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Evaluation of cowpea varietal response to bacterial blight in Burkina Faso: Implications for breeding and integrated disease management
No full textInternational audienceCowpea bacterial blight, caused by Xanthomonas citri pv. vignicola (Burkh.), is increasingly becoming a major constraint to cowpea productivity worldwide. The use of genotypes that are resistant and/or tolerant to the pathogen is an effective means of controlling the disease. In this study, we evaluated the response of 12 cowpea genotypes of Burkina Faso to three strains (CFBP 7111, CFBP 7112, and CFBP 7113) of X. citri pv. vignicola under greenhouse conditions. For each strain, an inoculum of 1 × 10⁸ CFU/mL⁻¹ was used to inoculate two-week-old trifoliate leaves. Parameters assessed included symptom percentage, bacterial population size, yield components, and leaf chlorophyll content. The results revealed that genotype Yiisyandé was the most affected by all strains, with approximately 50% leaf symptom coverage. In contrast, genotype KVx745-11P showed no symptoms for any of the strains. Strain CFBP 7113 generally reached the highest bacterial populations (7.17 log CFU/cm² for genotype Komcallé). KVx745-11P also exhibited the best yield, with an average per plant of 8.83 pods, 14.56 g pod weight, 90.92 seeds, and 13.37 g seed weight. These observations provide a solid basis for incorporating KVx745-11P into breeding programs aimed at developing broad-spectrum, durable resistant cowpea cultivars
Targeting resilience in Climate Smart Agriculture: A mini review
No full textInternational audienceResilience is a core concept of the second pillar of the Food and Agriculture Organisation's definition of Climate-Smart Agriculture (CSA). However, resilience is a complex concept admitting various definitions that feeds the confusion persisting around the concept of CSA. Given the stakes and the systemic and transformative changes that are needed to face climate change, especially in complex landscapes like Europe where urbanization and intensified agriculture intersect, the clarification of a unifying goal is crucial. In this mini-review, the authors propose to present the history and definitions of resilience to foster resilience in CSA strategies. This work highlights the existence of a network of operationalization attempts in literature, but disconnected from the holistic scale aimed for in CSA. Among all definitions of resilience, ecological resilience is the one adapted to bridge CSA and resilience with adequate governance integration both in urban and rural communities. When targeting resilience, the frameworks and indicators of social sciences have to come together with core disciplines related to agricultural management. In conclusion, this mini-review suggests to step back from the resilience conceptual debate and to invest more efforts towards creating indicators to capture early signals of social-ecological systems trajectories. This will help avoid brutal changes of management which could lead into a lack of societal cohesion within territories marbled by rural-urban gradients and lower their resilience
Les investissements numériques dans les exploitations agricoles françaises: Une classification selon les coûts totaux de possession farms
No full textInternational audienceDigital tool adoption depends, beyond the purchase price, on the total cost of ownership (TCO). Our analysis cross-references the commercial supply recorded in an original database (AgriTechCost_DB) and the usage observed in the 2020 agricultural census. The estimation of a TCO per farm, which depends on the combinations of adopted tools and their estimated cost, makes it possible to establish a classification of investment levels (low, medium or high). The results reveal a diversified supply of digital tools, primarily focused on crop production. In 2020, 59% of farms were using digital tools, mostly those with larger farmland and economic size. Low or moderate investments are predominant in specialized crop farming, whereas the share of high investments is larger in livestock farms.L’adoption d’outils numériques dépend, au-delà de leur prix d’achat, de leur coût total de possession (CTP). L’analyse des auteurs croise l’offre commerciale recensée dans une base de données originale (AgriTechCost_DB) et l’usage observé dans le recensement agricole de 2020. L’estimation, par exploitation, d’un CTP qui dépend des combinaisons d’outils utilisés et de leur coût estimé permet d’établir un classement des niveaux d’investissement (faible, moyen ou fort). Les résultats révèlent une offre variée, centrée sur la production végétale. En 2020, 59 % des exploitations étaient équipées d’outils numériques, surtout celles de surface agricole utile et de dimension économique plus élevées. Les investissements faibles ou moyens dominent en grandes cultures, tandis que les plus forts concernent les exploitations d’élevage
Isolation, Characterization and Genomic Analysis of PBC_MG88 and PBC_MG99 Bacteriophages and Their Antibiofilm Activity Against the Bacillus cereus Groups
No full textInternational audienceBacillus cereus is a major foodborne pathogen responsible for food spoilage and foodborne illness, including strains producing emetic toxins. In this study, two bacteriophages, PBC_MG88 and PBC_MG99, were isolated from wastewater using emetic B. cereus strains as hosts and were comprehensively characterized. Both phages formed clear plaques with halos and exhibited siphovirus morphology. Host range analysis against 172 B. cereus strains showed that PBC_MG88 and PBC_MG99 infected 50 and 60 strains, respectively. One-step growth experiments revealed efficient lytic activity, with latent periods of 20-25 min and burst sizes of 59-63 PFU per infected cell. More than 90% of phage particles adsorbed to host cells within 15 min. Both phages were stable across a wide temperature range (4-55 • C) and pH values (4-11). Genome sequencing revealed ~37 kb double-stranded DNA genomes lacking antibiotic resistance or virulence genes; however, the presence of lysogeny-related genes suggests a temperate lifestyle. Comparative genomic analyses indicated that both phages represent novel species within the genus Lwoffvirus. Biofilm assays demonstrated significant inhibition of B. cereus biofilm formation and reduction of pre-established biofilms. Overall, this study expands knowledge of B. cereus phage diversity and highlights the importance of genomic characterization in phage-based biocontrol research
Fine-scale fishery patterns reveal challenges and opportunities for coastal management and conservation in Madagascar
No full textInternational audienceThe blue economy agenda has generated tensions over marine space use, often marginalising small-scale fisheries in development policies. Boat tracking technology has only recently begun to be applied in these fisheries, but it offers a promising approach to accurately map fishing distribution. In this study, we explored how environmental, technological, and social factors influenced fishers’ spatial behaviour and catches at sea in one of the Madagascar's most heavily exploited coral reef fisheries. We recorded boat movements at 30 s intervals and reef fish catches simultaneously during a 12-month participatory survey. The spatial distribution of annual fishing effort (h·ha −1 ) and fish catch rates (kg·ha −1 ) was characterised by fishing community and gear type (beach seine, mosquito net trawl, gillnet, handline, and speargun) at 250−m resolution. A total of 75 reef fish families were recorded in catches (1,466 t·yr −1 ) across approximately 218 km 2 . Annual catch rates of the seven dominant families (comprising 62% of total catches) were highly variable and heterogeneous (mostly 1–391 kg·ha −1 ) across marine habitats. A total of 7,359 tracks by 521 boats were recorded. Fishing pressure was highly variable spatially (mostly 1−150 h·ha −1 ) among communities and gear types. The results revealed preferential target areas, informal marine tenure, limited travel distance to fishing grounds, and overexploitation patterns within the fishery, offering critical insights for fishery management and inclusive marine spatial planning. This study showed the usefulness and opportunities of deploying combined boat tracking and catch surveys in small-scale fisheries through participatory research
Shrimp hydrolysate-based palatability enhancer: A strategy to reduce fish-in fish-out ratio in marine fish species
No full textInternational audienceReducing aquaculture's reliance on wild fish remains a major challenge. Protein hydrolysates, often derived from food by-products, offer a promising, sustainable, and functional alternative to marine proteins. This study evaluated their use as a palatability enhancer (PE) by top-coating feeds with a low-dose liquid hydrolysate, primarily from shrimp, to reduce fish meal (FM) in juvenile red seabream (Pagrus major) diets. Experimental feeds included a high FM diet (HFM, 30 % FM), a low FM diet (LFM, 15 % FM) and two additional diets with 2 % PE top-coated (HFM+PE and LFM+PE). Six replicate tanks, each with 40 fish, were fed one of the diets twice daily to satiety for 15 weeks. Half the tanks experienced intermittent stress (1-min net chasing for one week, every 3 weeks). After the trial, fish were challenged with Edwardsiella tarda. Both basal diets resulted in comparable growth and feed efficiency. Reducing fish meal from 30 % to 15 % in the LFM diet resulted in a baseline reduction of approximately 25 % in wild fish use, as estimated by the economic Fish-In: Fish-Out (eFIFO) ratio. PE supplementation further improved growth (+5.6 % for SGR), health, and feed utilization (-7.5 % for FCR), enabling an additional 6 % reduction in wild-caught fish input compared to the LFM diet alone. The beneficial effects of PE were consistent despite intermittent stress, and survival following bacterial challenge was significantly higher with PE supplementation. In conclusion, liquid hydrolysate used as a PE provides a cost-effective way to reduce pressure on wild fish stocks while maintaining high feed performance
A safari across France: soil fauna insights from a nationwide soil quality monitoring program
No full textInternational audienceSoil biodiversity is fundamental to ecosystem functioning but remains underrepresented in conservation policies and large-scale monitoring. Here, we present RMQS-Biodiversity, a nationwide soil biodiversity survey integrated into the French Soil Quality Monitoring Network (RMQS), and illustrate its potential for soil ecology research. In this pioneer study, we examine three major ecological aspects: (i) how systematic grid-based sampling captures micro-food web patterns using nematode communities, (ii) the spatial turnover of detritivore communities (Collembola, Isopoda, Diplopoda) in response to environmental and geographic gradients, and (iii) the influence of macroecological drivers on predator (Carabidae) morphological traits. Across 69 sites, we identified a few widespread species coexisting with numerous rare taxa, underscoring the value of large-scale surveys for detecting cryptic biodiversity. Nematode indicators revealed high variability in food web structure across land uses, with increased facultative phytophagous nematodes in forests. Isopods and diplopods were strongly structured by dispersal constraints, while springtails exhibited weaker environmental responses, likely due to their higher dispersal capacity. Additionally, sexual size dimorphism in Carabidae varied by habitat, with female-biased dimorphism in closed habitats but no dimorphism in open environments, highlighting habitat stability's role in shaping morphological traits. This study demonstrates the value of multi-taxon, multi-trophic biodiversity assessments in long-term soil monitoring. RMQS-Biodiversity provides a robust framework for soil biodiversity monitoring and conservation, refining bioindicators of soil quality and informing policies such as the EU Soil Monitoring Law
Exploring the Landscape of Local and Distant Intra-vs. Inter-Chromosomal eQTLs Using TensorQTL and GCTA: A case study from 459 Liver Transcriptomes of Aged Laying Hens
No full textInternational audienceExpression quantitative trait loci (eQTL) mapping is a key approach in understanding how genetic variants influence gene expression and phenotypic variability. In this study, we compared the performance of two eQTL mapping tools: GCTA, widely used for quantitative traits, and TensorQTL, a recent method applied in human GTEx datasets. We assessed their performance in terms of eGene discovery, concordance, and computational efficiency using a large liver transcriptomic dataset from aged laying hens. Sustaining egg production in aging hens likely depends on efficient lipid synthesis, not only because yolk formation requires a large lipid supply, but also because lipids provide precursors for hormones and signaling molecules controlling ovulation and egg production. The liver is the central organ of lipid metabolism, making it a suitable tissue to investigate eQTLs influencing reproductive longevity. We investigated the genetic regulation of gene expression in the liver of 459 aged laying hens (90 weeks of age) from a single pure line, generating one of the largest eQTL datasets in livestock. Gene expression levels were derived from RNA-seq data that were inverse-normal transformed before association testing. Both GCTA and TensorQTL were used to map two types of eQTLs: i) local eQTLs defined as associations between an eGene and SNPs within ±500kb of its transcription start site (TSS), and ii) distant eQTLs defined as associations outside this region, including those on different chromosomes. To ensure robust detection, a 1Mb region was considered as an eQTL when at least five SNPs within a 100kb window exceeded a significance threshold and were in linkage disequilibrium (LD≥0.5). Bonferroni correction was applied to account for multiply testing considering 11,830 variables, and for distant eQTLs, 4,442 independent SNPs. Overall, 5,254 of the 11,830 genes expressed in the liver were regulated by at least one local eQTL across both methods. TensorQTL detected more eGenes (5,231) than GCTA (3,435), with 3,412 shared between both approaches, representing 65% and 99% of the eGenes detected by TensorQTL and GCTA respectively. This overlap for TensorQTL increased to 80% and 90% under more stringent p value thresholds (1e-9 and 1e-13), but the number of detected eGenes decreased within these ranges (4,038 and 3,054 respectively). The discrepancies likely originate from differences in model implementation and correction for population structure between the linear mixed model (GCTA) and linear regression without random effects (TensorQTL). TensorQTL’s GPU-based implementation drastically reduced computation time, identifying eQTLs in minutes instead of several days with GCTA.Beyond local associations, we identified 976 distant eQTLs with TensorQTL, most being intra-chromosomal (936) rather than inter-chromosomal (40). Around 75% of distant eQTLs were 500kb 1Mb from the eGene TSS, suggesting that most represent cis-regulatory effects rather than trans associations. These analyses are still ongoing.The liver eQTL map generated here provides a valuable resource for functional genomics in laying hens and offers insights into the genetic control of metabolic efficiency and reproductive persistence. Future work should include chromatin conformation analyses to better distinguish between distant cis-acting and trans-acting eQTLs.This project is funded by the European GEroNIMO N°101000236 and ANR ‘EFFICACE’ programs
Multi-year stability of spatial patterns in capelin otolith-edge chemical fingerprints in the Gulf of St. Lawrence, Canada
No full textInternational audienceIn the Gulf of St. Lawrence (GSL, Canada), the population structure and dynamics of capelin (Mallotus villosus), an abundant small pelagic forage fish, remain poorly understood, limiting the implementation of reliable stock assessment. Otolith-edge elemental signatures were analysed to identify regions with statically distinct element signatures and evaluate the potential of otolith chemistry as a tool for tracking capelin movements and life history events in the GSL. A total of 679 individuals were collected between 2022 and 2024, and their otolith elemental composition was analysed using Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Seven elements (lithium, boron, magnesium, potassium, zinc, strontium, and barium) were retained for discriminating among three regions: Estuary, South and Strait of Belle Isle (SBI). Quadratic discriminant analysis (QDA) assigned individuals to their region of origin with reallocation success rates of 64.3 % for the Estuary, 60.0 % for the South, and 80.5 % for the SBI. A sensitivity analysis confirmed the robustness of the results and indicated a negligible effect of individual length. Although some interannual variability was detected over the three-year period, spatial differences consistently exceeded temporal variation. Spatial differences in elemental signatures likely reflect underlying oceanographic drivers, such as water temperature and salinity, which influence otolith-edge chemistry. These results indicate that otolith-edge elemental fingerprints can provide significant discrimination among regions, supporting their potential use in studies of capelin movement and spatial population structure. Such information may ultimately contribute to improved stock assessment and management in the GSL
Integrated analysis of methylome and transcriptome highlights limited impact of DNA methylation on age-related gene regulation in laying hens
No full textInternational audienceUnderstanding how organisms respond to environmental challenges requires an integrat-ed view of gene expression and regulation. While transcriptome profiling captures dynamic shifts in gene expression, it does not reveal the underlying regulatory mechanisms. DNA meth-ylation, a key epigenetic modification sensitive to environmental factors, provides complemen-tary information on regulatory changes. Integrating methylome and transcriptome data from the same tissue enables a deeper understanding of how environmental stressors may shape gene regulation and phenotype. In a previous transcriptome study of the liver’s response to ageing in laying hens, we identified 634 and 941 differentially expressed (DE) protein-coding genes (PCG) that were respectively under- or over-expressed in 90-week-old laying hens (n=225) compared to 70-week-old (n=241). Here, we extend these results to examine the complex interplay between the transcrip-tome and the methylome, using Reduced Representation Bisulfite Sequencing (RRBS) obtained on a subset of 347 hens (n=174 at 90wk, n=173 at 70wk) from the first study. Among the 9.2M CpG sites identified with a minimum coverage of 10 reads, we selected those that fulfilled the following criteria: no overlap with known genomic variants (2M), at least 10 reads in 80% of samples (475,178), and methylation rate standard deviation >0.05, yielding 139,362 high-quality CpG sites located within 4,569 PCG including the 2kb promoter. A modest but significant global increase in DNA methylation with age was observed, with 906 differential-ly methylated CpG (DMC) sites, of which 557 were hypermethylated and 349 hypomethylated at 90wkcompared to 70wk, respectively corresponding to 89 and 57 genes.We then investigated relationships between methylation and expression using four com-plementary approaches: (i) overlap of DE genes with DMC-associated genes, (ii) multivariate linear models (Expr~site1+site2+…), (iii) unsupervised multi-omics factor analysis (MOFA2), (iv) weighted gene co-expression/co-methylation network analysis (WGCNA).As results, i) only a few DEGs overlapped with DMC-associated genes (<4%). Among them, we found SREBF2 gene harboring multiple DMCs, a key regulator of cholesterol synthesis that was previously reported to be impacted by age. Notably, although many of its target genes were also impacted by age, they were not associated with DMCs. ii) Among the 4,120 genes with paired data, only 406 (9.8%) showed significant associations between DNA methylation and gene ex-pression: 217 (53%) negative, 152 (37%) positive, 37 (9%) mixed. iii) MOFA2 analysis combin-ing all expressed genes and the 50k most variable methylation sites, highlighted a much larger proportion of the total variance accounted for by gene expression than methylation (50.1% vs 7.8%). iv) Using WGCNA with the full set of genes and methylation sites, we identified 20 co-expression and 8 co-methylation modules. A single methylation module correlated (R2>20%) with two expression modules, enriched in cell organization and transport functions, but with no shared genes.In summary, age exerts a modest but detectable effect on hepatic DNA methylation in laying hens, albeit with limited direct association to transcriptomic changes. Our results suggest that age-related transcriptional shifts may be driven by trans-acting methylation mechanisms rather than local CpG regulation.This project is funded by the European GEroNIMO N°101000236 and ANR ‘EFFICA-CE’ programs