Intérêt de l’efficacité digestive pour améliorer le progrès génétique de l’efficacité alimentaire chez le porc nourri avec une alimentation riche en fibres alimentaires

International audienceAméliorer l’efficacité alimentaire chez le porc : un levier majeur pour la durabilité des élevages :• Enjeu économique fort : le coût de l’alimentation représente 70 % du coût de production chez l’éleveur de porcs (Patience et al. 2015).• Objectif génétique prioritaire : l’efficacité alimentaire (EA) est un critère central de sélection (30–40 % des objectifs dans les lignées paternelles) (Verrier et al., 2020)Des régimes plus riches en fibres sont une option réaliste pour les années à venir, qui nécessitent peut-être d’adapter les schémas de sélection :• Les coefficients d’utilisation digestive (CUD) de la matière organique (CUDMO), de l’énergie (CUDE) et de l’azote (CUDN) : des indicateurs pertinents pour améliorer la digestion et donc l’EA dans ce contexte• Héritabilité : modérée en régime conventionnel (CO) (0,26–0,27) et élevée en régime fibreux (F) (0,54–0,56) (Déru et al., 2021)• Corrélations génétiques favorables avec l’indice de consommation (IC) (Déru et al., 2021)<br/

R-scripts for rabbit coprophagous behavior website

R-scripts used to analyse the data presented in the article "Coprophagia early in life tunes immune system gene expression in ileum after weaning in rabbit", Cauquil L., Beaumont M., Schmaltz-Panneau B., Liaubet L., Lippi Y., Bluy L., Poli M., Gress L., Lencina C. , Duranthon V., Combes S

Combining LD-Guided QTL Refinement, GEGA Annotation, and Tissue-Specific eQTL for Candidate Gene Prioritization

International audienceQuantitative trait loci (QTL) mapping is a powerful approach to dissect the genetic architecture of complex traits. However, the broad size of QTL intervals often hampers the identification of causal genes, limiting both functional interpretation and genomic selection. To overcome this limitation, we developed a workflow that refines QTL intervals using linkage disequilibrium (LD) between each SNP and its leader SNP. Once refined, the gene content of each region can be rapidly explored using the GEGA website (https://gega.sigenae.org/), which provides gene listing, functional annotations, and expression profiles across 47 tissues. Both protein-coding and long non-coding genes are included. This framework was applied to several traits of interest in hens to reduce QTL size and prioritize biologically relevant candidate genes.QTLs were obtained with GCTA and initially defined as ±500kb around the leader SNP. LD between each SNP and its leader SNP was computed chromosome by chromosome with PLINKv1.9, retaining SNPs with LD≥0.5. Refined boundaries were set by the most distal upstream and downstream SNPs still above this threshold. This LD-guided procedure greatly reduced QTL size. For example, the chromosome 12 QTL for Haugh unit (HU) shrank by 92% (from 1Mb to 76kb), reducing gene count from 143 to 9. The chromosome 18 QTL for egg weight (EW) decreased by 90% (from 1Mb to 102kb), reducing genes from 107 to 14.Following refinement, functional characterization was performed using GEGA. In the HU QTL, six protein-coding genes were identified, mostly ubiquitously expressed, with one gene showing specificity in the oviduct and blood, tissues relevant for albumen quality. Keyword searches related to viscosity, egg proteins or glycosylation did not retrieve genes in this interval. In the EW QTL, several genes showed tissue-specific expression in the oviduct or neuroendocrine axis (pituitary, hypothalamus). A keyword search related to hormonal regulation highlighted GALR2, consistent with its role in follicular growth and its expression in the gizzard and oviduct.Beyond this workflow, additional insights can be gained when transcriptomic data are available for tissues biologically linked to the phenotype. This is the case for traits related to lipid metabolism, for which the liver is the central organ. In the context of abdominal fat weight (AFW), we analysed a QTL located on chromosome 28 using hepatic RNA-seq data from 459 hens. After refining the QTL using LD, gene expression levels were used to detect local and distant-eQTL, and colocalization between QTL and eQTL signals was assessed. This strategy identified a lipid gene CRTC1 and its long-non-coding RNA as candidate genes, whose local-eQTLs showed LD profiles highly consistent with the AFW QTL LD pattern makes it biologically coherent with the phenotype. This example demonstrates how integrating tissue-specific eQTL enables prioritization of causal genes based on regulatory mechanisms.Overall, combining LD-guided QTL refinement, GEGA-based annotation, and tissue-specific eQTL colocalization provides an efficient strategy to narrow genomic intervals, identify functional candidates, and pinpoint regulatory variants underlying key production traits in poultry, enhancing interpretability and accelerating causal gene discovery.This project is funded by European GEroNIMO N°101000236 and ANR ‘EFFICACE’ projects

L’holobionte, une nouvelle dimension pour la sélection porcine ?

International audienceThe role of the microbiota, in particular the gut microbiota, on host performance is increasingly documented in farm animals. These advances have been made possible by the use of new high-throughput sequencing techniques and the development of data-analysis methods to characterize the microorganisms present (diversity, relative abundance, ecosystem assembly). They have provided new insights into the relations between host genetic diversity and host-microbiota interactions, as well as into the estimation of phenotypes or genetic values that consider microbiotic variability. These results fuel a new paradigm based on the definition of the holobiont as a biological system that assembles a host and its microbiota, thus providing a new vision of what an individual represents. We propose to assess the swine holobiont through modelling and experimental results to understand, predict and steer phenotypes to improve, for example, the health but also the productive and environmental efficiencies of pigs. These advances are also discussed as paving the way for developing selection strategies that simultaneously consider information about the host and its microbiota, while reflecting on the sustainable improvement of populations at the scale of a holobiont instead of an individual animal.Le rôle du microbiote et en particulier du microbiote intestinal sur les performances de l’hôte est de plus en plus documenté chez les animaux d’élevage. Ces avancées ont été permises par l’utilisation des nouvelles techniques de séquençage à haut débit et le développement de méthodes d’analyse des données pour caractériser les microorganismes présents (diversité, abondances relatives, assemblage en écosystèmes). Elles ont apporté de nouvelles connaissances sur les liens entre la diversité génétique de l’hôte et les interactions hôte-microbiote, mais aussi sur l’estimation des phénotypes ou des valeurs génétiques en prenant en compte la variabilité du microbiote. Ces résultats alimentent un nouveau paradigme fondé sur la définition de l’holobionte en tant que système biologique qui assemble un hôte et son microbiote, offrant une nouvelle vision de ce que représente un individu. Nous proposons de faire le point sur l’holobionte porc, en termes de modélisation et de résultats expérimentaux pour comprendre, prédire et piloter les phénotypes dans le but d’améliorer par exemple la santé mais aussi l’efficience productive et environnementale des animaux. Ces avancées sont également discutées comme ouvrant la voie pour élaborer des stratégies de sélection prenant simultanément en compte les informations sur l’hôte et son microbiote en raisonnant l’amélioration durable des populations à l’échelle non plus de l’individu mais de l’holobionte

Selective culling and the potential persistence of lumpy skin disease in cattle herds: insights from a mechanistic transmission model

International audienceThe first epidemic of lumpy skin disease (LSD) in France started in June 2025, with a total of 117 outbreaks recorded. This vector-borne disease affecting cattle is highly contagious, and prompted the implementation of strict control measures, including total depopulation of affected herds, resulting in the culling of more than 3,500 cattle. During the epidemic, total depopulation measures became increasingly unacceptable to cattle farmers, as they were perceived as unnecessary, leading to major protests. We use mathematical models to compare within-herd transmission dynamics under a selective culling strategy versus total depopulationIn this work, we propose a compartmental model of within-herd transmission, accounting for both cattle and vector populations. A test-and-cull strategy is implemented, relying on imperfect diagnostic tests capable of detecting infection in asymptomatic cattle, and different levels of test sensitivity and detection earliness are investigated. Alongside the test-and-cull strategy, a vector control strategy is implemented considering different levels of effectiveness in reducing the vector population.Our model shows that a selective culling strategy still results in 75% [26, 100] of the herd becoming infected, even in the best-case-scenario with highly efficient diagnostic tests and vector control. Given currently available tests, considered to have a sensitivity of 30% for subclinical animals within 2-3 days prior to their infectiousness onset, the predicted persistence is 60 days [34, 95], with 94% of the herd [44, 100] eventually becoming infected, representing only a marginal advantage compared with a total depopulation strategy. These metrics further deteriorate when the efficacy of insecticide products decreases

The fecal microbiota of lactating Holstein cows: A meta-analysis highlighting key microbial profiles and methodological challenges

International audienceIn cattle, the digestive microbiota has been poorly studied outside the rumen, despite its recognized role in animal physiology, health, and production. This study aimed to provide a comprehensive meta-analysis of the fecal microbiota of lactating Holstein dairy cows. A systematic PubMed online search identified 28 articles meeting strict inclusion criteria, along with 2 recently published articles, yielding more than 2,000 samples. Raw sequencing data targeting the 16S rRNA gene (V3-V4 region) were obtained either from public repositories or directly from the authors. The core microbiota was identified as the most prevalent and shared taxa, comprising 21 microbiota families that accounted for 82% of the relative abundance. A multigroup analysis was performed to correct for the article of origin effect and successfully identified 3 microbiota profiles. The meta-analysis approach is a rigorous method that ensures the independence of research results from experimental conditions, thereby enhancing the reliability and generalizability of the findings

Variability and uncertainty of data from genotoxicity test guidelines: what we know and why it matters

International audienceThis review comprehensively examines the variability and uncertainty associated with test guideline (TG)-conform genotoxicity data and explores the respective implications for the integration of non-animal-methods (NAMs) into regulatory frameworks. Historical amendments to OECD TGs are mapped to reveal the method’s evolution that improves the scientific quality of the data but also explains data heterogeneity within available databases. An analysis of the major genotoxicity databases ECVAM, ISSMIC, and OASIS demonstrates substantial variability in genotoxicity calls. Using the EFSA genotoxicity database, which currently harbours the best-curated (meta-) data, we estimate that 22–77% of compounds exhibit similarity of replicate results below 85%, depending on the assay. The potentially most important variables statistically explaining variability and sensitivity were analysed. The practical limitations to identify them with high reliability and to define their optimum needs to be accepted as a qualitative baseline uncertainty. These findings underscore the necessity of contextualizing NAM performance evaluations within the intrinsic variability and uncertainty of animal and in vitro reference data. We propose that this variability is explicitly considered in the development and validation of NAM-based Integrated Approaches for Testing and Assessment. This review provides a critical foundation for regulators and scientists aiming to enhance the acceptance and utility of NAMs in genotoxicity assessment

Recherches sur le pastoralisme en France : état des lieux des connaissances et questions vives

ANR‐23‐P012‐0009International audienceThis article provides an overview of the current state of knowledge on pastoral systems and territories in France, focusing on the key issues that affect them. It provides a comprehensive analysis of the factors contributing to the decline of pastoralism in a context of intensified production and herd expansion, adaptation to climate change and market fluctuations, and the return of wild predators. Five priority areas for research are identified: animal selection and breeding in pastoral environments; pastoralism as a specific agroecological model, with its strengths and weaknesses; multi‐stakeholder pastoral territories, as spaces for confrontation and development of collective projects; pastoralism occupations and their attractiveness; and data derived from methods for monitoring changes in vegetation, biodiversity, and livestock systems. While not identical, many of these issues are notably similar to those in pastoral contexts in other parts of the world, particularly West Africa.Cette synthèse dresse un état des lieux des connaissances sur les systèmes et territoires pastoraux en France au prisme des principaux enjeux qui les traversent. Le repli pastoral en situation d'intensification de la production et d'agrandissement des troupeaux, l'adaptation au changement climatique et aux fluctuations des marchés, ou encore le retour de prédateurs sauvages sont particulièrement discutés. Cinq champs de recherche prioritaires ont été dégagés : l'animal en milieu pastoral ; le pastoralisme comme modèle d'agroécologie avec ses forces et ses faiblesses ; les territoires pastoraux multi‐acteurs, espaces de confrontation et de projets collectifs ; les métiers du pastoralisme et leur attractivité, les données issues des méthodes de suivi de l’évolution des végétations, de la biodiversité et des systèmes d’élevage. Bien des sujets font écho avec les situations pastorales du reste du monde, notamment en Afrique de l'Ouest, sans pour autant les recouvrir exactement

Plan de Gestion de Données de l'entité "Plateforme GeT-TRiX"

Ce Plan de Gestion de Données décrit les divers produits de recherche générés par la plateforme GeT-TRiX dans le cadre de ses activités de prestations d'analyses transcriptomiques.- Les services de mise à disposition d'équipements auprès des utilisateurs- les services de génération et analyse de données transcriptomiques proposés par la plateforme- le développement de scripts d'analyse et d'une application we

Polyphenols as Modulators of the BMP Signaling Pathway to Counter Phenotypic Transformation of Colonocytes

International audienceABSTRACT The intestinal bone morphogenetic protein (BMP) pathway counteracts the Wnt pathway, which is overactivated in 90% of colorectal cancers (CRC) due to mutations in the adenomatous polyposis coli ( APC) gene. Our study aimed to identify a polyphenol that acts on the colonic BMP pathway and to evaluate its ability to mitigate the harmful effects of 4‐hydroxynonenal (HNE), a dietary genotoxic molecule, on normal colonocytes. We first evaluated the effect of 10 polyphenols on the expression of BMP pathway actors using a normal mouse colonocyte and fibroblast culture model. Apigenin (Apig) and resveratrol (Res) increased the production of BMP4 ligand and reduced expression of the Gremlin1 (Grem1) antagonist in fibroblasts. Apig also enhanced the expression of the bone morphogenetic protein receptor type 2 ( Bmpr2) in fibroblasts and that of the Smad1 effector in colonocytes. Finally, Apig inhibited the phenotypic transformation of colonocytes induced by HNE through a mechanism that involved the BMP pathway in both fibroblasts and colonocytes. Our findings suggest that targeting the colonic BMP signaling pathway through dietary factors could contribute to the prevention of CRC. Apig‐rich foods or supplements may play a role in this preventive nutrition, although further in vivo experiments are needed to confirm this potential