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The Maize ZmbHLH118 Transcription Factor Regulates Vacuolar Nitrate Loading by the NO <sub>3</sub> <sup>−</sup> Transporter ZmCLCa
No full textInternational audienceNitrate (NO 3-) is a major nutrient promoting plant growth and crop yield. Vacuolar nitrate storage is essential for nitrate acquisition and remobilization within the plant. However, the transcriptional regulation of transporters facilitating nitrate influx into the vacuole remains unclear. Here, we identified a bHLH transcription factor, ZmbHLH118, that negatively regulates the expression of ZmCLCa , thereby modulating nitrate vacuolar loading and uptake in maize ( Zea mays ). ZmbHLH118 overexpression and ZmCLCa loss-of-function in maize impaired root NO 3 -uptake, and further reduced nitrate content and plant growth.Moreover, ZmbHLH118 directly binds to the promoter and inhibits the expression of ZmCLCa , which encodes a tonoplast-localized nitrate transporter. Electrophysiological analysis showed that ZmCLCa mediates NO 3 -fluxes across the vacuolar membrane, indicating that ZmCLCa-mediated NO 3 -influx is required for vacuolar nitrate storage. Our data identify the ZmbHLH118 as a molecular actor of the transcriptional regulation of ZmCLCa in response to extracellular nitrate. This provides insights into the regulatory mechanisms acting upstream of the CLCa-mediated vacuolar nitrate transport. Finally, field assays showed that the regulation mechanisms of vacuolar nitrate affect maize growth and grain yield, highlighting their value for nitrogen use efficiency improvement in crop plants
CIRAD's advanced research towards marker assisted selection of high yielding resistant oil palm (E. guineensis Jacq.): Integrating plant genetics, phytopathology and genomics approaches
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/616431/)International audienceMarker-assisted selection (MAS) offers a powerful method for optimizing the development of diseaseresistant oil palm (E. guineensis Jacq.). An efficient and cost-effective approach involves investigating the genetic basis of resistance by directly exploiting data from ongoing breeding programs. Our results on Fusarium wilt, caused in Africa by Fusarium oxysporum F. sp. elaeidis, and on Basal Stem Rot (BSR), caused by Ganoderma boninense in Southeast Asia, illustrate the potential of this approach for identifying the genomic regions responsible for oil palm disease resistance. They provide key information not only on the genomic regions targeted by MAS, but also on the complexity of the genetic architecture of disease resistance, the genetic sources of favourable alleles, and the potential relationships between different traits of interest. MAS leverages as well knowledge of pathogens. In this context, the G. boninense–oil palm pathosystem is attracting increasing interest within the scientific community. An early inoculation test, enabling the induction of BSR in young seedlings under controlled conditions, allowed the identification of resistance Quantitative Trait Loci (QTL). This method, commonly used for selecting partially resistant progeny, allows for functional studies on the interactions between G. boninense and oil palm. Pathogen's genetic diversity data have led to a better understanding of the importance of sexual reproduction, scale of spore dispersal and of the demographic dynamics of the species in South- East Asia. A transcriptomic study performed on artificially inoculated oil palms showed that G. boninense expresses enzymes already known to be involved in the aggressiveness of other white rot fungi like CAZymes wood decay enzymes and detoxification proteins. The complete genome sequence of G. boninense further enhances our knowledge
Natural variation in Arabidopsis uncouples leaf and flower development and reveals massive transcriptomic heterochrony
No full textInternational audiencePlant development is a sequence of precisely timed and spatially coordinated events that produce organs such as leaves and flowers. In Arabidopsis thaliana, for example, the development of leaves (called bracts in the inflorescence) halts once the first flower forms. Understanding how this transition is regulated is key for decoding how developmental programmes are coordinated during the floral transition. In this study, we investigated a natural phenotypic variation that uncouples bract repression from flower initiation. We discovered that the continued formation of bracts after the floral transition involves complex genetic interactions across at least four loci. Interestingly, none of these loci included known floral identity genes previously linked to bract repression, pointing to novel regulators in the coordination of bract and flower development. Using time-series transcriptomics and curve registration, we found that differences in gene expression levels when bracts persist are mainly driven by a massive desynchronization of gene dynamics. This affects a wide range of biological processes beyond those associated with leaf identity. These findings align with the ‘inverse hourglass’ model, which proposes that transcriptomic divergence at transitional stages contributes to morphological variation. Our results suggest that this model may also explain trait variability within species, highlighting how transcriptome dynamics shape phenotypic robustness during developmental transitions
Monitoring liveweight and performance responses to nutrition in Sarda dairy ewes using a walk-over-weighing system
No full textIn Mediterranean dairy sheep systems, seasonal feed shortages can lead to periods of undernutrition, with negative consequences for animal performance and welfare, particularly during lactation. Liveweight (LW) is a practical indicator of nutritional status and body reserve dynamics, but conventional weighing is labour-intensive and typically performed at low frequency. Walk-over-weighing (WoW) systems integrated with electronic identification (EID) enable frequent, low-labour monitoring of individuals and may improve the detection of nutritionally driven LW changes.This study evaluated the sensitivity of a WoW system to detect moderate LW changes associated with contrasting nutritional levels in Sarda dairy ewes managed indoors or at pasture. Two experiments were conducted: (i) non-lactating ewes housed indoors and subjected to a short-term nutritional challenge; and (ii) lactating ewes managed on pasture with different daily access times and supplemented with hay and concentrate. In both experiments, ewes under the lower nutritional level exhibited lower LW, and WoW detected these differences over time. Under grazing and lactation, differences in nutritional level were also reflected in milk performance indicators.Overall, automated LW monitoring using WoW provides a feasible approach to track LW trajectories in dairy ewes under contrasting management conditions. Integration of LW with routinely collected production data (e.g. milk yield and composition) could support earlier identification of nutritional shortfalls and improve decision-making for welfare-oriented management
KGAP: An RDF Knowledge Graph of Agricultural Commodity Prices
No full textInternational audienceThis article presents the Knowledge Graph for Agricultural Prices (KGAP), which is a knowledge graph (KG) that integrates agricultural commodity prices data from three major Brazilian institutions: Cepea, Conab, and Ipea. The datasets, originally published in heterogeneous formats, were harmonized and converted into RDF/Turtle using the Almes Core metadata schema as the data model. Agricultural products were classified with the Agricultural Product Types Ontology (APTO), and geographic references were aligned with GeoNames identifiers, ensuring semantic consistency and adherence to the FAIR data principles. KGAP is archived on Zenodo and GitHub, and hosted on the Platform Linked Data Nederland (PLDN) with a public SPARQL endpoint. It contains metadata, price observations, product types, and location entities, allowing users to query and compare agricultural prices across institutions, regions, and time periods. The knowledge graph can potentially support applications in agricultural economics, policy analysis, journalism, data science, and machine learning. By explicitly modeling metadata such as reference quantities, KGAP enables semantically-aware queries that prevent common analytical errors and reveal insights previously obscured by data heterogeneity
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