economic viability of three sectors in the Auvergne-Rhône-Alpes region - field crops, herbivore livestock, and arboriculture - by 2050, in a context of climate change and agroecological transition. As part of this project, an inventory of structured projects in the Auvergne-Rhône-Alpes region was carried out to summarize the known responses of crop and livestock systems to non-conventional practices in the region. The objective was to identify the the levers used by projects in the region to adapt agriculture to climate change, and in particular to water constraints, which are likely to be a major challenge in the coming years. A characterization of these levers and a summary of the results obtained were also carried out.Research carried out mainly on the Internet identified 65 projects and highlighted 27 main levers grouped into four main categories: genetics, agricultural practices, functional diversity, and miscellaneous subjects for more forward-looking projects not focused on specific levers. A wealth of information was collected on these projects, especially through discussions with coordinators, in order to characterize them. Additionally, complete or partial results were obtained for 31 projects, and were the subject of a qualitative analysis summarizing their overall positive, negative, or neutral effects based on the lever studied and the variable measured.The levers studied were categorized by the sectors testing them. Thus, the miscellaneous subjects are the only ones to include projects involving several sectors, and otherwise only include livestock projects. The other groups include all three sectors, with more field crop projects for genetic levers, more arboriculture projects for agricultural practices, and a more balanced distribution for functional diversity levers. Regarding implementation dates and durations, projects focused on genetic or agricultural levers tend to be short, ongoing, and started after 2015, often tested on a reduced scale, primarily at specific sites. On the other hand, projects of miscellaneous subjects tend to be longer, also ongoing, and initiated between 2000 and 2020. They are implemented on a larger scale, often at the departmental or regional level, as are the projects on functional diversity, which also have the highest proportion of completed projects. These are relatively short and were typically initiated after 2015, although some are older. The structures managing these projects vary between groups. For example, research-focused institutions are more prominent in the agricultural practices and genetics groups, while the functional diversity and miscellaneous subjects include more associations. However, agricultural chambers are present in every groups. Moreover, the results of the experiments are generally positive or neutral for genetic strategies, more variable and nuanced with a positive trend for agricultural practices and functional diversity, and overall positive for the miscellaneous subjects, in a negative climatic context. These overall positive results may partially reflect a communication bias, with a tendency to highlight successes. Nevertheless, they are also supported by literature for several levers.Additionally, a comparison with work conducted in other parts of the AgriAuRA2050 project revealed that the practices and levers tested by groups of farmers or individual farmers in the Auvergne-Rhône-Alpes region are similar with those studied in structured projects. Thus, the issues explored by research institutions and technical or professional organizations overlap with those of farmers.Les prédictions climatiques prévoient une hausse générale des températures et une intensification des sécheresses, notamment dans les zones méditerranéennes qui remontent en France vers le nord. Ainsi, à l’horizon 2050, le climat de la région Auvergne-Rhône-Alpes devrait devenir plus méditerranéen, et son agriculture devra faire face à de nouveaux défis météorologiques. Par ailleurs, du fait du système mondialisé dans lequel s’inscrit cette agriculture, ce n’est pas le seul défi auquel elle va se confronter, et une transition agroécologique est en marche pour répondre à ces enjeux alimentaires, sanitaires, environnementaux, économiques et sociaux, entre autres.Dans ce contexte, le projet AgriAuRA2050 vise à concevoir des modes et itinéraires de production envisageables pour permettre la pérennité des exploitations agricoles et garantir la viabilité économique de trois filières de la région Auvergne-Rhône-Alpes, grandes cultures, élevage d’herbivores et arboriculture, à l’horizon 2050 dans un contexte de changement climatique et de transition agroécologique. Dans le cadre d’un des volets de ce projet, un travail de synthèse des réponses connues des systèmes de cultures et d’élevages avec des itinéraires techniques non conventionnels sur la région a été réalisé par un inventaire de projets structurés mis en place sur la région Auvergne-Rhône-Alpes. L’objectif était de dégager les leviers étudiés par les projets réalisés en région sur l’adaptation de l’agriculture au changement climatique, notamment à la contrainte hydrique qui s’annonce comme un enjeu majeur dans les années à venir. Une caractérisation de ces leviers et une synthèse des résultats obtenus a aussi été réalisée.Les recherches effectuées essentiellement sur internet ont permis d’identifier 65 projets, et d’en dégager 27 leviers principaux qui ont été rassemblés en quatre grands groupes : génétique, pratiques agricoles, diversité fonctionnelle et sujets divers pour les projets plus prospectifs ne s’intéressant pas à des leviers à proprement parler. De nombreuses informations ont été collectées sur ces projets, notamment par des échanges avec les coordinateurs, afin de les caractériser au mieux. De plus, des résultats complets ou partiels ont pu être obtenus pour 31 projets, et ont fait l’objet d’une analyse qualitative synthétisant un effet global positif, négatif ou neutre de chaque essai selon le levier étudié et la variable mesurée.Les leviers étudiés ont pu être caractérisés par les filières les testant. Ainsi, les sujets divers sont les seuls à comprendre des projets s’intéressant à plusieurs filières, et ne comptent sinon que des projets sur l’élevage. Les trois filières se retrouvent dans les autres groupes de leviers, avec davantage de projets en grandes cultures pour ceux génétiques, davantage de projets en arboriculture pour ceux sur les pratiques agricoles, et plus d’équilibre pour les leviers de diversité fonctionnelle. Concernant les dates et durées de réalisation, les projets avec des leviers génétiques ou de pratiques agricoles sont plutôt courts, en cours et commencés après 2015, testés à une échelle réduite, majoritairement au site. En revanche pour les sujets divers, ils sont plutôt longs, surtout en cours également, et leur commencement s’étale entre 2000 et 2020. Ils sont aussi réalisés à une échelle plus large, en grande partie départementale ou régionale, tout comme les projets sur la diversité fonctionnelle, qui comptent par ailleurs la plus grande proportion de projets terminés, plutôt courts, et ayant plutôt commencés après 2015 avec cependant des projets plus anciens. Les structures portant les projets varient également entre les groupes. Ainsi, les structures plus tournées vers la recherche se retrouvent surtout dans les groupes pratiques agricoles et génétique, tandis que les groupes Diversité fonctionnelle et Sujets divers comptent plus d’associations. Les chambres d’agricultures se retrouvent en revanche dans chacun des groupes. Concernant les résultats des essais, ils sont plutôt positifs ou neutres pour les leviers de génétique, plus variables et nuancés avec une tendance positive pour ceux des pratiques agricoles et de la diversité fonctionnelle, et globalement positifs pour les sujets divers, en notant un contexte climatique négatif. Ces résultats globalement positifs peuvent en partie s’expliquer par un biais de communication, avec une tendance à mettre préférentiellement en avant les réussites. Néanmoins, ils sont aussi appuyés par de la bibliographie pour plusieurs leviers.De plus, un croisement avec des travaux effectués dans d’autres volets du projet agriAuRA2050 a permis de se rendre compte que les pratiques et leviers testées par des collectifs d’agriculteurs ou des agriculteurs isolés sur la région Auvergne-Rhône-Alpes rejoignent ceux auxquels les projets structurés s’intéressent. Ainsi, les problématiques explorées par la recherche et les instituts techniques ou professionnels croisent celles des agriculteurs