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Structural variations, gene polymorphism and expression reveal major candidate genes associated with pod and seed size variation during peanut (Arachis hypogaea L.) domestication
No full textData availability: The raw RNA-Seq data generated and analyzed in the current study are publicly available in the ArrayExpress collection in BioStudies under the accession number: E-MTAB-15520 (https:/www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15520).Tribute: The authors would like to pay tribute to their colleague, Professor Djibril Sane, who passed away in September 2020. He was involved in the supervision of Mounirou H. Alyr.International audienceBackground: Pod size is a key agronomic trait in peanut (Arachis hypogaea) that underwent strong selection during domestication. In a previous study, we fine-mapped a quantitative trait locus (QTL) for pod and seed size to a 168.37 kb region on chromosome A07. Here, we integrated structural variation analysis, gene sequence comparison, and transcriptomic profiling to refine candidate genes and uncover molecular mechanisms underlying domestication-related differences in pod size.Results: Comparative genomic analyses among Arachis duranensis, A. monticola, and four cultivated varieties (Fleur11, Tifrunner, Shitouqi, Fuhuasheng) revealed multiple structural variations in the QTL interval, including a ~ 25 kb inversion between the wild species (A. duranensis and A. monticola) and all cultivated genotypes. This inversion altered the orientation of a candidate gene, Aradu.DN3DB/Arahy.5EZV1I (SAP), which also carried a non-synonymous SNP distinguishing wild and cultivated lines. RNA-Seq profiling of two parental lines (Fleur11 and 12CS_091) and two near-isogenic lines (NILs) at 20 and 40 days after flowering (DAF20, DAF40) identified two differentially expressed genes in the QTL region: Aradu.SFU0J/Arahy.VEUG4Z (phytochromobilin synthase) and gene.15763 (mitochondrial ribosomal protein), both showing higher expression in large-pod genotypes. GO enrichment analysis revealed contrasting strategies between pod size groups: small-pod genotypes emphasized early maturation and storage metabolism, while large-pod genotypes maintained prolonged growth through hormonal signaling and cell division, supporting greater pod expansion.Conclusions :This study identifies three promising candidate genes for seed and pod size variation during peanut domestication: Aradu.DN3DB/Arahy.5EZV1I, gene.15763, and Aradu.SFU0J/Arahy.VEUG4Z. The ~25 kb inversion affecting Aradu.DN3DB/Arahy.5EZV1I and the expression differences in Aradu.SFU0J/Arahy.VEUG4Z between large- and small-pod genotypes suggest structural and transcriptional mechanisms contribute to phenotypic variation. These findings advance understanding of domestication-related traits in peanut and provide a foundation for functional validation, which could guide breeding strategies to optimize pod and seed size
Multifunctionality of agroecological vineyards: complex interactions between functional and taxonomic diversity of service crops and ecosystem services
No full textInternational audienceHighlights: • Agroecological practices shaped the taxonomic and functional diversity of service crops. • Service crops improved soil structure and natural enemies' abundance. • Service crops reduced soil fertility and limited grapevine growth and yield. • Adaptive management is needed to limit grapevine–service crop competition.Abstract: Agroecological practices in vineyards can enhance agroecosystems multifunctionality, by reducing pesticides use and their adverse effects on human health and the environment. However, growers remain concerned about potential negative impacts of plant diversification on grapevine performance, and existing literature report conflicting findings. This study employs both taxonomic and functional approaches to characterize weed communities in inter-rows of agroecological vineyards and assesses the effects of different plant diversification strategies-tillage (Tviti), service crop (Aviti), service crops and agroforestry (Dviti)- on soil quality, grapevine performance, and natural regulation processes over a two-year period in the south of France. Management practices shaped weed communities functional traits, with high tillage (Tviti) favoring acquisitive strategies plant communities. Those traits directly affected several of the indicators of services: service crops competed for soil resources, particularly nitrogen, affecting negatively grapevine yield and vigor. However, in 2023, more diverse systems (Aviti, Dviti) exhibited improved soil aggregate stability and increased natural enemy diversity. However, results varied significantly across years, highlighting the importance of environmental factors. Finally, no clear agroforestry effect was observed, likely due to the young age of the trees. A deeper understanding of the relationships between functional diversity and multiple ecosystem services in vineyards could help mitigate potential trade-offs associated with plant diversification. Furthermore, adapting management practices to local abiotic conditions and growers’ requirements is essential for optimizing both vineyard productivity and ecological sustainability
Banques et fintechs : le capital-investissement comme éléments de différenciation entre groupes bancaires coopératifs et à capital-actions
No full textInternational audienceThis paper examines how French banking groups engage in fintech financing, distinguishing cooperative banks from shareholder-owned banks. Drawing on agency theory and the resource- based view, we analyze whether organizational form shapes banks’ investment strategies toward fintechs. Using an original dataset covering the period 2000-2025 and binomial and multinomial logit models, we show that differences between bank types lie less in the decision to invest than in how they invest. In particular, cooperative and shareholder-owned banks differ in terms of geographic focus, timing of entry, and the types of fintechs they finance.Cet article analyse les stratégies de financement des fintechs mises en oeuvre par les groupes bancaires français, en distinguant banques coopératives et banques à capital-actions. En mobilisant la théorie positive de l'agence et l'approche fondée sur les ressources, nous étudions si la forme organisationnelle influence la manière dont les banques s'engagent dans le financement des fintechs par capital-investissement. À partir d'une base de données originale couvrant la période 2000-2025 et de modèles logit binomial et multinomial, les résultats montrent que les différences portent moins sur la décision d'investir que sur les modalités d'intervention, notamment en termes de localisation, de stade d'entrée et de profil des fintechs financées
Agrainer les animaux sauvages : manipulations et recompositions des assemblages entre humain.es et non-humain.nes
No full textInternational audienceCet article explore la pratique de l’agrainage – l’apport de grains à la faune sauvage – grues cendrées, sangliers, canards et flamants roses, dans trois territoires : la Camargue et le lac du Der en France, et Vattenriket en Suède. Utilisé pour détourner les animaux des cultures ou les fixer à des fins cynégétiques ou touristiques, l’agrainage interroge les frontières du « sauvage », traditionnellement associé à l’autonomie animale. À partir d’une enquête socio-ethnographique multi-située, nous montrons que le sauvage relève d’un gradient relationnel, façonné par des pratiques humaines. Ces interventions produisent une nature partiellement fabriquée, dans laquelle les espèces sont catégorisées selon des critères locaux : espèces protégées ou nuisibles, gibier. Nous proposons la notion de « suffisamment sauvage » qui éclaire les seuils implicites qui rendent ces compromis acceptables. Pour autant, l’agentivité animale – par la résistance, l’adaptation ou l’imprévisibilité – continue de perturber les dispositifs humains, faisant de la coexistence un équilibre toujours instable, situé et renégocié
Architectural singularities in wild Coffea species: integrated morphological perspectives for climate-resilient coffee cultivation
No full textInternational audienceBackground: Global coffee production faces increasing threats from climate change, including rising temperatures, prolonged droughts, and the spread of diseases. Wild coffee species, notably those growing in seasonally highly arid environments in Madagascar, represent a critical genetic resource to address these challenges. Understanding adaptive traits allowing these species to establish into arid environments is essential to guide breeding strategies for creating resilient coffee varieties.Aims: We identified structural strategies likely to explain drought tolerance in wild Malagasy Coffea species.Methods: We used architectural analysis to describe three Baracoffea species, Coffea ambongensis, C. bissetiae, and C. boinensis, and compare them to known cultivated Coffee. Structural and functional traits were measured across developmental stages.Results: Our results suggest that, in addition to rhythmic growth and terminal flowering on shoots, Baracoffea species possess unique architectural characteristics including a complex architectural unit made of four different stem types, reflecting a high level of functional specialisation. Species-specific developmental strategies reflect different pathways into edifying plant architecture mainly depending on primary and secondary growth trade-offs.Conclusion: These findings highlight the architectural diversity of Baracoffea, identify potentially important drivers of ecological adaptation through development pathways and therefore highlight the potential of this group of species for breeding climate-resilient coffee varieties
Modeling breeding programs considering social behavior in large groups of farmed fish
No full textBreeding programs are essential in aquaculture, improving economically and environmentally important traits. In aquaculture systems, animals are raised in large groups, where social interactions are frequent and can influence individual performance. In these circumstances, indirect genetic effects can play an important role in the response to selection, and consequently, their effects on selection outcomes must be analyzed.This study aimed to evaluate the implications of heterogeneous social interaction effects on fish breeding programs using stochastic simulations. We simulated a fish breeding program with 2000 selection candidates from 1000 families formed by a partial mating design of 100 males and 100 females. Social interactions were simulated, affected by the target phenotype and two latent-personality traits. We investigated how genetic gains and phenotypic variances are affected by the magnitude and direction of social interaction effects on the target phenotype, different selection strategies, and the genetic correlations between the target phenotype and personality traits. Our results showed that increased social interaction effects lead to greater phenotypic variability in the target trait. Under mass selection, the genetic means of personality traits change, and these changes depend on the strength and direction of genetic correlations between the focal and personality traits. Conversely, group selection did not increase phenotypic variability but reduced genetic gain for the focal trait compared to mass selection. Moreover, group selection did not alter the genetic means of personality traits. However, this approach increased the rate of inbreeding per generation, which could be mitigated by optimizing the number of families per group..</div
Predictions of wheat phenotypic variability by integrating high-throughput phenotyping observations into a crop growth model
No full textInternational audienceAccurate prediction of phenotypes across genotypes and environments is crucial for accelerating crop improvement. Process-based crop growth models (CGMs) can capture complex genotype-by-environment interactions, but their use is limited by labor-intensive genotypic parameter measurements. Here, we developed a faster data assimilation pipeline integrating high-throughput phenotyping (HTP) observations with the Sir-iusQuality wheat model to efficiently estimate key genotypic parameters and predict genotype performance. Using time-series RGB imagery from a ground-based Phenomobile, we assimilated intercepted photosynthetically active radiation (fIPAR), heading date, and final grain yield to jointly assimilated to calibrate twelve genotypic parameters governing phenology, canopy development, light interception, biomass accumulation, and grain filling. Two data assimilation strategies-a Bayesian DREAM (zs) algorithm and a lookup table (LUT) inversion-were compared through both in silico experiment and eight years of multi-environment field trials of nine durum wheat cultivars. The LUT method demonstrated superior computational efficiency, with prediction accuracy comparable to Bayesian inference on real field data. Multi-year field trials showed that two environments (year/site) were sufficient to reliably characterize genotypic parameters and predict performance across environments. By combining time-series HTP data with ecophysiological modeling, our data assimilation pipeline offers breeders a powerful tool for genotype characterization. It streamlines the process of capturing environmental variance and phenotypic stability, reducing time and effort in crop improvement
Dehydration-driven organization of metabolites into NaDES-like assemblies in orthodox seeds
No full textà paraitre dans New PhytologistInternational audienceDesiccation tolerance in plants, especially during orthodox seed dehydration, relies on compatible solute accumulation, complex molecular mechanisms, and intermolecular organizations that remain poorly understood. We combined metabolite profiling, mass spectrometry imaging (MSI), and electrospray and cold-spray ionization mass spectrometry (ESI/CSI) to investigate metabolite organization into natural deep eutectic solvent-like assemblies during oilseed rape seed dehydration. We show that sucrose co-localizes and interacts with organic and amino acids in seed tissues to form hydration-dependent, sucrose-centered assemblies, whose formation is promoted by water loss and reproduced in bioinspired artificial mixtures displaying NaDES-like physicochemical properties. These findings support the idea that seed metabolites, with sucrose as preferential matrix, organize into eutectic-like supramolecular networks during dehydration, suggesting a physicochemical basis for cytoplasmic stabilization in desiccation-tolerant seeds
