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Robustness of high‐throughput prediction of leaf ecophysiological traits using near infrared spectroscopy and poro‐fluorometry
No full textData availability statement: The datasets supporting the conclusions of this article are available in the Recherche Data Gouv repository at https://doi.org/10.57745/WVAPOL. The scripts for prediction analyses are publicly available in GitLab: https://forgemia.inra.fr/eva.coindre/robustness_ht_prediction_ecophysiological_traits.International audienceAbstract:Water scarcity is a major threat to crop production and quality. Improving drought tolerance through variety selection requires a deeper understanding of plant ecophysiological responses, but large-scale phenotyping remains a bottleneck. This study assessed the potential of high-throughput tools (spectroscopy and poro-fluorometry) to predict leaf morphological and ecophysiological traits in a grapevine diversity panel grown in pots under well-watered outdoor conditions and under three contrasting soil water treatments in a greenhouse. We found a certain complementarity between measuring devices. Spectrometers could accurately predict leaf mass per area, water content, and water quantity (R2 > 0.58), while the poro-fluorometer was efficient for predicting net CO2 assimilation (R2 > 0.72), regardless of the water treatment. The prediction of leaf mass per area using spectrometers appeared to be quite robust across both outdoor and greenhouse experiments, while the prediction of water use efficiency was dependent on the water treatment, with much better predictions under moderate (R2 > 0.73) than severe water deficit. Calibrated models were then applied to the full diversity panel using only high-throughput measurements to estimate trait values and their broad-sense heritability. Leaf mass per area, also measured directly, showed similar heritability whether based on observed or predicted data. Heritability estimates for predicted traits reached up to 0.5. Overall, our findings support the use of spectroscopy and poro-fluorometry as reliable, nondestructive tools for high-throughput phenotyping, enabling genetic studies on drought-related traits in grapevine.Plain Language Summary: Drought is a major challenge for crop production. To breed grapevines that can better tolerate dry conditions, it is crucial to evaluate how plants respond to water stress using quick phenotyping tools. In this study, we tested two fast, nondestructive tools, near-infrared spectroscopy and poro-fluorometry, on grapevines grown with different water levels. Spectroscopy was accurate for evaluating leaf thickness and water content, while poro-fluorometry was better at predicting photosynthesis. These tools were effective even across different growing environments. The results demonstrate that these methods can aid in estimating genetic variability in drought-related traits, facilitating the selection and improvement of drought-tolerant grapevines
Vegetative and reproductive bud burst in adult mango trees: effects of light and growth unit architectural traits
No full textInternational audienceHighlights: • Mango tree crown receives more light prior to regrowth flush than before flowering. • Architecture and light affect differently vegetative and reproductive bud burst. • The effects of architectural traits and light are additive or in interaction. • Light quantity and quality affect differentially bud burst occurrence and dynamics.Abstract: Tree growth and reproduction results from the balance between internal and environmental factors. Knowledge is lacking on this balance in evergreen fruit trees characterised by a permanent contrasted light environment within the crown. This study hypothesised that architectural traits and light environment of terminal growth units (GUs) affected their vegetative and reproductive bud burst in the mango tree. Bud burst was monitored on terminal GUs of four adult mango trees, cv. 'Cogshall', during vegetative growth and flowering. Some GUs architectural traits (diameter, apical vs lateral position, outer vs inner location within the crown) and their light environment (quantity: relative transmitted PPFD, TrPPFD, and quality: red to far-red ratio, ζ) were measured at sampling. Factors affecting the occurrence, intensity and dynamics of bud burst were evidenced using generalised linear mixed models. The occurrence of vegetative and reproductive bud burst increased with ζ. For vegetative buds, it also increased with GU diameter at medium to high ζ values. The occurrence of reproductive bud burst was higher in the outer than the inner part of the crown, and on the apical than the lateral GUs. Two vegetative and reproductive flushes occurred. The dates of vegetative and reproductive bud burst were globally delayed by low ζ and high TrPPFD. For GUs that burst during the main reproductive flush, bud burst occurred earlier in the outer than the inner part of the crown. The interplay between the signals leading to the observed spatial and temporal patterns of bud burst is discussed
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
The R4multidata project: Comparison of R tools for multidimensional data analysis. Example with RGCCA and mixOmics for supervised methods
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Detection of an anadromous fish demonstrates the potential of passive environmental DNA sampling for monitoring migratory fish
No full textPassive environmental DNA sampling (PEDS) is a new method that is increasingly used to inventory aquatic biodiversity through environmental DNA (eDNA). In contrast to active filtration (AF) to obtain eDNA, which can require batteries and electronics to actively pump water, PEDS involves simply exposing a material to water to passively collect eDNA particles from the environment. As the duration of sampling takes place over several days, this could detect species missed during active filtration. However, its potential to spatially and temporally detect mobile fauna has been little investigated to date. To explore this, this study evaluated its potential to monitor a migratory fish, the first study of this kind. After a preliminary experiment in a fish pass equipped with cameras to validate our workflow, we monitored in the field the upstream migration of an anadromous fish, the twaite shad Alosa agone. The field study was carried out across 25 km of the Aude River in the south of France over a period of seven weeks (February to April 2025). This monitoring period was chosen based on historical direct observations to cover an initial phase without twaite shad in the river, followed by the first adult arrivals, and subsequent confirmed observations in the spawning area. Using a metabarcoding approach with 12S rRNA MiFish-U primers, we successfully detected twaite shad both with PEDS (22%) and AF (10%), finding no significant difference between the methods. At the ecological level, no clear upstream migration pattern could be characterized as no significant effects of environmental covariates (temperature, water flow) were found on twaite shad detection. Nonetheless, these results are encouraging for PEDS monitoring of fish species both spatially and temporally, especially considering that migration of this fish was incredibly low in the study area in 2025 (3 spawning events recorded in 2025 compared to a mean of 314 per year between 2021 and 2024). Moreover, our occupancy model indicates that the sampling design could be further optimized for future monitoring by increasing the number of PEDS replicates (to up to 11). The low cost, ease of deployment and effectiveness of passive samplers (for mobile species, in turbid waters, etc.) make these tools an additional asset for eDNA biodiversity surveys in a variety of environments
Early root-root interactions weaken foliar defense responses against Septoria tritici blotch in a durum wheat varietal mixture
No full textInternational audienceThe interactions between co-cultivated plant cultivars are increasingly recognized as influencing their susceptibility to pathogens in mixtures. However, the underlying mechanisms remain largely unexplored. Using a model of durum wheat cultivar mixtures where susceptibility to Septoria foliar disease is increased, we combined aerial and root phenotyping with transcriptional analyses and untargeted metabolomics to elucidate the potential signaling cascade driving this modulation of susceptibility. We observed contrasting root architectures between cultivars in mixture. Molecular analysis showed a delayed induction of defense-related genes and metabolites following pathogen inoculation in plants grown in mixture compared to pure stand. The findings suggest that root architecture potentially triggers a competitive response that could delay the induction of defense responses following pathogen inoculation. Altogether, these results point to a possible interplay between root architecture, resource competition, plant metabolism, and defense modulation in shaping plant–pathogen interactions within varietal mixtures
First-ever data on space use by breeding Whiskered Terns Chlidonias hybrida using bio-logging
No full textInternational audienceWetlands are critical ecosystems for many species of conservation concern, including migratory birds. These species face resource depletion and unpredictability in the context of global change and are expected to adjust their space use accordingly. Understanding how waterbirds use space and identifying their foraging needs are essential for guiding conservation efforts. Here, we present preliminary results on the fine-scale space use of a wetland flagship species, the Whiskered Tern Chlidonias hybrida, in La Brenne, a historical French breeding stronghold. The species is listed as 'Vulnerable' in France and breeds in only a few large wetlands. For the first time, we equipped four adult terns with miniature GPS tracking devices, providing unique, high-resolution data on their daily movements throughout the breeding season (i.e. pre-incubation, incubation, rearing, and post-breeding). Our results showed that most daily foraging trips did not exceed 2-3 km, resulting in relatively small home ranges (ranging from 2.00 km2 to 14.95 km2). Values were higher during the post-breeding period (up to 8 km from the nest and home range size up to 74.45 km2). Furthermore, we found that Whiskered Terns remained faithful to their foraging areas throughout the season and preferentially foraged in ponds - especially those near their colony - compared with other potential foraging habitats. On average, 91% of foraging positions occurred in ponds and 9% in grasslands. We also provide practical details on bird capture and device attachment methods. Finally, this pioneering bio-logging study offers promising prospects for future research on the movement ecology of Whiskered Terns, which could be invaluable for their conservation
A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution
No full textData availability: Raw data from long-read sequencing and genome assemblies of C. micrantha, C. medica and C. reticulata were deposited at EBI under the following accession numbers: - CITMI (C. micrantha): Raw data: PRJEB78372 - Assemblage: PRJEB78515 - Umbrella: PRJEB78526 - CITME (C. medica): Raw data: PRJEB78445 - Assemblage: PRJEB78498 - Umbrella: PRJEB78525- CITRE (C. reticulata): Raw data: PRJEB78477 - Assemblage: PRJEB78537 - Umbrella: PRJEB78524Resequencing raw reads derived from 58 citrus accessions were deposited in the EBI database under AC experiment accessions ERX12760151, ERX12780957, ERX12791201 and ERX12817346 to ERX12817400 (supporting information, Table 1).The raw RNA-seq data for C. medica, C. reticulata, C. maxima and C. micrantha were deposited in the European Nucleotide Archive under accession code PRJEB77075. The pseudochromosome and chloroplast genome assemblies of C. medica, C. reticulata and C. micrantha and their annotations are available on: https://citrus-genome-hub.southgreen.fr.International audienceThe main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies of C. medica, C. reticulata and C. micrantha, released for the first time alongside a published chromosome-scale assembly of C. maxima. Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA-satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra- and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research
Doping feruloylated arabinoxylan covalent hydrogels with cellulose nanocrystals
No full textInternational audienceTo improve the viscoelastic properties of Feruloylated Water Extractable Arabinoxylan (F-WEAX) gels, F-WEAX was crosslinked using a laccase in the presence of cellulose nanocrystals (CNC). The CNC/F-WEAX weight ratio ranged from 0 to 1.5, with a constant F-WEAX concentration of 1% (w/v). The addition of CNC increased gel stiffness and the elastic modulus scales as [CNC]³. CNC also affects the relaxation behaviour, enhancing significantly the loss factor at low frequencies. QCM-D measurements shows that F-WEAX adsorbed irreversibly onto CNC with the same affinity as non-feruloylated ones. In the presence of CNC, the action of laccase produces double the quantity of elastically active oxidation products, which are the dimer and trimer forms of ferulic acid (FA). As a consequence, the swelling capacity of the F-WEAX-CNC gels decreases, however less than anticipated from the increase in shear modulus. The synergistic enhancement of elasticity, while maintaining swelling capacity, is tentatively attributed to the formation of high-functionality junctions through the irreversible adsorption of F-WEAX onto CNC
About identifiability and observability for a class of dynamical systems
No full textInternational audienceWe present novel results and constructive methods on the observability, identifiability and joined observability-identifiability analysis of autonomous dynamical systems, with a special focus on nonlinear systems. While most existing works treat rational systems, the study of general nonlinearities remains less developed, up to our knowledge. Moreover, even in rational systems, a rigorous and unified theoretical argument ensuring the identifiability of parameters from input-output equations is still lacking. To address these gaps, we extend existing results in the literature. The key ingredient of our methods is a test of the linear independence of some functions of the observations and their derivatives. We furthermore describe constructive procedures to retrieve the unknowns based on the resolution of linear systems of equations. Finally, we apply our approach to several illustrative cases, including two non-rational cases that highlight its relevance. In particular, we show how our results allow the treatment of general nonlinearities and may complement existing techniques