Scientific publication

[hal-05131958] Protein signatures of feed restriction and spontaneous lipolysis in skimmed ewe milk

Milk lipolysis refers to the breakdown of triacylglycerols by lipoprotein lipase. Our aim was to identify the drivers of spontaneous lipolysis in skimmed ewe milk. To achieve this, feed restriction was used as a lever to generate contrasting samples with respect to lipolysis. We combined multivariate statistical methods to identify the effects of feed restriction on ewes, the molecular composition of skim milk, and the drivers of spontaneous lipolysis in milk. The high spontaneous lipolysis in skimmed ewe milk was driven by a combination of variables consisting of 12 milk proteins (ANGPT1, FN1, COL14A1, W5PDQ9, W5QH04, CLSTN1, PPIB, PLIN3, ITIH2, ASAH1, SMPD1 and FST), 7 milk fatty acids (C6:0, C14:0, C14:1 cis9, C10:1 cis9, C10:0, C11:0 and C12:0), milk urea, plasma acetate, plasma urea, plasma IGF1, milk yield, and NEL. In particular, the proteins ANGPT1, SMPD1, and ASAH1 were identified as participants in the lipolytic process in milk, whatever the level of nutrition, which could be considered in future tools to manage milk lipolysis.

ano.nymous@ccsd.cnrs.fr.invalid (Mylène Delosière) 26 Jun 2025

https://hal.science/hal-05131958v1

[hal-05131572] Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression: a pilot study

Climate change, with its repercussions on agriculture, is one of the most important adaptation challenges for livestock production. Poultry production is a major source of proteins for human consumption all over the world. With a growing human population, improving poultry's adaptation to environmental constraints becomes critical. Extensive evidence highlights the influence of environmental variations on epigenetic modifications. The aim of this paper is therefore to explore chickens' molecular response to maternal heat stress. We employed Reduced Representation Bisulfite Sequencing to generate genome-wide single-base resolution DNA methylation profiling and RNA sequencing to profile the transcriptome of the brains of embryos hatched from dams reared under either heat stress (32 ∘ C) or thermoneutrality (22 ∘ C). We detected 289 significant differentially methylated CpG sites (DMCs) and one differentially methylated region (DMR) between heat stressed and control groups. These DMCs were associated with 357 genes involved in processes such as cellular response to stimulus, developmental processes, and immune function. In addition, we identified 11 genes differentially expressed between the two groups of embryos, and identified ATP9A as a target gene of maternal heat stress on offspring. This study provides a body of fundamental knowledge on adaptive mechanisms concerning heat tolerance in chickens.

ano.nymous@ccsd.cnrs.fr.invalid (Keyvan Karami) 26 Jun 2025

https://hal.science/hal-05131572v1

[hal-05042762] Co-conception d’outils d’observation et d’évaluation du bien-être animal

Le réseau SBEA INRAE s’est engagé dans un projet de co-conception d’outils d’observation quotidienne pour le suivi des animaux et d’évaluation du bien-être, adapté à nos contextes expérimentaux. Les grilles, basées sur les protocoles de Welfare Quality, rapportent les signaux de détresse et signalent les animaux nécessitant une attention particulière. Elles assurent ainsi une documentation précise et facilitent la communication entre équipes. Le projet souligne l’importance de la collaboration continue entre intervenants pour améliorer le bien-être des animaux.

ano.nymous@ccsd.cnrs.fr.invalid (Elodie Guettier) 22 Apr 2025

https://hal.inrae.fr/hal-05042762v1

[hal-05040032] PIGLOW, une application pour évaluer le bien-être animal en élevage porcin

Dans le cadre du projet européen PPILOW (2019-2024, https://www.ppilow.eu/), l’application PIGLOW, qui bénéficie d’un développement pour téléphones portables, a été mise en place. Elle permet de réaliser des évaluations du bien-être animal (BEA), dans les élevages pour les femelles gestantes, les femelles allaitantes et leurs porcelets, les porcelets en post-sevrage et les porcs charcutiers en croissance. L’évaluation est réalisée sur environ 60 critères. Une synthèse est générée automatiquement et les principaux résultats sont représentés graphiquement, dont un « radar bien-être ».

ano.nymous@ccsd.cnrs.fr.invalid (Stéphane Ferchaud) 18 Apr 2025

https://hal.inrae.fr/hal-05040032v1

[hal-05050868] Prise en compte du bien-être animal dans les développements du Cati SICPA

Le Cati SICPA a pour mission principale de fournir des systèmes de collecte, de stockage et de gestion des données de phénotypage animal, pour les unités expérimentales «animales» et les chercheurs. Ces systèmes comprennent un volet logiciel et un volet matériel, que SICPA peut être amené à intégrer ou à développer. Cet article présente 3 exemples de réalisations qui illustrent les types de contributions du collectif SICPA dans les expérimentations menées dans les UE/ IE des départements GA et Phase : SICPA Environnement, SICPA Sanitaire et Alimentation, Nid électronique pour les poules.

ano.nymous@ccsd.cnrs.fr.invalid (Jean-François Bompa) 29 Apr 2025

https://hal.inrae.fr/hal-05050868v1

[hal-05003464] Le chantier « Agroécologie & Marché » conduit par les groupes filières INRAE

Innovations agronomiques 100 (2025), 1-12 <div>Résumé<p>Le secteur agroalimentaire fait l'objet d'une segmentation croissante du marché avec la multiplication de démarches dites de qualité, publique ou privée, qui engagent les filières dans la construction de pratiques de production, de transformation ou de distribution différenciées. Nous connaissons peu de choses sur la manière dont ces démarches inscrivent leurs pratiques dans l'agroécologie, et en particulier pour les filières ayant une mention valorisante autre que l'agriculture biologique. De 2022 à 2023, la Direction Scientifique Agriculture INRAE a engagé un chantier exploratoire, avec 11 groupes filières INRAE, pour analyser comment se construisent des démarches de filières différenciées sur le marché et leur engagement en faveur de l'agroécologie. Ce chantier dénommé « Agroécologie et Marché » s'est appuyé sur une analyse documentaire et une série d'entretiens auprès de plus de 60 acteurs, représentatifs d'interprofessions et de différents maillons de diverses filières. Cet article introductif présente la réflexion initiale de ce chantier, la mission des groupes filières et les 28 cas d'études retenus à titre illustratif, pour conduire cette analyse exploratoire au regard d'une diversité de contextes de production et de filières.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 24 Mar 2025

https://hal.inrae.fr/hal-05003464v1

[hal-05003526] Méthode d'analyse de la transition agroécologique à l'échelle des filières

Cet article propose un cadre analytique du processus de transition agroécologique à l'échelle des filières agrialimentaires, en mobilisant des approches issues des transition studies et de l'économie de l'innovation. Ce cadre vise à questionner la manière dont les différents maillons des filières peuvent se coordonner pour construire un processus d'apprentissage collectif de conception et valorisation sur le marché de systèmes agrialimentaires durables. Un ensemble de fonctions clés telles que la coconstruction des connaissances, la mise en place de cahiers de charges en lien avec des mentions valorisantes, la sécurisation de l'approvisionnement au travers de contrats, sont considérées. La pertinence d'utilisation de ce cadre d'analyse pour comprendre ces dynamiques de filière, s'est renforcée au fil de sa construction pour l'étude de 28 cas de démarches de filières déclarant se différencier par des pratiques reliées à des principes de l'agroécologie.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 24 Mar 2025

https://hal.inrae.fr/hal-05003526v1

[hal-04838897] In vitro evaluation of intestinal barrier function after exposure to digested pea ingredients -food matrix effect

Dietary fibres (DF) are important components of human and animal diets. However, they can decrease protein digestibility and absorption, and thus the nutritional value of a food. The aim of this study was to investigate how the form of delivery of pea DF impacted the integrity of the intestinal barrier and thereby the potential absorption of molecules. To this end, two pea flours, with either intact or ruptured cell walls, and two controls, pea fibres and pea protein, were digested in vitro and the digesta obtained applied onto a jejunum porcine cell line (IPEC-J2 cells). Cell viability and integrity were evaluated by transepithelial electrical resistance measurement, colorimetric assay (MTS), and immunohistochemistry for tight junction proteins. Additionally, the diffusion of FITC-dextran (FD4) and lucifer yellow (LY) through the epithelial cell monolayers was monitored. The digested pea samples did not alter IPEC-J2 viability and permeability. For instance, no difference in the diffusion of molecules either FD4 or LY across the monolayers was observed between the different digesta and the control. Similarly, no effect was observed in ZO-1 labelling intensity compared to the control. This study demonstrated that intestinal integrity was maintained whether or not pea cell walls were intact or ruptured.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Hélène Perruchot) 18 Dec 2024

https://hal.inrae.fr/hal-04838897v1

[hal-05006836] Sauvegarde d'une race locale porcine par la filière Noir de Bigorre

Si la grande majorité de la production porcine française est relativement homogène, une offre de produits issus de systèmes d’élevage alternatifs incluant, entre autres, les signes officiels de qualité s’est progressivement structurée en filière. L’exemple de la filière Noir de Bigorre, organisée autour de la préservation et de la valorisation de la race Gascon, éclaire sur la construction d’une démarche dont les principes apparaissent en cohérence avec les éléments de l’agroécologie proposés par l’organisation des nations-unies pour l’alimentation et l’agriculture (FAO). Interrogés sur leur organisation, les représentants de cette filière et d’un salaisonnier partenaire se sont largement retrouvés dans ces différentes dimensions de l’agroécologie. Un des principes fondateurs partagé par tous est celui des valeurs humaines et sociales et, bien que reposant sur la valorisation de pratiques ancestrales, le succès de cette filière repose sur de nombreuses innovations techniques et organisationnelles.

ano.nymous@ccsd.cnrs.fr.invalid (Bénédicte Lebret) 26 Mar 2025

https://hal.inrae.fr/hal-05006836v1

[hal-04951257] Effect of temporal water restrictions on drinking behavior and time budget in lactating dairy cows according to their position in the social hierarchy within the herd

On dairy farms, milking practices can temporarily restrict cows from accessing drinking water. This study examined how different types of temporary water restriction, similar to those commonly encountered on farms, may affect the individual behavior and physiological dehydration status of cows and whether these effects could differ according to the cow's position in the social hierarchy of the group. Four treatments were applied (CTRL = free access to the drinker and feed fence, HL = 2 h of headlock at the feed fence after morning and evening milking, D2H = free access to the feed fence and no access to water for 2 h after milking, and D4H = free access to the feed fence and no access to water for 4 h after milking) to 4 groups of 10 lactating dairy cows using a 4 × 4 Latin square design. Each treatment period lasted 1 wk. The cows were housed within a freestall barn, and each group was in a pen equipped with 1 electronic drinker, 10 individual feeders, and 2 cameras. Cow social dominance hierarchies were characterized using normalized David's scores, which were calculated from video-detected replacements at each pen's drinker. During the last 4 d of each treatment period, drinking behavior was measured using interconnected drinkers, and eating, idle, and lying times were measured using accelerometers. On d 6 of each treatment period, during the morning and evening milkings, blood and then milk samples were collected to analyze bioindicators of dehydration and milk composition, respectively. The daily water intake of cows was unaffected by either social dominance or treatment type. Drinking rate and drinking bout frequency were higher during the HL, D2H, and D4H treatments than during the CTRL treatment, and drinking time was lower during the D4H treatment than during the CTRL treatment. Hourly lying time decreased at the end of the water restriction periods, that is, at 1000 h in HL, at 1100 h in D2H, and at 1200 and 1300 h in D4H, which was not observed in CTRL, which could be interpreted as a sign of cow discomfort. For blood collected before the morning milking, hematocrit levels were lower in the D4H treatment than in the HL treatment. For blood collected before the evening milking, creatinine concentrations were lower in the D4H treatment than in the D2H treatment, with a greater difference seen for dominant cows than for subordinate cows. For both milkings, milk freezing point was higher in the HL, D2H, and D4H treatments than in the CTRL treatment, indicating dilution. In contrast to the other social categories, subordinate cows made more daily visits to the drinker during the D4H treatment than during the CTRL treatment but displayed no differences in drinking bout duration or the duration of drinking interruptions within bouts in the D2H treatment compared with the CTRL treatment. Overall, cows were able to maintain their water intake despite the temporary water restrictions when they had access to the number of drinkers recommended by animal welfare guidelines. That said, their idle and lying time appeared to be disturbed.

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 17 Feb 2025

https://hal.inrae.fr/hal-04951257v1

[hal-04951317] A conceptual mechanistic model of amino acid fluxes in the small intestine, taking the example of pig

During digestion, almost 50% of absorbed essential amino acids (AAs) are metabolised by intestinal tissue, thus not appearing directly in the portal vein. This value, which is referred to as first-pass metabolism, seems high in relation to the overall efficiency of AA use considered in growth models. Experimental studies of first-pass metabolism are complicated due to the presence of numerous metabolic fluxes in the intestine and to the dynamics of digestion and absorption. The aim of this study was to integrate current knowledge of the metabolic AA fluxes in the small intestine in a conceptual model of intestinal AA metabolism. The model was built as a series of 200 intestinal segments, each having the same structure. Each segment was composed of seven pools, representing the fate of a generic AA according to their location (i.e., luminal or intestinal), origin (i.e., dietary or endogenous), and form (i.e., as protein or as a free AA). The pools were connected by fluxes, representing the main fates of AA, such as saturable transport of luminal AA or homeostasis of free or protein-bound AA in intestinal tissue. To parameterise the model, data from the literature were used, as well as values considered as reasonable. Simulations were carried out over 24 h, with five meals during the day and fasting during the night. Representing the small intestine as a series of segments allowed to account both for its tubular structure and for changing luminal environment. During the day, the model simulated the uptake of AA from the intestine and export to the blood, while during the night it simulated the uptake of AA from the blood to ensure intestinal homeostasis. Approximately, half of dietary AAs absorbed were metabolised in first-pass by intestinal tissue (i.e., used for intestinal protein synthesis). Part of this intestinal protein was secreted in the lumen as endogenous protein, which was driven by the presence of digesta, and endogenous protein can be digested and absorbed in more distal segments. In vivo, only the apparent first-pass metabolism of AA can be measured due to the dynamics of AA recycling and the tubular structure of the small intestine. This model can be a valuable tool for research and education to simulate the impact of nutrition on intestinal AA metabolism. (c) 2025 The Authors. Published by Elsevier B.V. on behalf of The animal Consortium.

ano.nymous@ccsd.cnrs.fr.invalid (Clément Garçon) 17 Feb 2025

https://hal.inrae.fr/hal-04951317v1

[hal-04590313] Environmental trade-offs of meeting nutritional requirements with a lower share of animal protein for adult subpopulations

Decreasing the share of protein contributed by animal-based foods is recommended to move towards more sustainable and healthier diets. This study aimed to assess potential environmental impacts of diets with a lower share of animal protein. The diets were modeled to include the minimum share of animal protein in total protein that met nutrient requirements and did not increase costs. The new diets also minimized the difference in the quantity of food from those of observed (OBS) diets. They were modeled for five adult subpopulations (defined by sex and age) using mathematical optimization. The model was created by combining the INCA2 database (to model OBS diets in the French population) and a database of 207 food items to adjust nutritional and price parameters. All modeled diets satisfied nutritional and cost constraints. A low-animal-protein (LAP) diet was identified for each subpopulation by progressively decreasing the share of animal protein by steps of 5% until the recommended quantity of protein and/or consumption constraints were no longer satisfied. Potential environmental impacts of the LAP diets in eight impact categories were calculated using life cycle assessment (LCA) and life cycle inventories from Agribalyse® 3.0. A LAP diet for the entire population was calculated as a weighted mean of the subpopulations’ LAP diets. The share of animal protein decreased from 70% in the OBS diet to 50% in the LAP diet. Compared to the OBS diet, the LAP diet decreased five environmental impacts: climate change (greenhouse gas emissions), acidification (emissions of acidifying compounds) and land occupation (all by more than 30%), cumulative energy demand (by 23%) and marine eutrophication (by 13%). Conversely, it increased three environmental impacts: freshwater eutrophication and water use (both by ca. 40%) and biodiversity damage potential (potential loss of species associated with land use) (by 66%). These results suggest that decreasing the share of animal protein to 50% is compatible with nutritional requirements, affordability and consumption constraints, but would have mixed effects on the environment.

ano.nymous@ccsd.cnrs.fr.invalid (Joël Aubin) 28 May 2024

https://hal.science/hal-04590313v1

[hal-04874121] Sensitivity analysis of the INRA 2018 feeding system for ruminants by hybrid local and global approaches: Comparing the contribution of dietary input variables to multiple response prediction in dairy cattle

We conducted sensitivity analysis (SA) of the French National Institute of Agricultural Research (Institut national de la recherche agronomique; INRA) 2018 feeding system for ruminants applied to dairy cows. We evaluated which dietary input variables contribute most to changes in each output variable, considering the potential interactions presence among input variables. We applied a quantitative analysis (one-at-a-time analysis, OAT; i.e., local SA) and a relative comparative analysis (global SA; GSA) through variance-based SA considering potential interactions and nonmonotonicity. The 5 likely influential dietary input variables were selected: CP, gross energy (GE), OM apparent digestibility (OMd), effective degradability of nitrogen assuming a passage rate of 6%/h, and true intestinal digestibility of nitrogen. The sensitivity of 5 selected animal responses (output variables) to input variables was analyzed: DMI, milk protein yield (MPY), energy in methane (ECH4), nitrogen utilization efficiency (NUE), and the ratio between urine and total N excretion (UN/TN). Six diets for dairy cattle, reflecting the diversity of diets commonly used in practice, were formulated to meet 95% of the potential milk production (37.5 kg/d) of a multiparous dairy cow at wk 14 of lactation. For each diet, the 5 input variables were randomly sampled around the INRA 2018 feed table values (reference point), and the animal responses around this reference situation were calculated using the rationing software INRAtion V5. In OAT, the sensitivity of animal responses was quantified by calculating the normalized tangent value at the reference point, and in GSA, the Sobol indices were calculated for relative influence of each input and their interaction. The influence of the 5 key input variables on the 5 main animal responses predicted from the INRA feeding system was consistent across both SA approaches. With the 6 diets, GE and OMd appeared as the main contributors to changes in DMI, MPY, ECH4, and NUE. Crude protein was the main contributor to changes in UN/TN and another major contributor to changes in NUE. When considering OAT, the sensitivity of outputs showed differences depending on diet, more particularly for DMI and MPY. With grass hay–based diets (GH), DMI was less sensitive and MPY was more sensitive to variations in input variables than other diets. When considering GSA, interactions between input variables were also noticeable for DMI and MPY; the interactions were high with the GH diets for DMI, and with fresh ryegrass and grass silage diets for MPY. On the other hand, for MPY, the non-GH diets were less sensitive to variations in input variables, and the interaction between inputs was higher than with GH diets. Our results support the hypothesis that MPY, unlike DMI, is more responsive to energy-related factors at a high true intestinal digestible protein (PDI) to net energy for lactation (UFL) ratio (e.g., GH diets &gt;117 g PDI/UFL), than at a lower PDI/UFL ratio. Hence, hybridizing the SA methods can help to interpret the system and facilitate a more precise evaluation thereof, especially GSA, which is amenable to nonmonotonic models such as those characterizing complex feeding systems integrating multiple nutritional and animal factors.

ano.nymous@ccsd.cnrs.fr.invalid (Seoyoung Jeon) 08 Jan 2025

https://hal.inrae.fr/hal-04874121v1

[hal-04802793] Comparative genomics and epigenomics of transcriptional regulation

Transcriptional regulation in response to diverse physiological cues involves complicated biological processes. Recent initiatives that leverage whole genome sequencing and annotation of regulatory elements significantly contribute to our understanding of transcriptional gene regulation. Advances in the data sets available for comparative genomics and epigenomics can identify evolutionarily constrained regulatory variants and shed light on noncoding elements that influence transcription in different tissues and developmental stages across species. Most epigenomic data, however, are generated from healthy subjects at specific developmental stages. To bridge the genotype-phenotype gap, future research should focus on generating multidimensional epigenomic data under diverse physiological conditions. Farm animal species offer advantages in terms of feasibility, cost, and experimental design for such integrative analyses in comparison to humans. Deep learning modeling and cutting-edge technologies in sequencing and functional screening and validation also provide great promise for better understanding transcriptional regulation in this dynamic field.

ano.nymous@ccsd.cnrs.fr.invalid (Huaijun Zhou) 03 Dec 2024

https://hal.science/hal-04802793v1

[hal-05051425] Enrichir le milieu de vie des porcs

Enrichir le milieu de vie permet de stimuler les comportements naturels des porcs, ainsi que leur cognition. Pour que l'enrichissement soit adapté à l'espèce, il faut bien connaître ses besoins comportementaux et son mode de vie. Les porcs sont des animaux qui sentent très bien, ont une audition performante mais voient surtout en 2D et sont myopes. Leur groin leur sert à explorer leur environnement. Ils forment des liens sociaux avec leurs congénères et peuvent se bagarrer en présence d'individus qu'ils ne connaissent pas, pour établir une hiérarchie. Capables d'apprendre et mémoriser sur du long terme, ils sont très performants au niveau cognitif. Souvent, nos situations d'élevage sont pauvres ou bien vont proposer des enrichissements inadaptés. Dans cet article nous montrons qu'il existe de nombreuses façons d'enrichir l'environnement des porcs et que certaines modalités (auditive, olfactive) ont été très peu prises en compte pour enrichir. Les enrichissements sociaux et cognitifs sont également encore peu considérés, même si quelques possibilités existent. Finalement, Il reste encore énormément de choses à développer, et les exemples de nos élevages expérimentaux devront être amenés à se généraliser.

ano.nymous@ccsd.cnrs.fr.invalid (Céline Tallet) 29 Apr 2025

https://hal.inrae.fr/hal-05051425v1

[hal-05122259] Early life reproductive investment affects longevity in ewes

To increase lifetime production of ewes, it has been suggested to mate ewe lambs. However, research on the effect of age at first lambing on longevity has shown conflicting results. This study investigated the impact of early life reproduction (i.e., the effect of age at first lambing and litter size) and environmental conditions on longevity in a prolific sheep breed traditionally bred as lambs. Lifetime performance data were obtained from 550 884 Norwegian White Sheep born between 2000 and 2013 spread across Norway. All ewes lambed their first litter either as 1-year-old or 2-year-olds. Longevity was investigated using a linear mixed model with age at first lambing, litter size, county, the covariates early- and late parturition, and two categorical variables describing cross-fostering and success in weaning as fixed effects. Herd x year was fitted as a random effect. The lifespan of the ewes was affected both by age of the ewe at first reproduction and the reproductive investment (i.e., litter size). The predicted lifespan for ewes mated as lambs was 1 548 days (4.2 years) whereas the lifespan for those mated as 2-year-olds was 1 700 days (4.7 years). There was a curvilinear relationship between lifespan and litter size. Lifespan increased from 1 272 days (3.5 years) to 1 618 days (4.4 years) when litter size increased from 0 to 1 lamb. Further increased reproductive investment resulted in a decreased lifespan with a litter size of 4 having the shortest lifespan of 1 468 days (4.0 years). The relation between litter size and lifespan was similar but at different levels for both age groups of ewes, except for ewes rearing less lambs than they gave birth to. In that group, ewes mated as lambs had a peak predicted lifespan at 1 504 days (4.1 years) with a litter size of one lamb, whereas those first mated as 2-year-olds had their peak predicted lifespan of 1 650 days (4.5 years) with a litter size of two lambs. The relationship between longevity and reproductive investment was in some cases affected by environmental conditions. However, the effect was not consistent with latitude. In conclusion, ewes mated as lambs, in general, live shorter lives compared to those first mated as 2-year-olds but environmental importance for longevity and reproduction needs further investigation.

ano.nymous@ccsd.cnrs.fr.invalid (L.S. Kierkegaard) 20 Jun 2025

https://hal.inrae.fr/hal-05122259v1

[hal-05131593] Nitrogen and truly digestible protein efficiencies of dairy cows fed fresh herbage- or maize forage-based diets: a meta-analysis

Understanding how dietary forage influences dairy cows' use of nitrogen (N) and protein resources may help decrease N losses to the environment, which is a major issue in the livestock sector. The present study evaluated the effects of cow and diet characteristics on N use efficiency and the efficiency of truly digestible protein in the intestine (PDI) (i.e., protein use efficiency at the metabolic level), depending on whether the base forage is fresh herbage or maize forage. To this end, a meta-analysis was performed of a dataset composed of 22 experiments that included 266 observations of individual in vivo whole-tract digestibility and N balance for lactating dairy cows fed either fresh herbage diets indoors (Fresh herbage, n = 113) or maize forage diets (Maize, n = 153). The dataset compiled dietary and zootechnical variables such as feed intake, chemical composition of the diet, milk yield (MY), milk composition and cow characteristics. The nutritional value of diets, cow protein requirements and PDI use efficiency were calculated for all diets according to the INRA 2018 feeding system for ruminants. The dataset was then analysed using mixed-effect models, considering the experiment and the cow as random effects. Feed intake, MY and dietary PDI concentration were greater for Maize diets than Fresh herbage diets, while dietary N and energy concentrations were greater for Fresh herbage diets. Dietary N concentration influenced N use efficiency the most, while the ratio of dietary protein concentration to energy concentration influenced PDI efficiency the most. N and PDI use efficiency averaged 23.9 and 72.0%, respectively, for the Fresh herbage diet type, and 30.6 and 74.7%, respectively, for the Maize diet type. This study highlighted that cows use N and PDI in similar ways regardless of whether they are fed fresh herbage or maize diets. In the range of variation studied, each increase in N use efficiency increased PDI use efficiency by the same degree, regardless of the type of diet. This suggests that PDI use efficiency can be predicted from N use efficiency, which is easier to calculate.

ano.nymous@ccsd.cnrs.fr.invalid (Manon Ferreira) 26 Jun 2025

https://hal.inrae.fr/hal-05131593v1

[hal-04964242] Refining the soil and water component to improve the MoSt grass growth model

Knowledge of previous and future grass growth is an important factor for grassland management decision making. It allows the farmer to predict the availability of grass for the herd on a short-term basis and adapt grassland management practise accordingly. The Moorepark St Gilles Grass Growth Model (MoSt GG) is used to predict grass growth weekly on 84 grassland farms across Ireland. The repeated use of the model on these farms has identified areas for improvement that have been addressed in this paper. Among these improvements, the soil sub-model component has been further developed to better represent different soil types and to account for different soil depths, improving the simulations of water and soil nitrogen fluxes (V2V1+soil). A soil sub-layer of 10 cm was added to better simulate growth recovery after a drought period (V3V2+water). The radiation component was improved by including the day length in the grass growth estimation (V4V3+rad) instead of only accounting for daily cumulative solar radiation. These improvements were evaluated against several experiments conducted in Ireland and France. The developments improved model accuracy for every experiment evaluated. The RMSE in the original version of the model ranged from 322 to 1011 kg of DM/ha, whereas in the latest version of the MoSt GG model (V4V3+rad), the RMSE ranged from 312 to 671 kg of DM/ha. The further consideration of soil characteristics resulted in a higher variability in grass production and N leaching depending on soil type and weather conditions, leading to improved growth trend representation. The addition of the soil sub-layer (V3V2+water) improved the accuracy in drier years (French experiment) due to the more realistic grass growth recovery after a drought. The latest version of the model (V4V3+rad) simulates grass production more accurately than the previous versions and increases the reliability of grass growth prediction.

ano.nymous@ccsd.cnrs.fr.invalid (L. Bonnard) 24 Feb 2025

https://hal.inrae.fr/hal-04964242v1

[hal-05109749] Myogenic and adipogenic potential of porcine muscle satellite cells isolated by flow cytometry

Skeletal muscle mesenchymal stromal cells (MSCs) are resident cells in the stromal, interstitial or perivascular areas, with satellite cells (SCs) acting as essential precursors for muscle growth and regeneration. This study firstly aimed to phenotype freshly isolated SCs using cell surface markers and gene expression and to assess their ability to differentiate in myogenic or adipogenic conditions. Then, refined SCs populations sorted according to the myogenic CD56 cell surface marker were characterized. SCs were isolated from the longissimus muscle of 5-7day-old piglets and analyzed using flow cytometry. The hematopoietic CD45 + cells represented 20 % of the total isolated cell population. The myogenic CD29 and CD56 positive cell populations were the most abundant (80 % and 50 % respectively). Mesenchymal CD90 positive cells were also highly present (34 %) while the proportions of fibro-adipogenic CD140a and CD34-positive cells were low (&lt;3 %). In this study, we showed that total isolated muscle-derived SCs were able to differentiate into myotubes in both myogenic and adipogenic media. Transcriptional profiles were similar, except for PPAR gamma, PGC1 alpha, and Myosin Heavy Chain 2B witch present a higher induction during differentiation in the adipogenic medium. Interestingly, non-hematopoietic CD45-sorted cells further separated in CD45-/CD56+ and also CD45-/CD56-sub-populations mostly formed myotubes under both conditions, with CD56-cells showing potential and gene expression profile of myoblasts. Mature adipocytes were found in the CD45-/CD56+ group after differentiation in adipogenic medium. This study increases knowledge on myogenic cell surface marker and underscores the complexity and heterogeneity of muscle SCs.

ano.nymous@ccsd.cnrs.fr.invalid (Annie Vincent) 12 Jun 2025

https://hal.inrae.fr/hal-05109749v1

[hal-05042739] L'introduction d'animaux en vergers et en vignes : une solution agroécologique pour gérer les adventices ?

Le projet REVE avait pour objectif d'explorer les multiples aspects des interactions entre l'élevage et les productions végétales. Celles-ci se révèlent notamment productrice de nombreux services dont ceux de régulation des bioagresseurs. Cet article fait un focus sur l'introduction d'animaux en vignes et vergers pour gérer les adventices. Le but de cette étude est d'analyser, pour différentes espèces animales introduites, les services rendus en termes de gestion de l'enherbement, versus les disservices en termes de dommages causés aux sols, aux plants de vignes et aux arbres dans les vergers.

ano.nymous@ccsd.cnrs.fr.invalid (Gentiane Maillet) 22 Apr 2025

https://hal.inrae.fr/hal-05042739v1

[hal-05051412] À l’écoute des cochons

Interview de Céline TALLET, directrice de recherche à INRAE et responsable de l’équipe Bien-être de l’UMR PEGASE.

ano.nymous@ccsd.cnrs.fr.invalid (Céline Tallet) 29 Apr 2025

https://hal.inrae.fr/hal-05051412v1

[hal-04966411] ECL Method for the Determination of Skatole in Pig Plasma

Skatole is one of the compounds responsible for the unpleasant odor found in tainted boar meat. Its quantification in blood plasma could allow for the identification of tainted carcasses for selective breeding or research purposes with measures in live animals. Toward this goal, we demonstrate that skatole may be quantified after extraction in blood plasma by electrochemiluminescence (ECL) using boron-doped diamond electrodes. First, a method for extracting skatole from plasma into acetonitrile for further analysis has been developed. Additionally, for the first time, native skatole has been detected in pig plasma samples using ECL for the determination of boar taint in pigs. A double extraction was achieved using an intermediate step with commercial rapeseed oil at a ratio of 1:4:10 (plasma/rapeseed oil/acetonitrile). Using standard solutions of deionized water spiked with skatole (50-1000 nM), a calibration curve demonstrated good linearity with a coefficient of determination (R 2 ) of 0.9948, a limit of detection of 37 nM (4.84 ng/mL), and a limit of quantification of 227 nM (29.69 ng/mL). Then, 24 pig plasma samples were analyzed, and the resulting skatole concentrations were compared with those contained in the fat of the same animals and determined using the "gold standard" technique, HPLC. The results reported here indicate a Pearson correlation coefficient (R 2 ) of 0.96. All of the pig samples that displayed an elevated skatole concentration above the consumer acceptance threshold can be identified from plasma analysis alone, thus demonstrating that plasma detection with ECL can be utilized for the determination of boar taint.

ano.nymous@ccsd.cnrs.fr.invalid (Samuel Stewart) 25 Feb 2025

https://hal.inrae.fr/hal-04966411v1

[hal-04891786] CowComfort: A R-shiny app to visualize the evolution of thermal comfort of dairy cows under climate change and the associated uncertainty

We present CowComfort, an R-shiny app developed to assist researchers, stakeholders and policy makers in the spatialized visualization of the evolution of the thermal comfort of dairy cows under climate change. The application is designed to take into account the uncertainty associated with the climatic projection and the calculation of the thermal indices. This app and its associated data can be used in modelling research and to communicate about the impact of climate change on dairy cows and the required adaptations. An illustration is given for French climatic data and for an evaluation of the thermal stress based on several calculations of the temperature humidity index. It can be easily repeated and extended to other climate situations and thermal stress evaluations.

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Isabelle Graux) 16 Jan 2025

https://hal.inrae.fr/hal-04891786v1

[hal-05081949] The Denver call for action

In October 2022, the Dublin Declaration of Scientists on the Societal Role of Livestock was initiated during the International Summit on the Societal Role of Meat, held in Dublin. The Declaration has since been signed by more than 1,200 scientists from around the world, each verified to hold relevant scientific credentials. The Declaration begins with the words: “Livestock systems must progress on the basis of the highest scientific standards. They are too precious to society to become the victim of simplification, reductionism or zealotry. These systems must continue to be embedded in and have broad approval of society. For that, scientists are asked to provide reliable evidence of their nutrition and health benefits, environmental sustainability, socio-cultural and economic values, as well as for solutions for the many improvements that are needed. This declaration aims to give voice to the many scientists around the world who research diligently, honestly and successfully in the various disciplines in order to achieve a balanced view of the future of animal agriculture.” Today, two years later, these words have lost none of their importance. Renewed urgency led to this Denver Call for Action.

ano.nymous@ccsd.cnrs.fr.invalid (Wilhelm Windisch) 23 May 2025

https://hal.inrae.fr/hal-05081949v1

[hal-04867271] Polar lipids and proteins in milk fat globule membranes as players in spontaneous lipolysis in cow’s milk

A study of the lipidome and proteome was performed on milk fat globule membranes (MFGM) originating from milk samples from high (HL) and low (LL) lipolysis groups of cows. Combined univariate and multivariate statistical analyses proposed a set of variables highly associated to contrasted samples with regard to milk lipolysis. Milk from HL group were related to 4 phosphatidylinositols, 8 phosphatidylcholines, 1 sphingomyelin and 27 proteins, among them the phosphatidylcholine/phosphatidylethanolamine ratio and ORM1 may contribute to the membrane remodeling of the MFGM. The abundance of CP, CHI3L1, NECTIN2, A2M were strongly positively correlated with HL. Conversely, 3 phosphatidylinositols, 1 phosphatidylcholine and 2 phosphatidylethanolamines were assigned to the LL group. The HL group in cows is associated with a specific MFGM phospholipids and proteins profile, suggesting an impact on membrane fluidity and lipid rafts composition intervening in LPL anchoring and activation, as well as on pro-inflammatory lipids and proteins.

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Bernard) 06 Jan 2025

https://hal.inrae.fr/hal-04867271v1

[hal-05045421] Genetic regulation of gene expression across multiple tissues in chickens

The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.

ano.nymous@ccsd.cnrs.fr.invalid (Dailu Guan) 24 Apr 2025

https://hal.inrae.fr/hal-05045421v1

[hal-04998059] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

Scientific publishing has undergone a tremendous change in recent years. We, a group of Editors-in-Chief of scientific journals owned by scientific bodies, want to communicate some of our values. We represent animal, animal -open science, animal -science proceedings, JDS Communications, Journal of Animal Science, Journal of Applied Poultry Research, Journal of Dairy Science, Poultry Science and Translational Animal Science. Our values motivate our involvement in society-, association-or scientific institutionowned journals in animal science and shape our practices in scientific publishing, in the light of the tremendous changes in the landscape of scientific publishing over the last decade.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 20 Mar 2025

https://hal.inrae.fr/hal-04998059v1

[hal-05104838] Chickens perceive humans as social buffers and may follow human-given cues: A pilot study

Positive perception of humans, extensively documented in domestic mammals, remains comparatively underexplored in domestic birds like chickens, with existing studies largely focusing on fear reduction. This research evaluated whether chickens perceive humans positively, accounting for interaction types and breed differences. Two breeds (Lohmann LSL Classic, Brown Classic) experienced physical contact (PC), visual-only contact (VC), or minimal human contact (MC) over 13 days (Days 35-51; PC and VC: 1-2 min/day). Birds were assessed using three behavioral tests. During the separation-reunion test (Days 52-53), individuals underwent two 3-min separations (experimenter absent) and reunions (experimenter present) in an open-field setting. Subsequently, the experimenter attempted up to six standardized capture attempts to catch the birds (the capture test). Lastly, the local enhancement test (Days 120-137) assessed birds' ability to use human presence/gestures to locate food. In the separation-reunion test, PC birds exhibited calmer/positive behaviors, such as reduced vigilance and increased foraging, in the presence of the experimenter compared to being alone. Conversely, MC birds displayed fewer calm behaviors and greater withdrawal when the experimenter was present. Brown birds showed more calm behaviors, reduced movement, and spent more time near the experimenter than white birds. The capture test supported these results, with PC and brown birds being easier to capture. In the local enhancement test, two PC individuals and the brown PC group as a whole successfully used human-given cues to locate food rewards. These results indicate that, as observed in other species, chickens-especially those with positive human experiences-can associate humans with rewarding outcomes. Positive interactions may also lead chickens to perceive humans as social buffers-that is, as factors that help mitigate stress in challenging situations. Although fundamental, this study highlights the potential of breed-sensitive approaches to improve poultry welfare and opens the discussion on adapting human-animal interactions to breed-specific characteristics. These insights can inform welfare-enhancing practices and provide practical tools for on-farm management that benefit both animals and farmers.

ano.nymous@ccsd.cnrs.fr.invalid (Vitor Hugo Bessa Ferreira) 10 Jun 2025

https://hal.science/hal-05104838v1

[hal-05128106] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

Scientific publishing has undergone a tremendous change in recent years. We, a group of Editors-in-Chief of scientific journals owned by scientific bodies, want to communicate some of our values. We represent animal, animal -open science, animal -science proceedings, JDS Communications, Journal of Animal Science, Journal of Applied Poultry Research, Journal of Dairy Science, Poultry Science and Translational Animal Science. Our values motivate our involvement in society-, association-or scientific institutionowned journals in animal science and shape our practices in scientific publishing, in the light of the tremendous changes in the landscape of scientific publishing over the last decade.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 24 Jun 2025

https://hal.inrae.fr/hal-05128106v1

[hal-05057234] Towards a ‘One quality’ approach of pork: A perspective on the challenges and opportunities in the context of the farm-to-fork continuum – Invited review

A substantial amount of research on pork production and consumption highlights an interplay between the intrinsic qualities that are inherent to the product and the extrinsic qualities related to how it is produced, which together contribute to the perception and evaluation of fresh pork. However, studies have emphasised difficulties in defining their relative importance depending on the countries, consumers' knowledge, experience and personal beliefs, as well as their dynamic changes over time. A joint and multidimensional consideration of the intrinsic and extrinsic quality dimensions is critical to achieve sustainable development goals that ensure healthy, nutritious, fair and environmentally friendly pork produced in a profitable manner. However, very few studies have investigated the synergies and antagonisms between the multiple dimensions of intrinsic and extrinsic qualities of pork. This perspective aims to define and promote the concept of ‘One Quality’ pork, as an approach to meeting the multiple and divergent expectations of stakeholders in the pork value chain, while jointly considering pork quality and sustainability. It aims to discuss how the changing expectations of consumers, citizens and public action including policy makers are currently promoting a holistic definition and evaluation of pork quality. It also seeks to explore how the multiple dimensions of pork quality, including their intrinsic and extrinsic dimensions, can be considered simultaneously. The opportunities and challenges of implementing a ‘One Quality’ approach to pork for an integrated sustainability assessment of the farming systems, i.e., by jointly addressing the intrinsic quality attributes, ensuring sustainable farming practices, economic viability for stakeholders, and alignment with consumer and citizen expectations, are then discussed along the farm-to-fork continuum.

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 06 May 2025

https://hal.inrae.fr/hal-05057234v1

[hal-04993749] The Changes in Grassland Animal Husbandry and Herdsmen’s Life in the Qinghai Pastoral Area of China Based on the Perspective of Changes in the Grassland Property Rights System

Based on the historical background of the changes made to the grassland property rights system, the first part of this study restores the changes in property rights systems in six major autonomous counties of grassland animal husbandry production in Qinghai region, while the second part qualitatively analyzes the changes in grassland animal husbandry operations and herdsmen’s life under the changes in property rights. The results show that, with the reform of the property rights system, the range of livestock grazing has changed from large-scale nomadic grazing to regional rotational grazing. The herds are mainly yaks and Tibetan sheep, accounting for more than 90%, with the proportion of Tibetan sheep being higher than that of yaks. The numbers of total livestock and those on the market first rose and then declined, showing a dynamic balance in recent 10 years, while the number of breeding female animals has increased year by year. Artificial grass planting has gradually become popularized in pastoral areas. The time span of livestock supplementary feeding has increased and is more scientific, and the output value of animal husbandry has increased year by year, showing a strong peak associated with intensification. The proportion of the population engaged in animal husbandry has decreased gradually with increasing population in the region. The income sources of herdsmen have become more and more diversified and are increasing year by year, and the Engel coefficient presents a downward trend. The human environment in pastoral areas has improved. Based on the above analysis, suggestions for the sustainable and high-quality production of animal husbandry under the current grassland property rights system are put forward, as well as for the construction of green organic agricultural and livestock product export land in Qinghai Province.

ano.nymous@ccsd.cnrs.fr.invalid (Yujiao Gou) 17 Mar 2025

https://hal.inrae.fr/hal-04993749v1

[hal-05087086] Ordre de distribution de deux fourrages chez la chèvre : effets sur l’ingestion, la production et le comportement alimentaire

La capacité des chèvres à s’adapter à l’ordre de distribution de deux fourrages différents dans la même journée n’est pas connue, alors que cette pratique est très répandue. Une série de 5 essais, combinant chacun 2 fourrages, ont été conduits pour déterminer les effets de l’ordre de distribution de ces fourrages sur l’ingestion volontaire journalière, la production laitière et le comportement d’ingestion de chèvres laitières Alpine en milieu de lactation. Les combinaisons testées ont été les suivantes : herbe verte et ration semi-complète (ensilage de maïs - tourteau de soja), foin de luzerne de bonne qualité et ensilage de maïs, enrubannage de graminées et foin de luzerne de bonne qualité, foins de luzerne de bonne et de moyenne qualité, et enfin herbe verte et foin de graminées de mauvaise qualité. Dans chaque essai, 24 chèvres ont été étudiées au cours de 3 ou 4 périodes successives, avec 300 à 600 g de concentré par jour selon les essais. Les chèvres ont montré des réactions très différentes selon les combinaisons de fourrages étudiées, avec parfois aucune préférence marquée entre les deux fourrages, et parfois une nette préférence pour l’un des deux fourrages (ratio de 50:50 à 90:10 dans la ration). Un fourrage a toujours été plus ingéré lorsqu’il a été distribué le soir plutôt que le matin (+53% en moyenne), l’ordre de distribution affectant largement la proportion de chaque fourrage dans la ration. En moyenne, l’ingestion totale a eu tendance à augmenter, mais faiblement, lorsque le fourrage préféré a été distribué le soir, en lien avec un temps d’accès au fourrage plus élevé. Les effets de l’ordre de distribution sur la production laitière ont varié selon les essais, en fonction de l’écart de préférence et de valeur alimentaire entre fourrages, ainsi que des variations d’ingestion totale.

ano.nymous@ccsd.cnrs.fr.invalid (Remy Delagarde) 27 May 2025

https://hal.inrae.fr/hal-05087086v1

[hal-05087066] Edito. Valorisation des fourrages en élevage caprin : des modalités de distribution à leurs impacts sur la qualité des produits

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Bertrand Bluet) 27 May 2025

https://hal.inrae.fr/hal-05087066v1

[hal-04880108] The Kerbernez long-term experiment: A dataset on crop yield and soil organic matter evolution in forage crop rotations and permanent grasslands in a temperate oceanic climate

Forage crop rotations including grasslands, common in dairy systems, are known to ensure good productivity and limit the decrease of soil organic matter frequently observed in permanent arable land. A dataset was built to compile data from the Kerbernez long-term experiment, conducted in Brittany(France) from 1978 to 2005. This experiment compared the effect of different forage crop rotations fertilized with ammonium nitrate and/or slurry, with or without grassland, on forage production (quantity, quality) and changes in soil physio-chemical characteristics. These forage crop rotations were based on silage maize and cut monospecific grasslands of Italian ryegrass (Lolium multiflorum L.) or perennial ryegrass (Lolium perenne L.). More precisely, the experiment compared silage maize monocultures, rotations with silage maize and Italian ryegrass established for 6 to 18 months, and rotations with silage maize and perennial ryegrass established for three to more than 10 years. They are representative of the forage crop rotations and permanent grasslands that were at the heart of Brittany's forage revolution in the 1970s. The dataset includes information about the climate and soil conditions, the management of crops and grasslands, the evolution of topsoil organic carbon and nitrogen stocks, the inter-annual variations in crop and grassland dry matter yields and nitrogen contents. The dataset also includes characterisation of soil structural stability, particle-size soil organic matter fractions and potential soil carbon and nitrogen mineralisation at the end of the trial. It consists of fourteen csv files. This dataset can be used for a variety of purposes, namely for assessing the ability of mechanistic models to simulate soil organic matter dynamics and associated fluxes, and to estimate the influence of grassland presence and duration in forage crop rotations on such fluxes.

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Isabelle Graux) 10 Jan 2025

https://hal.science/hal-04880108v1

[hal-04964254] Characterization of grazing Holstein-Friesian dairy cows based on a combination of nitrogen use efficiency and nitrogen balance

Awareness and interest in the use of nitrogen in dairy production systems is intensifying. Cows with high nitrogen use efficiency (NUE; nitrogen used and stored divided by nitrogen available) are generally considered to have a lower nitrogen footprint. This, however, may not always be true on a per-animal basis. The objective of this study was to characterize lactating dairy cows based on the combination of NUE and nitrogen balance (Nbal; nitrogen available less the nitrogen used and stored). Data were available for 1,472 weekly NUE and Nbal estimates from 711 lactations of 278 Holstein-Friesian grazing dairy cows. Random solutions for each cow from separate mixed model analyses of NUE and Nbal were used to categorize each cow into 1 of 2 strata for NUE and separately for Nbal; cows were then categorized on a combination of strata for NUE and Nbal. Data from 248 cows were used. Marginal means for a range of production traits were computed for each of the 4 strata. The population mean (SD) for NUE and Nbal was 21.3% (4.4) and 436 (97) grams of nitrogen per day, respectively. The correlation coefficient between NUE and Nbal was −0.47 demonstrating that the relationship between efficiency (i.e., NUE) and excretion (i.e., Nbal) is, indeed, not perfect. Cows with high NUE and low Nbal were assumed more desirable cows because they had, on average, a higher (i.e., better) or similar NUE to the other 3 strata and excreted, on average, 53 g of nitrogen less per day (SE = 5.1 g N/d) compared with the cows stratified as high NUE and high Nbal. Nevertheless, cows with high NUE and low Nbal were, on average, in greater negative energy balance than cows with low NUE and high Nbal, with the former also having, on average, a lower BCS than both strata of cows with low NUE, suggesting potential poorer health or reproductive capabilities compared with their counterparts. In conclusion, it is important to consider both NUE (high is desirable) and Nbal (low is desirable) when defining nitrogen-efficient dairy cows.

ano.nymous@ccsd.cnrs.fr.invalid (E. Tavernier) 24 Feb 2025

https://hal.inrae.fr/hal-04964254v1

[hal-05122302] A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats

Animal behaviour is a significant component in the evaluation of animal welfare. Conducting continuous observations of animal behaviour is a time-consuming task and may not be feasible over extended periods for all animals. Thus, new technologies like sensors and cameras can be used to assess individual behaviour continuously. Combined with Artificial Intelligence (AI), accelerometers are promising to continuously and individually detect animal behaviour from the acceleration signals and characteristics of the behaviour. Such devices are commercialised for cattle but they have not been widely developed for small ruminants. Being able to automatically monitor behaviour at an individual scale represents a crucial step towards an objective assessment of animal welfare. This paper aims to present the use of a pipeline called ACT4Behav (Accelerometer-based Classification Tool for identifying Behaviours) involving a supervised classification algorithm for automatically characterising specific animal behaviours using accelerometer data, and to explore the best pre-processing steps for each behaviour. This algorithm is designed to be general-purpose and applicable with different species, behaviours and accelerometers. This paper presents the use of this pipeline with eight indoor-housed goats equipped with ear-mounted accelerometers. Rumination, head in the feeder, standing and lying behaviours were continuously sampled from camera recordings for 11 consecutive hours for each goat using The Observer software. The developed pipeline was used to identify optimal descriptive features and data preparation steps for each prediction model, one for each behaviour. A sensitivity analysis was conducted to assess the impact of the processing techniques and parameter value on the resulting AUC (Area Under the Curve) score, used as the performance score of the models. This analysis allowed the identification of the adequate filtering techniques, time-window segmentations, application of various transformations to raw data, and feature selections for each behaviour. Tuning the data pre-processing for each behaviour enhanced the ability to predict rumination (AUC score=0.800), head in the feeder (AUC score=0.819), lying (AUC score=0.829) and standing (AUC score=0.823) behaviours. When the application of the models on goats that did not participate in the training was tested by training the models on six goats and testing it on the two other goats, the AUC score for the four behaviours decreased (0.644, 0.733, 0.741 and 0.749 respectively for rumination, head in the feeder, lying and standing).

ano.nymous@ccsd.cnrs.fr.invalid (Sarah Mauny) 20 Jun 2025

https://hal.inrae.fr/hal-05122302v1

[hal-05100241] Oral-stomach sampling as an alternative to rumen canula for the inoculation of in vitro batch fermentation systems

The standard method to collect rumen fluid (RF) serving as inoculum for in vitro rumen fermentation assays and using ruminally cannulated animals is less and less accepted in some countries, and oral-stomach sampling (OSS) could be an alternative that needs to be validated. The objective of this study was to compare the in vitro rumen fermentation parameters of a large set of substrates with contrasted fermentation profiles using inocula obtained by OSS and from different sampling sites in the rumen of cannulated dairy cows. Rumen fermentation assays were conducted using twelve different substrates (six forages and six total mixed rations) and three types of inoculum consisting in fresh RF sampled in the reticulum (RF ret ), sampled both in the reticulum and the ventral sac (RF mix ) and using OSS (RF tub ) during three feeding periods creating variability in RF composition (control and acidogenic diets). There was a strong effect of substrate on all the parameters (P &lt; 0.001) and a limited effect of the type of RF on the overall fermentability of substrates, particularly between RF mix (standard method) and RF tub that had similar values for dry matter (DM) and fiber degradabilities, gas production (including proportion of methane (CH 4 ) in the gas produced), total volatile fatty acids (VFA) and ammonia (NH 3 ). Above all, we did not detect any interaction between the substrate and the type of RF, highlighting the possibility to measure confidently relative differences among substrates or treatments. Overall, our results showed that fresh OSS can be a relevant alternative to the fresh RF sampling using cannulated animals. To keep OSS as a research tool on the long term, efforts should be continued to improve the standardization and the refinement of the OSS method.<p>Abbreviations: ADF, acid detergent fibre; Bic, bicarbonate; C, cocksfoot; Ca, calcium; CH 4 , methane; CP, crude protein; DM, dry matter; GP, gas production; IVADFD, in vitro acid detergent fibre degradability; IVDMD, in vitro dry matter degradability; IVNDFD, in vitro neutral detergent fibre degradability; MgO, magnesium oxide; MF, meadow fescue; NDF, neutral detergent fibre; NH 3 , ammonia; NIR, near infrared reflectance; OM, organic matter; OSS, oral-stomach sampling; P, potassium; PG, permanent grassland; RC, red clover; RF, rumen fluid; RF mix , rumen fluid sampled in different sites of the rumen; RF ret , rumen fluid sampled in the reticulum; RF tub , rumen fluid sampled using tubing OSS; S, sainfoin; TMR, total mixed ration; TMRA, acidogenic total mixed ration; TMRF, total mixed ration rich in fibers; VFA, volatile fatty acids; WC, white clover.</p>

ano.nymous@ccsd.cnrs.fr.invalid (Vincent Niderkorn) 06 Jun 2025

https://hal.inrae.fr/hal-05100241v1

[hal-05012247] Optimizing the MoSt GG model a sensitivity-driven calibration for better grass growth forecasting

Grasslands offer an efficient and eco-friendly way to produce high-quality feed for ruminants, benefiting both livestock production and human nutrition. However, its high sensitivity to its environment makes its management challenging for farmers. Predicting week ahead grass growth results in better-informed decision making on farms. The Moorepark St Gilles Grass Growth Model (MoSt GG) has been used since 2018 to predict weekly grass growth on grassland farms across Ireland with 84 farms involved in 2023. The repeated use of the model on these farms has identified a need to improve its accuracy, which has been addressed in this study. First, a sensitivity analysis using the Morris method was conducted to identify the parameters that have the most influence on the model’s grass growth output, both on an annual and monthly time step. From that analysis, ten parameters were selected, all of which related either to temperatures, day length or nitrogen demand and availability for the grass. These ten parameters were calibrated using a semi-automatic iterative method of calibration on a dataset of 14 commercial farms containing four years of grass measurements. Nine iterations were necessary to calibrate the model resulting in a reduction of MAPE from 30.0% to 19.8% in its final calibrated version, and notably increasing the final R2 from 0.58 to 0.71. Finally, the model was evaluated over a new dataset of ten commercial farms for four years. The evaluation confirmed the improvement of the model with a final MAPE of 19.1% and a R2 of 0.67 compared to 30.1% and 0.57 respectively before the calibration. The calibration process of the MoSt GG model has significantly improved the model accuracy to predict on farm grass growth. This improvement is expected to be particularly valuable for farmers in their decision making process, providing them with more reliable on farm grass growth predictions.

ano.nymous@ccsd.cnrs.fr.invalid (L. Bonnard) 31 Mar 2025

https://hal.inrae.fr/hal-05012247v1

[hal-04702523] Electrical stimulation to improve meat quality: Factors at interplay, underlying biochemical mechanisms and a second look into the molecular pathways using proteomics

Ensuring consistent beef eating quality is paramount for meeting consumer demands and sustaining the meat industry. Electrical stimulation (ES) is a post-slaughter intervention used to accelerate post-mortem glycolysis, to avoid cold shortening, to control the tenderization rate of meat through sophisticated physical, chemical and biochemical mechanisms including proteolysis, to improve beef tenderness and to achieve normal pHu that might lead to positive impact on color. This review comprehensively examines the multifaceted effects of ES on beef quality, encompassing factors and settings influencing its efficacy and the underlying biochemical mechanisms revealed using traditional biochemistry methods. It then delves into the molecular pathways modulated by ES, as unveiled by muscle proteomics, aiming to provide a second look and an unprecedented understanding of the underlying biochemical mechanisms through an integrative proteomics analysis of low-voltage ES (LVES) proteomics studies. The proteins changing as a result of ES were gathered in a compendium of 67 proteins, from which 14 were commonly identified across studies. In-depth bioinformatics of this compendium allowed a comprehensive overview of the molecular signatures and interacting biochemical pathways behind electrically stimulated beef muscles. The proteins belong to interconnected molecular pathways including the ATP metabolic process and glycolysis, muscle structure and contraction, heat shock proteins, oxidative stress, proteolysis and apoptosis. Understanding the intricate interplay of molecular pathways behind ES could improve the efficiency of beef production, ensuring consistent meat quality and meeting consumer expectations. The integrative analysis approach performed in this study holds promise for the meat industry's sustainability and competitiveness.

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 19 Sep 2024

https://hal.inrae.fr/hal-04702523v1

[hal-04865671] Effects of intramuscular fat on the flavor of fresh sheep and goat meat: Recent insights into pre-mortem and post-mortem factors

Sheep and goat meat products are becoming increasingly popular among consumers due to their unique flavor derived from intramuscular fat (IMF), which contributes to formation of the distinctive odor. However, there is currently a dearth of reviews on the impact of IMF on the flavor of sheep and goat meat. The present review aims to discuss the relationships between IMF and flavor through lipid composition and fatty acid (FA) distribution, provide an overview of characteristic flavor compounds affecting the flavor of sheep and goat meat, and shed light on the impacts of pre-mortem and post-mortem factors on meat flavor attributed to changes in FAs and flavor compounds. Controlling pre-mortem practices and adjusting post-mortem harvesting methods are key factors in shaping and/or driving the flavor of sheep and goat meat products. This review enhances the comprehensive understanding of the impact of IMF on the flavor of sheep and goat meat.

ano.nymous@ccsd.cnrs.fr.invalid (Tianyu Su) 07 Jan 2025

https://hal.inrae.fr/hal-04865671v1

[hal-05019793] Research note: double digest Restriction site Associated DNA sequencing is a suitable alternative to high density SNP chips for genomic selection of layers

For the genomic selection of laying hens, the costs of genotyping are still a challenge. Alternative genotyping approaches as low density SNP chips have been developed by breeding companies to avoid the use of the high-density SNP chip (HD). Another approach called double digest restriction site associated DNA sequencing (ddRAD-seq), associated with an appropriate quality control was also proven to be reliable to genotype laying hens. From this perspective, the use of ddRAD-seq genotypes as an alternative to HD SNP chip genotypes was studied for the genomic evaluation of 179 candidate individuals in a commercial pure line of laying hens of Rhode Island. Genomic evaluations based on ancestry were performed in three different scenari and for four egg quality traits. The first scenario is the reference scenario using only HD SNP chip genotypes. The genomic estimated breeding values (GEBV) were calculated for the 179 candidates with 437 individuals as the reference population (GEBVHDchip437). In the second scenario, the reference population included only the 50 individuals with true ddRAD-seq genotypes and GEBVddRAD-seq50 were calculated for the 179 G1 candidates, based on their ddRAD-seq genotypes. Finally, for the third scenario of genomic evaluation, the reference population was constituted of 437 individuals, with simulated ddRAD-seq genotypes. The GEBVddRAD-seq437 were calculated for the 179 G1 candidates based on their true ddRAD-seq genotypes. Then, Spearman correlations were calculated between GEBVddRAD-seq50 or GEBVddRAD-seq437 and the reference GEBVHDchip437. The mean rank correlation between GEBVHDchip437 and GEBVddRAD-seq50 was 0.92. The mean correlation between GEBVHDchip437 and GEBVddRAD-seq437 was 0.98. The reduced reference population of the GEBVddRAD-seq50 scenario didn't permit for a good representation of the genetic diversity in the population. But, with an equivalent reference population, genomic evaluation based on ddRAD-seq genotypes achieves similar results as genomic evaluation based on HD SNP chip genotypes.

ano.nymous@ccsd.cnrs.fr.invalid (Mathilde Doublet) 22 May 2025

https://hal.science/hal-05019793v1

[hal-05042837] The application of near‐infrared spectroscopy to predict composition, gross energy yield, and methane production of natural forages on the Qinghai–Tibet Plateau

Background Yak ( Poephagus grunniens ) production on the Qinghai–Tibet Plateau is influenced heavily by the quality of the natural forage, which can vary significantly in both quality and quantity. Therefore, timely and accurate monitoring of forage variables is essential for optimizing livestock production in this region. Methods This study investigated the use of near‐infrared spectroscopy (NIRS) as a tool for estimating the composition and quality of natural forage. A total of 301 natural forage samples were collected, and their spectral data were acquired using NIRS. Conventional methods were used to measure the forage composition, and predictive models were developed based on the spectral data. Results Our findings indicate that NIRS can accurately predict the contents of crude protein, acid detergent fiber, and neutral detergent fiber. However, it demonstrated less accuracy in predicting dry matter digestibility, gross energy yield, and methane production. Conclusions The application of NIRS for assessing the nutritional composition of forages on the Qinghai–Tibet Plateau is a key advancement for the livestock industry. Understanding forage nutrition enables informed feeding strategies and improvement of livestock production. Future research should refine predictive models to ensure sustainable forage management and enhance livestock productivity in this unique ecological environment.

ano.nymous@ccsd.cnrs.fr.invalid (Runze Wang) 22 Apr 2025

https://hal.inrae.fr/hal-05042837v1

[hal-05087203] Pâturage estival de mûrier blanc (Morus alba) par les chèvres laitières : effets sur les performances zootechniques, le lait et le fromage

Face aux sécheresses estivales, de plus en plus fréquentes, les arbres fourragers apparaissent comme une solution permettant aux éleveurs d’offrir un fourrage vert à leurs animaux. L’effet de l’intégration de ces essences, et plus particulièrement du mûrier blanc, dans l’alimentation des chèvres laitières est peu connu. Deux essais, en 2021 et 2022, ont été conduits sur la ferme caprine du Pradel (07) pour déterminer l’impact du pâturage de mûrier blanc sur les performances zootechniques et sur les caractéristiques des laits et des fromages de chèvre. Chaque année, deux lots de 24 chèvres laitières ont été soit conduits sur un pâturage de mûrier blanc, soit nourries à l’intérieur avec une ration à base de foin de luzerne, avec la même complémentation en concentré (750 g/j). Le lait de chaque lot a été transformé séparément, soit par lot (2021), soit par sous-lot (2022), pour vérifier l’aptitude à la transformation fromagère jusqu’à la dégustation des Picodons AOP par des consommateurs naïfs (2021) ou un panel expert (2022). Les feuilles de mûrier ont eu une bonne valeur alimentaire et ont constitué environ les deux tiers de la ration fourragère du lot Mûrier (estimation grâce aux alcanes), avec un maintien de la production laitière entre les lots. Dans les deux essais, les taux butyreux et protéique du lait ont été supérieurs sur le lot Mûrier. Par conséquent le rendement fromager au démoulage a été supérieur pour les fromages du lot Mûrier. Les dégustations des Picodons AOP entre 12 et 15 jours d’affinage n’ont montré aucune différence entre les fromages des deux lots. Le Picodon répond aux attentes des consommateurs et conserve toutes les caractéristiques de son AOP.

ano.nymous@ccsd.cnrs.fr.invalid (Claire Boyer) 27 May 2025

https://hal.inrae.fr/hal-05087203v1

[hal-05121191] Clarifying grazing management methods: a data-driven review

Grasslands, particularly permanent grasslands, provide vital ecosystem services and, therefore, focus a number of management challenges. Grassland management revolves around organizing how livestock graze in both space and time, using various grazing methods. However, international research describes these grazing methods using diverse and sometimes inconsistent terminologies. This lack of standardization may create ambiguity and hinder comparative research on grazing methods. Here, to address this issue, we conducted a literature review aiming to identify common patterns of grazing methods based on shared grazing management criteria. Through multivariate analysis, we analyzed 249 experimental datapoints derived from 102 studies. We ran principal component analysis followed by hierarchical clustering on principal components on seven management criteria. This review identified 4 broad families of grazing methods: continuous grazing, conventional rotational grazing, deferred rotational grazing, adaptative multi-paddock grazing. This work distinguishes rotational from continuous grazing methods, as commonly described in the literature. Furthermore, it identifies adaptative multi-paddock grazing as a distinct and innovative group of rotational grazing. The approach developed here could serve as support to characterize and compare different grazing methods.

ano.nymous@ccsd.cnrs.fr.invalid (Robin Russias) 19 Jun 2025

https://hal.inrae.fr/hal-05121191v1

[hal-05114435] Efficient pigs do not always have less environmental impacts: insights from an individual-based model to assess environmental, economic and technical performances

Pig production is facing economic and environmental challenges. In previous studies, the environmental impacts of pig farming have mainly been assessed with group-feeding strategies. A feeding strategy applied to a group of pigs results in unequal animal responses and environmental impacts due to inter-individual variability in lean growth potential and nutritional requirements. The present work aimed at fairly evaluating pigs’ responses in a given production system. We designed a methodological approach able to (i) virtually assess technical, economic and environmental performances of each fattened pig within a population; and (ii) help determine the pig characteristics resulting in contrasted environmental performances in a conventional system including feedstuffs classically used on French commercial farms. For that purpose, experimental data collected on 732 entire Large White males were used to adjust growth profiles using InraPorc® software and to estimate amino acid (AA) requirements of pigs. Each individual profile was used to generate a virtual population of 1 000 pigs. For each population, technical performances were simulated with an individual-based model, economic and environmental evaluations were applied to these performances, and then averaged to assess the individual performance of each of the 732 original pigs. Climate change, use of fossil resources, acidification, eutrophication potentials and land use impacts were evaluated per kg live body weight at farm gate through life cycle assessment. A principal component analysis was applied to the correlation matrix between environmental and economic performances to identify their main drivers. Hierarchical clustering was used to group pigs with similar responses. Three clusters of pigs were distinguished. Cluster 1, with best environmental and economic performances, combined low feed conversion ratios, relatively low-impact feeds and high protein deposition potential (PDm). Clusters 2 and 3 displayed worst environmental performances. Cluster 3 had similar feed efficiency and economic performances as Cluster 1, but higher initial AA requirements, resulting in high-impact feeds and a lower protein deposition. Cluster 2 had the lowest-impact feeds due to the lowest initial AA requirements, and were the least efficient. Feed efficiency, PDm and AA requirements of pigs at the beginning of fattening were the main factors affecting environmental performances. Contrary to previous studies where group feeding was modelled, we show that feed efficiency alone cannot be retained to identify pigs with the lowest impacts. Other pig characteristics such as AA requirements, PDm and environmental impacts should be accounted for to lower the environmental impacts of pig production.

ano.nymous@ccsd.cnrs.fr.invalid (Estelle Janodet) 16 Jun 2025

https://hal.inrae.fr/hal-05114435v1

[hal-05128077] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

Scientific publishing has undergone a tremendous change in recent years. We, a group of Editors-in-Chief of scientific journals owned by scientific bodies, want to communicate some of our values. We represent animal, animal -open science, animal -science proceedings, JDS Communications, Journal of Animal Science, Journal of Applied Poultry Research, Journal of Dairy Science, Poultry Science and Translational Animal Science. Our values motivate our involvement in society-, association-or scientific institutionowned journals in animal science and shape our practices in scientific publishing, in the light of the tremendous changes in the landscape of scientific publishing over the last decade.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 24 Jun 2025

https://hal.inrae.fr/hal-05128077v1

[hal-05079670] Dynamics of the lactose content and other osmotic agents in milk throughout lactation according to the cow's parity

Milk lactose content (LC) is known to vary due to metabolic disorders and udder inflammation. To assess its ability to serve as a marker of these 2 disorders, it is important to first understand its dynamics for healthy cows, particularly its relation with milk osmolarity, because it is the main osmotic agent. To assess the dynamics of LC, we studied relations among contents of lactose and other major osmotic agents in milk throughout lactation in different parities. Cows were fed a constant TMR diet throughout lactation. The profile of osmotic agents in morning milk (lactose, K, Na, Cl, and protein) was measured in the milk of 30 cows (17 primiparous and 13 multiparous). To avoid confounding effects due to udder inflammation, data from cows with unhealthy udders (i.e., 2 or more milk samples with SCC &gt;200,000 cells/mL) were excluded (n = 2 primiparous and 3 multiparous). From 12 to 235 DIM, 8 to 9 samples per cow were first taken 2 wk apart, and then taken monthly. A regression model that included cow parity, DIM, their interaction, and random cow effect was used to illustrate the dynamics of milk osmolarity and each osmotic agent throughout lactation. Milk osmolarity remained stable throughout lactation (279 +/- 0.3 mOsm/L), with no significant difference between primiparous and multiparous cows. The contents of lactose, K, Na, Cl, and protein explained 86.4% of milk osmolarity. Milk LC was lower for multiparous compared with primiparous cows over the entire lactation period, except at 12 DIM, when both parity cows had similar LC. For multiparous cows, the lower LC was compensated by higher Na content. Principal component analysis of all osmotic agents explained 82% and 83% of the cumulative variance throughout lactation for primiparous and multiparous cows, respectively. At 12 DIM, multiparous cows had lower LC and Cl and K contents compared with primiparous cows, which exhibited only lower LC compared with the rest of the lactation period. From 40 to 235 DIM, however, milk from the 2 parities had similar dynamics of osmotic agents: K content decreased and protein content increased. This study revealed that in cows with healthy udders, the dynamics of LC and other osmotic agents contents in milk differed between parities and throughout lactation to maintain a constant milk osmolarity.

ano.nymous@ccsd.cnrs.fr.invalid (Auxane Hamon) 23 May 2025

https://hal.inrae.fr/hal-05079670v1

[hal-05087116] Fréquence de distribution des fourrages chez la chèvre laitière : effets sur l’ingestion, la production et le comportement

En élevage caprin, les fourrages sont souvent distribués plusieurs fois par jour, pour des raisons d’organisation et pour stimuler les chèvres à ingérer davantage. L’influence de la fréquence de distribution sur l’ingestion des chèvres est mal connue. Quatre essais ont été conduits pour déterminer les effets de la fréquence de distribution sur l’ingestion volontaire, la production laitière et le comportement d’ingestion de chèvres laitières Alpine en milieu de lactation. Les essais comparaient 1 et 2 distributions (un essai sur herbe affourragée en vert), 2 et 3 distributions (un essai sur foin de luzerne et un essai sur deux types de ration complète, à base d’ensilage de maïs ou de pulpes de betterave), ou 1, 2 et 3 distributions (un essai sur foin séché en grange de prairies multi-espèces). De 24 à 96 chèvres ont été utilisées par essai, au cours de 3 périodes successives, selon des schémas expérimentaux en inversion, avec 400 à 800 g de concentré par jour selon les essais. Dans tous les essais, la fréquence de distribution n’a eu aucun effet sur l’ingestion ni sur les durées journalières d’ingestion ou de repos couché, et ce malgré une reprise importante de l’activité d’ingestion après chaque nouvelle distribution. La production laitière n’a pas varié avec la fréquence de distribution dans trois des essais, et a légèrement augmenté de 60 g/jour dans un des essais, en passant de 2 à 3 distributions par jour. Les taux butyreux et protéique du lait ont peu ou pas varié avec la fréquence de distribution. Il semble donc possible de réduire le nombre de distributions quotidiennes sans pénaliser les performances laitières des chèvres, à condition que le système d’auge soit de volume suffisant et permette un accès permanent au(x) fourrage(s).

ano.nymous@ccsd.cnrs.fr.invalid (Remy Delagarde) 27 May 2025

https://hal.inrae.fr/hal-05087116v1

[hal-05049047] Comportement social du porc domestique et son importance pour le bien-être animal en élevage

Le porc est une espèce sociale, qui évolue au sein de groupes dont la structure hiérarchique est régulée par un ensemble d’interactions agonistiques, comme les agressions, et non agonistiques, comme les contacts du groin. Cette revue vise à i) faire un bilan des connaissances sur le comportement social du porc domestique, ii) décrire l’impact de certaines pratiques d’élevage sur l’expression de ces comportements, et iii) proposer des perspectives de recherche sur le comportement social pour améliorer le bien-être animal en élevage. De nombreuses conditions et pratiques d’élevage, comme les allotements successifs, la constitution de groupes de taille ou de composition inadéquates, et des infrastructures inadaptées, impactent les comportements et les relations sociales entre les porcs. Jusqu’à récemment, la recherche sur le comportement social du porc s’était principalement focalisée sur les interactions agonistiques. Ainsi, leur rôle dans les relations de dominance et la défense des ressources, ainsi que l’impact des pratiques d’élevage sur ces comportements, ont été particulièrement bien caractérisés. Au contraire, les comportements non agonistiques ont reçu un intérêt beaucoup plus récent. Pourtant, leur prévalence est bien plus élevée que celle des comportements agonistiques, et ils seraient impliqués dans de nombreux processus biologiques, comme la reconnaissance et la communication sociale, l’affinité ou la réduction du stress. En favorisant des états mentaux positifs, ces comportements pourraient être d’une importance capitale pour le maintien du bien-être des porcs en élevage, et il est nécessaire de mieux comprendre leurs fonctions et déterminants. Ces connaissances devraient être prises en compte pour faire évoluer les pratiques dans les systèmes d’élevage.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Clouard-Mésange) 28 Apr 2025

https://hal.inrae.fr/hal-05049047v1

[hal-05003496] La transition agroécologique à l'échelle sectorielle : un long processus de convergence vers un nouveau paradigme

L'agroécologie constitue un paradigme pour transformer notre système agricole et alimentaire vers plus de durabilité. Les transformations à la fois techniques, organisationnelles et commerciales, supposent une convergence de nouvelles règles cognitives, normatives et réglementaires. Après avoir rappelé quelques éléments d'institutionnalisation de l'agroécologie à l'échelle internationale et dans la législation française, nous exposons un cadre heuristique pour penser la transition agroécologique à l'échelle sectorielle, en mobilisant l'approche multi-niveaux des transition studies. Cette approche de la transition sectorielle ouvre sur la nécessité de construire un cadre analytique à l'échelle des filières pour approfondir la compréhension des leviers et freins à la transition agroécologique.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 24 Mar 2025

https://hal.inrae.fr/hal-05003496v1

[hal-04829504] Work in agriculture: A blind spot in reducing pesticide use on dairy farms?

CONTEXT: Implementing alternative practices to the use of pesticides involves work issues that can limit adoption of these practices, particularly on dairy farms. Depending on how practices change, work organization may completely change, additional skills and knowledge may be required, and system complexity may increase, inducing a higher mental workload. This can result in an excessive total workload for already overburdened farmers. OBJECTIVE: The present study examines whether work limits the implementation of alternative practices to reduce pesticide use on dairy farms, depending on the amount of change the practices require. Three work dimensions were considered: work organization, skills and knowledge, and physical and mental workload. METHODS: We used nine semi-structured interviews with crop and livestock experts in Brittany (France’s leading region for dairy production) to classify multiple categories of practices by their degree of difficulty and the type of work dimension involved, with a specific focus on three practices: using resistant crop varieties, mechanical weed control and extending crop rotations. RESULTS AND CONCLUSIONS: First, experts emphasized certain alternative practices over others depending on the institution to which they belonged. Second, the need to balance the feeding system and an increase in herd size, which is not compatible with all alternative practices, were barriers specific to dairy farms. Third, all three practices we focused on were skill- and knowledge-intensive, but in different ways. Using resistant crop varieties requires access to the right information, while mechanical weed control raises issues of training, investment or outsourcing. Finally, extending crop rotations, considered as a redesign of the production system, requires obtaining the resources, time and autonomy to think about new rotations. SIGNIFICANCE: This study shows that, in addition to work organization, other work dimensions are crucial for reducing pesticide use on dairy farms.

ano.nymous@ccsd.cnrs.fr.invalid (Julia Denantes) 10 Dec 2024

https://hal.science/hal-04829504v1

[hal-04998547] Editorial : Values shared by journals of learned societies, associations, and scientific institutions in animal science

Scientific publishing has undergone a tremendous change in recent years. We, a group of Editors-in-Chief of scientific journals owned by scientific bodies, want to communicate some of our values. We represent animal, animal -open science, animal -science proceedings, JDS Communications, Journal of Animal Science, Journal of Applied Poultry Research, Journal of Dairy Science, Poultry Science and Translational Animal Science. Our values motivate our involvement in society-, association-or scientific institutionowned journals in animal science and shape our practices in scientific publishing, in the light of the tremendous changes in the landscape of scientific publishing over the last decade.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 20 Mar 2025

https://hal.inrae.fr/hal-04998547v1

[hal-04959534] A mass balance model to predict the fate of copper and zinc in pig farming systems to reduce environmental impacts: Application to French context

CONTEXT: Although copper (Cu) and zinc (Zn) are essential for pig health, they also represent an environmental risk. A better understanding of the influence of feeding and manure management practices on Cu and Zn flows is required to optimise the whole pig farming system. OBJECTIVE: For this purpose, a model was built to predict Cu and Zn flows from the feed to the spread products to be able to account for the influence of swine production and manure management. METHODS: The parameters used to model Cu and Zn flows during the treatments were mainly obtained from the literature and, when not available, based on expert knowledge. A sensitivity analysis was performed to identify critical parameters and to select sets of parameters to quantify uncertainty of the results. RESULTS AND CONCLUSION: The use of feed containing only 15 and 80 mg/kg feed of Cu and Zn, respectively, would allow to reduce Cu and Zn contents in stored raw manure of 41 and 36 %, respectively, compared to the use of feed with current EU regulations. However, concentrations of Cu and Zn relative to DM in effluents increase with the application of effluent treatments. Feed is therefore the most effective lever for reducing Cu and Zn concentrations in organic fertilisers from swine systems, and will directly influence manure concentrations before and after treatments.

ano.nymous@ccsd.cnrs.fr.invalid (Emma Gourlez) 20 Feb 2025

https://hal.inrae.fr/hal-04959534v1

[hal-04986525] Editorial: Values shared by journals of learned societies, associations and scientific institutions in animal science

Scientific publishing has undergone a tremendous change in recent years. We, a group of Editors-in-Chief of scientific journals owned by scientific bodies, want to communicate some of our values. We represent animal, animal -open science, animal -science proceedings, JDS Communications, Journal of Animal Science, Journal of Applied Poultry Research, Journal of Dairy Science, Poultry Science and Translational Animal Science. Our values motivate our involvement in society-, association-or scientific institutionowned journals in animal science and shape our practices in scientific publishing, in the light of the tremendous changes in the landscape of scientific publishing over the last decade.

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 11 Mar 2025

https://hal.inrae.fr/hal-04986525v1

[hal-04757159] Mastitis has a cumulative and lasting effect on milk yield and lactose content in dairy cows

Milk lactose content (LC) physiologically decreases with parity order in dairy cows, but also after udder health inflammation(s) and/or in presence of elevated milk SCC in subclinical cases. Therefore, the progressive decrease in milk LC observed along cows' productive life can be attributed to a combination of factors that altogether impair the epithelial integrity, resulting in weaker tight junctions, e.g., physiological aging of epithelium, mechanical epithelial stress due to milking, and experienced clinical or subclinical mastitis. Mastitis is known to affect the udder synthesis ability too, so our intention through this study was to evaluate if there is a cumulative and lasting effect of mammary gland inflammation(s) on milk yield (MY) and LC. For this purpose, we used diagnoses of clinical mastitis and milk data of Austrian Fleckvieh cows to evaluate the effect of cumulative mastitis events on LC and MY. Only mastitis diagnoses recorded by trained veterinarians were used. Finally, we investigated if cumulative mastitis is a heritable trait and whether it is genetically correlated with either LC or MY. Estimates were obtained using univariate and bivariate linear animal models. A significant reduction in LC and MY was observed in cows that suffered from mastitis compared with those that did not experience udder inflammation. The h2 of cumulative mastitis is promising and much greater (0.09) than the h2 of the binary event itself (≤0.03). The genetic correlations between cumulative mastitis with LC and MY were negative, suggesting that cows with a great genetic merit for MY and LC are expected to be more resistant to repeated inflammations and less recidivist. When we used number of lifetime SCC peaks (≥200,000 or 400,000 cells/mL) to calculate cumulative inflammation events, h2 was even higher (up to 0.38), implying that also subclinical mastitis has a relevant negative impact on both LC and MY. Finally, the present study demonstrated how repeated mastitis events can permanently affect the mammary gland epithelial integrity and synthesis ability, and that the number of cumulative mastitis is a promising phenotype to be used in selection index in combination with other indicator traits toward more resistant and resilient mammary glands.

ano.nymous@ccsd.cnrs.fr.invalid (A. Costa) 28 Oct 2024

https://hal.inrae.fr/hal-04757159v1

[hal-04832467] Impact of UV pre-treatment on the Longissimus thoracis et lumborum muscle proteomes of dry-aged beef cuts: A characterisation within two sampling locations

This research aimed to explore the changes in two sampling locations (internal and external) of the Longissimus thoracis et lumborum (LTL) beef muscle proteomes subjected to ultraviolet light before dry-aging. It further compared the biological processes and associated proteins at interplay at the external locations of UV pre-treated and control dry-aged samples. Before dry-aging, proteins related to external stimuli were differentially abundant between both locations possibly due to the early post-mortem energy metabolism attempting to compensate for energy deficiencies and stress derived from slaughter and processing. The biochemical status of muscle during chilling and hanging of the carcasses and the impact of the UV pre-treatment may have also influenced the abundance of these proteins before dry-aging. Proteins associated to muscle structure, energy and fatty acids metabolism were differentially abundant between locations after 21 days of dry-aging. These dynamic changes in the meat proteome and related biological processes suggested that both evolved differently between the two sampling locations during dry-aging, and these may underlie the development of dry-aged beef properties. The proteome of the external locations sampled from UV pre-treated beef loins was compared to control counterparts during dry-aging. The results show that aging time appeared to outweigh the effect of UV since the differentially abundant proteins between both groups decreased as dry-aging progressed. These proteins were associated with mRNA stabilization, the matrisome, energy pathways and heat shock proteins (HSPs). Further research is warranted to better understand the role of these proteins in the production of dry-aged beef and their relation to the UV pre-treatment.

ano.nymous@ccsd.cnrs.fr.invalid (Sara Álvarez) 12 Dec 2024

https://hal.inrae.fr/hal-04832467v1

[hal-04999356] Transitioning to low chemical nitrogen perennial ryegrass white clover pastures on wetland grazing dairy systems

Context Reductions in chemical nitrogen fertiliser applications in agricultural systems within the European Union will have a significant role in reducing greenhouse gas emissions related to agriculture. Aims The current study investigates the transition from old permanent perennial ryegrass (PR) swards (PR-old) to newly established PR (PR-new) receiving high levels of chemical nitrogen (N) application or PR white clover swards (PRWC) receiving lower levels of chemical N application on wetland soils in the border, midland and western region of Ireland over 3 years (2021–2023, inclusive). Methods The experimental site, which consisted of old PR swards, was transitioned to either new PR swards receiving up to 250 kg N/ha per annum or PRWC swards receiving up to 125 kg N/ha annually. Key results In the year of establishment, PR-new and PRWC-new swards has a significantly reduced total pasture DM yield (8925 and 8561 kg DM/ha) compared to older PR swards (14,182 kg DM/ha) while PRWC oversown (PRWC-over) swards were intermediate (11,330 kg DM/ha). In subsequent years, PR-new, PRWC-new and PRWC-over swards achieved increased DM yield (14,891, 15,642 and 15,218 kg DM/ha) compared to older swards. Within PRWC, white clover contents increased from 0 g/kg DM in early 2021 to 250 and 190 g/kg DM in 2022 and 2023, respectively. Consequently, significant reductions in chemical N fertiliser applications were achieved, from 229 and 200 kg N/ha for PR-old and PR-new swards, respectively, and 124 and 84 kg N/ha for PRWC-over and PRWC-new swards, respectively. The PRWC system tended (P &lt; 0.08) to have increased milk and milk fat plus protein yield (5197 and 473 kg/cow, respectively) compared to the PR (5092 and 461 kg/cow, respectively) during the 3 year study period. Conclusion These results highlight the potential for PRWC systems to increase pasture production and milk production, while reducing chemical N applications in comparison to PR only systems on a wetland soil. Implications The extent of sward renewal and initial reduction in pasture production may result in shortages in winter feed production during the transition to low chemical N PRWC systems.

ano.nymous@ccsd.cnrs.fr.invalid (H. Walsh) 20 Mar 2025

https://hal.inrae.fr/hal-04999356v1

[hal-04821220] Postmortem proteolysis and its indicators vary within bovine muscles: Novel insights in muscles that differ in their contractile, metabolic, and connective tissue properties

This study assessed postmortem proteolysis over 14 d in bovine Masseter (MS), Longissimus thoracis (LT), and Cutaneous trunci (CT) muscles. First, the metabolic, contractile, and connective tissue properties were characterized to establish their intrinsic differences. The MS contained the highest levels of oxidative markers and myosin heavy chain-I (MyHC-I), whereas the CT possessed the greatest glycolytic capacity, MyHC-IIx, and connective tissue proteins (P &lt; 0.05). The LT had intermediate metabolic characteristics, a heterogeneous mixture of MyHC isoforms, and the lowest amount of connective tissue proteins (P &lt; 0.05), confirming the muscles' intrinsic divergence. Proteolytic analysis revealed increased desmin and slow troponin-T (TT-slow) degradation, with a higher 110 kDa band intensity in the MS than in the CT (P &lt; 0.05). In comparison, the CT exhibited greater TT-fast degradation and higher 30 kDa fragment intensity (P &lt; 0.05). The LT demonstrated the greatest overall proteolysis, indicated by increased TT-fast and TT-slow degradation and the highest intensity of the 30 kDa band (P &lt; 0.05). This is likely due to protease activity, as the LT and MS exhibited more calpain-1 autolysis and less calpastatin abundance than the CT (P &lt; 0.05). However, caspase-3 activity was highest in the MS and lowest in the LT. A principal component analysis incorporating proteolytic indicators further demonstrated the distinct proteolytic profiles in the three muscles. Overall, findings suggest that the progression of postmortem proteolysis is muscle-specific and that a single proteolytic indicator does not sufficiently describe proteolysis when comparing muscles differing in contractile and metabolic properties.

ano.nymous@ccsd.cnrs.fr.invalid (Chandler Stafford) 05 Dec 2024

https://hal.inrae.fr/hal-04821220v1

[hal-04718511] Stocking density at feeders and drinkers and temporal feed restriction affects dairy cows’ drinking behavior

Water is an essential resource for dairy cows and its consumption is closely linked to feed intake. Social competition can lead to changes in drinking behavior, especially for subordinate cows. We studied how changes in stocking density at the feeder (varied between 1 or 2 cows per feeder), and drinker (varied between 6 or 12 cows per drinker) and a temporal feed restriction (14 or 24 h access) impacts drinking in 4 groups of 6 cows each, following a Latin Square design. Within each group of 6 focal cows, we recorded drinking behavior and 2 were identified as most dominant, 2 as most subordinate, and the 2 others as intermediate, based on success in agonistic interactions at the drinker. Cows drank less water when feed availability was restricted (on average 5.3 L/d less ± 3.4; 4.5% average difference). Subordinate cows also spent less time drinking when overstocked (9.3 min/d less ± 6.7; 24.3% difference). During treatments with more competition, cows were more likely to be observed drinking in the hours after the peak in drinking observed for the control treatment. A high level of competition among group-housed animals is considered a welfare problem and can lead to injuries and reduced production. Our findings provide evidence that feed restriction and higher stocking density of cows at the drinker and feeders changes the drinking behavior of cows, with subordinate animals experiencing more pronounced effects.

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 02 Oct 2024

https://hal.inrae.fr/hal-04718511v1

[hal-05051419] L’enrichissement du milieu de vie

Les conditions captives empêchent souvent l’animal de satisfaire pleinement ses besoins physiologiques et éthologiques, par exemple du fait de la maîtrise de la reproduction ou de la constitution des groupes sociaux par les humains. De plus, certaines pratiques inhérentes à l’élevage (ex. les déplacements des animaux) sont source de stress pour les animaux, car ils les perçoivent comme des menaces lorsqu’elles sont imprévisibles et donc incontrôlables, ou très éloignées de leurs attentes. Enfin, les stimulations sensorielles et cognitives sont plus rares qu’en milieu naturel. Or, un milieu pauvre en stimulations induit chez les animaux un stress chronique du fait de leur incapacité à accomplir certains comportements ou besoins physiologiques. Ce stress chronique est en lui-même problématique pour le bien-être animal, mais aussi pour les résultats des recherches scientifiques menées sur ces animaux...

ano.nymous@ccsd.cnrs.fr.invalid (Céline Tallet) 29 Apr 2025

https://hal.inrae.fr/hal-05051419v1

[hal-05084798] A pilot study on alternative blood sampling methods in pigs

Background The collection of blood samples allows the monitoring of animal health and can be achieved by puncture or catheterization of specific veins. However, this process raises ethical concerns regarding animal welfare. As an alternative to traditional invasive blood collection methods, we tested the use of kissing bugs (Dipetalogaster maxima, a blood-sucking insect) and devices derived from human medicine, such as vascular imaging (VeinViewer®) and prick lancets used for finger pricking. These methods were compared against the catheter collection method, which is considered the gold standard method for repeated blood sampling. The blood collection methods were tested in six female Large White pigs at four time points. Methods were compared for ease of collection, animal stress indicators, and obtained concentrations of plasma cortisol and glucose. <div>Results<p>Among the methods, the catheter and insects were the least stressful, followed by the prick lancet, and the VeinViewer®. The VeinViewer® was the most stressful, mainly because the pig had to be restrained with a snout rope. According to the operators, the VeinViewer® and prick lancet sampling were the most difficult methods to perform, whereas catheter and kissing bug sampling were easier. However, kissing bug sampling took up to 50 min compared to other methods (2-3 min). The method of sampling has a significant effect on glucose concentrations, with lower concentrations obtained with prick lancet (6.1 mg/dL, p &lt; 0.05) and kissing bugs (73.8 mg/dL, p &gt; 0.05) compared to the catheter method (93.2 mg/dL) and the VeinViewer® (94.7 mg/dL). Glucose concentrations obtained by catheter were significantly correlated with those obtained by the VeinViewer® (r = 0.47) or kissing bugs (r = 0.54). Differences in cortisol levels were less pronounced, with only the prick lancet method showing lower concentrations (2.9 ng/dL, p &lt; 0.05) compared to the other methods (catheter 19.3 ng/dL, kissing bugs 20.8 ng/dL, and VeinViewer® 20.4 ng/dL). Significant Spearman's correlations were observed between cortisol concentration of samples obtained by catheter and VeinViewer® (r = 0.64) or prick lancet (r = 0.52).</p></div> <div>Conclusions<p>These findings underscore the reliability of catheterization as the gold standard, although the prick lancet appears promising to reduce pig's stress. However, the method could be further refined, both in terms of animal acceptability and especially analytical procedures.</p></div>

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Xavier) 26 May 2025

https://hal.inrae.fr/hal-05084798v1

[hal-05109811] Replacing hexane with 2-methyloxolane for defatting soybean meal fed to dairy cows: Effects on dairy performance and nitrogen partitioning

2-Methyloxolane (MeOx) is a promising candidate for replacing hexane as a solvent for defatting soybean meal (SBM). However, the use of MeOx requires adjustments of the oil extraction process that may affect the nutritive value of SBM. This study aims to ensure that process modifications due to the use of MeOx do not affect the protein value of SBM for dairy cows. Sixteen primiparous Holstein dairy cows were included in a 4 × 4 Latin square design experiment. The 4 dietary treatments consisted of hexane-defatted SBM, MeOx-defatted SBM, or a combination in various proportions: 100% hexane-defatted SBM (control diet, HEX), 67% hexane-defatted SBM plus 33% MeOx-defatted SBM (33MeOx), 33% hexane-defatted SBM plus 67% MeOx-defatted SBM (67MeOx), and 100% MeOx-defatted SBM (100MeOx). The diets contained 16% SBM and were iso-CP. Feed, rumen fluid, blood, urine, feces, and milk samples were collected. The traits measured were indicators of ruminal protein degradation (NH3 concentration and branched-chain volatile fatty acid proportion in the rumen fluid), N metabolism (plasma concentrations of essential AA, 1-methylhistidine, and 3-methylhistidine), N partitioning and N use efficiency (N use efficiency for milk production, N isotopic discrimination between plasma and diet), and milk quality (protein and fat contents, N fractions, hexane and MeOx residues). Statistical analyses used difference and equivalence tests. Replacing hexane-defatted SBM with MeOx-defatted SBM resulted in likely equivalent dairy performance, N partitioning, and N use efficiency for milk production, although some indicators suggested slight rumen and digestive alterations that may have subtly affected whole-body N metabolism. A subset of 6 cows was selected for analysis of solvent residues in milk. Even though hexane-defatted SBM contained only 11 mg/kg DM of n-hexane residues, 5 out of 6 milk samples from cows fed HEX presented detectable n-hexane residues, whereas only 1 out of 6 milk samples from cows fed 100MeOx presented detectable n-hexane residues. Therefore, n-hexane residues in milk tended to be detected more often when cows were fed hexane-defatted SBM compared with MeOx-defatted SBM. The MeOx-defatted SBM contained 977 mg/kg DM of MeOx residues, but only 2 out of 6 milk samples from cows fed 100MeOx and 0 out of 6 milk samples from cows fed HEX presented detectable MeOx residues. These results raise prospects for using MeOx as a hexane substitute for defatting SBM fed to dairy cows, although further studies are needed to confirm the slight differences observed here in N metabolism.

ano.nymous@ccsd.cnrs.fr.invalid (Valentin Menoury) 13 Jun 2025

https://hal.inrae.fr/hal-05109811v1

[hal-05100159] How does feeding strategy affect the aromatic volatile compounds profile and sensory properties of organic fresh pork?

This study aimed to evaluate two feeding strategies on pork quality in organic farming using 77 non-castrated male pigs (Piétrain × Large White) reared in two batches, each including two groups. Male littermates were allocated to either a Control group (C, n = 37), fed following the organic specifications, or to a group receiving an organic test feed mainly based on French raw materials and containing more fibre and omega-3 fatty acids (Bio+, n = 40). Within batch, each group was reared in one pen from the same building on deep straw bedding with free outdoor access, with ad libitum feeding from around 33 kg until slaughter at around 128 kg of live weight. Loin meat samples were analysed by a trained sensory panel and by SPME-GC–MS to identify the main volatile compounds. Meat from Bio+ pigs showed a significantly more intense red colour (P &lt; 0.01), but lower aromatic persistency (P &lt; 0.05) and tended to be less tender (P = 0.08) than meat from C pigs. None of the samples were qualified as boar tainted. A total of 27 volatile compounds were quantified, with more compounds present in Bio+ pigs, probably due to the greater diversity of raw ingredients in the feeds. The multi-dimensional analyses enabled to observe relationships between volatile compounds and sensory traits but did not differentiate the two feeding strategies. Bio+ feeding strategy compared to C influenced some organoleptic characteristics (red colour of raw meat, aromatic persistency) without modifying the texture, odour and flavour of organic cooked pork.

ano.nymous@ccsd.cnrs.fr.invalid (Chloé Van Baelen) 06 Jun 2025

https://hal.inrae.fr/hal-05100159v1

[hal-05077824] Application of machine learning for optimizing biomarker combinations and guiding decisions on meat authentication

This paper tested the relevance of two machine learning approaches (decision trees, DTs; and random forest models, RFs) applied to meat authentication. DT allow to select and rank potential biomarkers according to their respective discriminatory power, optimize their combinations, and guide decisions on classification of samples according to their production systems, all of which has so far been under-researched. RFs were also developed as they are particularly robust. We applied both methods on 19 compounds/variables measured on different tissues (perirenal fat (PF), dorsal fat (DF) and longissimus thoracis et lumborum (LTL) muscle) in an experiment using Romane male lambs pasture-finished on lucerne for four durations pre-slaughter (n = 34–36 lambs per group). Several DTs/RFs were constructed including measurements that are relatively easy to carry out in the abattoir/point of sale, or measurements requiring laboratory analyses. The DTs/RFs distinguished carcasses of lambs pasture-finished from stall-fed lambs with an accuracy of up to 95.1–95.7 %, and showed that PF skatole and PF carotenoid pigment content (out of 19 variables) played a prominent role in classification. The DT/RF designed for use at the point of sale, which was based on DF spectrocolorimetric characteristics and LTL muscle colour coordinates, achieved 84.3–85.4 % accuracy. This is the first research to use DTs for meat authentication, and threshold values for classification decisions will probably need to be validated further on larger databases. These findings nevertheless raise prospects for broad application of decision trees for authentication.

ano.nymous@ccsd.cnrs.fr.invalid (Lucille Rey-Cadilhac) 22 May 2025

https://hal.inrae.fr/hal-05077824v1

[hal-05049982] Bioaccessibility and associated concepts: Terminology in the context of in vitro food digestion studies

In vitro gastrointestinal models are widely used to study food digestion, in combination with analytical methods to determine the physicochemical and biochemical fate of food compounds. The in vitro bioaccessibility determined with these models is often used as an indicator of the in vivo bioavailability. However, the bioaccessibility concept is not used consistently within the scientific literature, leading to confusion and making it difficult to compare the results from different studies.<p>The aim of this article is to provide standardized definitions of in vitro digestibility and bioaccessibility, detailing the main processes involved, including physical release, solubilization, and biochemical/metabolic reactions. The terminology of complementary cellular, ex vivo, and animal/human in vivo experiments is also given. Application of the in vitro terminology to different nutrients is discussed, including lipids, proteins, carbohydrates, vitamins, and other bioactive compounds. The proposed definitions unify most concepts related to the gastrointestinal fate of ingested food compounds.</p>

ano.nymous@ccsd.cnrs.fr.invalid (Myriam M.-L. Grundy) 28 Apr 2025

https://hal.science/hal-05049982v1

[hal-05087181] Luzerne et/ou fétuque déshydratées chez la chèvre : effets sur l’ingestion, la production et les aptitudes fromagères

Utiliser de la luzerne sous forme déshydratée dans les systèmes alimentaires caprins permet d’augmenter l’ingestion totale et donc la production laitière. En revanche, les bénéfices de la luzerne déshydratée sur les caractéristiques du lait et des fromages ne sont pas connus. L’objectif de cet essai a été de quantifier les effets spécifiques de la luzerne déshydratée, en comparaison avec de la fétuque déshydratée, sur l’ingestion, la production laitière, la composition fine du lait de chèvre, son aptitude fromagère et sur les fromages de type faisselle. Trois traitements ont été comparés sur 3 lots de 12 chèvres Alpine multipares en milieu de lactation pendant 6 semaines, avec un régime à base de fourrage déshydraté constitué de 100 % de fétuque (FET), de 50 % de fétuque et 50 % de luzerne (MIX), ou de 100 % de luzerne (LUZ). Le fourrage a été complémenté avec 820 g de matière sèche (MS)/jour de concentré à base de maïs grain, mais comprenant 15, 11 et 7 % de tourteau de soja pour FET, MIX et LUZ, respectivement, pour obtenir des rations iso-azotées. L’ingestion de fourrage déshydraté et l’ingestion totale ont été d’autant plus élevées que la proportion de LUZ était importante (+ 0,52 kg MS/j entre FET et LUZ). Le traitement LUZ n’a pas permis d’augmenter la production laitière. Les taux butyreux et protéique ont augmenté de manière linéaire avec l’accroissement de l’apport de luzerne dans la ration et ce dès la semaine 3 (+3,8 et +1,7 g/kg de lait entre FET et LUZ, respectivement). Le rendement fromager de laboratoire de type présure en frais a été significativement plus élevé avec LUZ en semaine 6. Cette augmentation du rendement a été associée à un taux de matières utiles plus élevé. L’analyse sensorielle n’a pas permis de discriminer les traitements alimentaires malgré un effet significatif de la luzerne sur la texture des fromages. Le remplacement de la fétuque déshydratée par de la luzerne déshydratée dans l'alimentation des chèvres a donc permis une augmentation de l’ingestion, une amélioration de la composition du lait et de meilleurs rendements fromagers en frais.

ano.nymous@ccsd.cnrs.fr.invalid (Catherine Hurtaud) 27 May 2025

https://hal.inrae.fr/hal-05087181v1

[hal-05087156] Prévision de la composition chimique du fourrage ingéré par des chèvres laitières selon sa nature et le taux de refus

Les élevages caprins présentent la particularité de valoriser une diversité de ressources alimentaires, variables en termes de qualité et de forme d’apport. La chèvre est réputée pour sa capacité à trier le fourrage distribué de manière plus prononcée que les autres ruminants, et à adapter son comportement alimentaire au type d'alimentation qu'elle reçoit. Cette capacité de tri peut modifier la valeur alimentaire du fourrage ingéré au regard de celle du fourrage distribué. Cette caractéristique animale combinée à un contexte de rations diversifiées rend difficile la prévision des réponses des chèvres aux apports alimentaires, ainsi que la maîtrise des quantités de refus. À partir d’une base de données rassemblant les résultats d’essais de 4 sites expérimentaux, des équations de prévision de la composition chimique du fourrage ingéré sont proposées. Cette base de données comporte 8 types de fourrages et 260 couples de compositions chimiques et quantités de fourrage distribué et refusé. Ces fourrages ont été répartis en 3 groupes en fonction de leur capacité à être triés. Cette étude confirme que la capacité d’un fourrage à être trié et le taux de refus affectent la composition chimique de l’ingéré. Un effet important a été observé avec du foin de luzerne (+ 8 g de MAT/kg MS pour 10 % de refus supplémentaire) et un effet moindre avec des fourrages peu triés, tel que le foin de graminées (+1 g de MAT/kg MS pour 10 % de refus supplémentaire). Pour les autres fourrages qualifiés de triables, on observe un gain de +5 g de MAT/kg MS pour 10 % de refus supplémentaire. Des réponses similaires ont été observées sur les teneurs en NDF et ADF, avec une diminution de leur teneur dans le fourrage ingéré lorsque le taux de refus augmente. Cette étude confirme la capacité de la chèvre à trier les fourrages et qu’il est possible de mieux prévoir la composition chimique du fourrage ingéré en fonction de sa nature et du taux de refus.

ano.nymous@ccsd.cnrs.fr.invalid (Romain Guyard) 27 May 2025

https://hal.inrae.fr/hal-05087156v1

[hal-05079463] Dry matter intake and production efficiencies of dairy cows rotationally grazing a perennial ryegrass monoculture, a perennial ryegrass-white clover sward, or a multispecies sward

The objective of this study was to evaluate the effect of sward diversity on individual cow DMI, milk production, and milk production efficiency. In this context, 3 swards were compared: a perennial ryegrass monoculture (Lolium perenne L.; PRG), a PRG with white clover (Trifolium repens L.; PRGWC), and a multispecies sward (MSS) composed of grasses, legumes, and herbs. The experiment followed a randomized block design, encompassing 56.1 ha divided into 20 blocks. Three herds of 49 dairy cows were created, 1 for each sward, and were composed of both pure Holstein-Friesian (HF) and HF crossbred with Jersey (JFX) dairy cows. All the cows were distributed among the 3 treatments according to parity, expected calving date, overall Economic Breeding Index, and milk subindex within each breed. The study monitored pasture production and quality, milk production, DMI, and feed conversion efficiency over a 2-yr period. Results indicated that pregrazing herbage yields and daily herbage allowance were similar across sward types. Daily milk yield (MY) was significantly influenced by sward type, with PRG yielding less than both PRGWC and MSS (13.9, 15.5, and 15.5 kg/ cow, respectively). Sward type had a significant effect on DMI, with PRG having the lowest DMI (16.3 kg DM/ cow), compared with MSS (18.7 kg DM/cow), which was the highest whereas PRGWC was intermediate (17.5 kg DM/cow). Consequently, feed efficiency was greatest for PRGWC [91 g/unit &amp; eacute; fourrag &amp; egrave;re lait (UFL) intake], intermediate for the MSS (87 g/UFL), and lowest for the PRG (83 g/UFL). Breed also had a significant effect on MY and composition, with JFX having a lower MY than HF (14.6 and 15.3 kg/cow, respectively) but with increased milk fat (5.31% and 5.72%, respectively) and protein (4.08% and 4.24%, respectively) concentration. Consequently, milk solids (MlS) production was similar for the 2 breeds. The JFX animals were more feed efficient, producing 89 g MlS/UFL intake compared with 84 g for HF. The study highlighted the potential for more diverse swards to improve animal performances in grazing systems while reducing the use of chemical N fertilizer, therefore improving the sustainability of such systems.

ano.nymous@ccsd.cnrs.fr.invalid (A. Jezequel) 22 May 2025

https://hal.inrae.fr/hal-05079463v1

[hal-04998536] Oxidative stress‐induced changes in wooden breast and mitigation strategies: A review

Wooden breast (WB) is a multifactorial muscular abnormality resulting from the interplay between genetic predispositions for rapid growth, physiological stress, and anatomical impairments. This myopathy has been a persistent challenge in the poultry industry since its initial identification a decade ago. WB negatively impacts meat quality, leading to increased toughness and reduced nutritional value. Building on foundational research utilizing multiomics technologies, hypoxia‐induced oxidative stress has been identified as a key early event driving the pathological processes of WB. This review provides a comprehensive overview and the state‐of‐the‐art evidence on the pivotal role of oxidative stress in WB myopathy. It begins by examining the generation of reactive intermediates that induce oxidative damage and the host's defense mechanisms aimed at mitigating these threats. The discussion then focuses on the consequences of oxidative damage for mitochondria, protein and lipid oxidation, connective tissue remodeling, and inflammation—pathological hallmarks of WB‐affected muscles. Additionally, the review highlights how oxidative stress influences satellite cell behavior, impairing the repair and regeneration of muscle tissues, a process implicated in WB. Finally, efforts to prevent or mitigate WB myopathy are summarized, with particular attention to potential intervention strategies targeting oxidative stress. These include innovative feed formulations and gut microbiota modulation, which show promise in alleviating the severity of the condition.

ano.nymous@ccsd.cnrs.fr.invalid (Yaqin Wang) 25 Mar 2025

https://hal.inrae.fr/hal-04998536v1

[hal-05109827] Corrigendum to “Association between body condition profiles, milk production, and reproduction performance in Holstein and Normande cows” (J. Dairy Sci. 107:11621–11638)

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Dezetter) 12 Jun 2025

https://hal.inrae.fr/hal-05109827v1

[hal-05010133] Analyse transversale de 28 démarches de filières agrialimentaires : des dynamiques d'innovation variables au travers de leur engagement dans l'agroécologie

Depuis de la loi de 2014 dédiée au développement de l’agroécologie, les filières végétales et animales françaises mobilisent des principes de l’agroécologie de façon variée. Cet article synthétise l’analyse transversale de 28 cas de démarches de filières déclarant se différencier par des pratiques reliées à des principes de l’agroécologie, dans différents domaines de production de l’animal ou du végétal. Le cadre d’analyse mobilisé est basé sur des fonctions d’innovation mises en œuvre par ces filières. Ces différentes actions conduites dans la filière peuvent alimenter un processus d’apprentissage collectif dans la transition vers l’agroécologie. Les résultats présentés montrent une capacité transformative variable des filières, mais permettent d’avancer un ensemble de régularités sur lesquelles semble reposer la transition agroécologique des filières en France. L’article conclut par des pistes d’actions collectives pour soutenir la transition agroécologique en France.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 28 Mar 2025

https://hal.inrae.fr/hal-05010133v1

[hal-05109774] Integrated multi-omic analyses of bovine milk identify biomarkers of negative energy balance

Dairy cows are susceptible to negative energy balance, which can lead to metabolic disorders such as ketosis. Negative energy balance (NEB) often occurs in early lactation, but can also be due to food scarcity. Its quantification is difficult and prone to error, justifying the need to identify biomarkers instead. The effect of NEB on milk composition is known to be directly related to its intensity, impacting major and minor milk constituents. As such, one promising approach may be to identify non-invasive biomarkers in milk. To identify potential biomarkers of NEB, we performed an integrative multi-omic study of milk production and composition in two feed restriction trials of different lengths and intensities. Multivariate data integration using a redundancy analysis enabled an exploration of the linear relationships between variation in energy balance and milk production and composition. A highly correlated multi-omic signature of NEB was then identified using a multi-block partial least squares discriminant analysis. Early and late integration of data from the two feed restriction trials enabled the identification of a robust multi-omic panel of biomarkers of NEB. Taken together, these analyses showed that feed restrictions led to consistent decreases in milk yield, lactose content and uric acid concentration, as well as increased isocitrate and serotransferrin concentrations and differentially abundant microRNAs in both whole milk and milk fat globules. These findings are promising for the development of a panel of non-invasive biomarkers for monitoring animal energy status, and enhance our understanding of adaptations to NEB.

ano.nymous@ccsd.cnrs.fr.invalid (Antoine Leduc) 12 Jun 2025

https://hal.inrae.fr/hal-05109774v1

[hal-04925986] Grazing time of dairy cows recorded using two devices based on accelerometers

Investigating grazing behaviour of dairy cattle requires accurately recording their daily grazing time. Unfortunately, commercially available devices are often not validated for the degree of precision required in animal science at the cow x day level. In two studies, the ability of the Feed'Live (R) device (New Medria) to accurately estimate daily grazing time of dairy cows was investigated. It contains a triaxial accelerometer whose raw data, once processed by New Medria, provides the dominant activity for 5-min periods: intake, rumination, over- activity or other activity. Feed'Live data were compared to those from the Lifecorder Plus (Kenz) device, which contains a uniaxial accelerometer, used in the study as reference values for actual grazing time due to its known high accuracy thanks to a large external validation. Twenty four dairy cows were simultaneously equipped with both devices for several weeks in study 1 (spring 2021) and study 2 (spring 2022), for a total of 1224 cow x day datapoints. Daily access time to pasture was either 19 h/day (861 cow x day datapoints) or 7 h/day (363 cow x day datapoints) according to the experimental treatments investigated. On the whole database, compared to the Lifecorder Plus, Feed'Live underestimated daily grazing time by 15 % (65 min/day), with a lower underestimation for cows having 19 h/day of access to pasture (11 %, 48 min/day), and a greater underestimation for cows having only 7 h/day of access to pasture (31 %, 107 min/day). The bias in the estimated grazing time between the two devices was strongly and positively correlated with the time of other activity. This is because Feed'Live failed to identify grazing as the main activity during several grazing sequences and sometimes missed entire grazing sequences. Most of the grazing activity that the Feed'Live failed to detect was classified as other activity, with no misclassification as rumination. Correcting grazing time by adding other activity time to it provided a much more accurate estimate of actual grazing time, with no more bias and an average mean prediction error of only 9 % at the cow x day level vs. 23 % without correction on the entire database. For cows having access to pasture only during daytime, the mean prediction error was reduced from 40 % to 6 % thanks to this correction. For scientific purposes, when data are available, actual grazing time can thus be estimated accurately by the Feed'Live by summing the times of grazing and other activity.

ano.nymous@ccsd.cnrs.fr.invalid (Romain Guyard) 03 Feb 2025

https://hal.inrae.fr/hal-04925986v1

[hal-04843455] Révéler et valoriser vos données avec le thésaurus INRAE

Dans un contexte de surabondance de l'information, disposer d'outils d'aide à l'indexation et à la recherche documentaire s'avère de plus en plus indispensable. La construction d'un thésaurus couvrant les thématiques d'un institut de recherche comme INRAE (Institut national de recherche pour l'agriculture, l'alimentation et l'environnement) a pour objectif de décrire finement les productions institutionnelles. Ce type de vocabulaire permet de mieux valoriser ces productions en facilitant leur découverte et leur réutilisabilité. Le thésaurus INRAE contient plus de 16 000 concepts en français et en anglais, des synonymes et des définitions et sert actuellement à indexer des publications, codes et données scientifiques avec des mots-clés. Après avoir présenté le thésaurus INRAE, en détaillant sa structure, son contenu et les divers moyens d'y accéder, nous illustrons son utilité à travers cinq témoignages provenant de collectifs d'utilisateurs scientifiques ou d'appui à la recherche.

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Aubin) 17 Dec 2024

https://hal.inrae.fr/hal-04843455v1

[hal-04820215] Améliorer conjointement la santé et le bien-être des animaux dans la transition des systèmes d’élevage vers la durabilité

Cet article présente les travaux et les recherches à conduire pour placer la santé et le bien-être au cœur de la transition agroécologique des systèmes d’élevage. Il souligne la nécessité de considérer la santé dans une perspective plus large qu’aujourd’hui et la question des expériences émotionnelles positives en matière de bien-être. Les interactions positives entre santé et bien-être mais aussi les tensions possibles entre ces deux dimensions sont discutées. L'amélioration conjointe de la santé et du bien-être des animaux pose des questions à différentes échelles. Au niveau de l'animal, sont à explorer les compromis entre les fonctions physiologiques de production, de reproduction et d'immunité, le rôle du microbiote ainsi que les mécanismes psycho-neuro-endocriniens qui relient l'état mental et la santé. Au niveau de l'exploitation, il conviendrait de considérer l’expertise des éleveurs et d’évaluer l’effet des changements de pratiques sur leur bien-être au travail. Au niveau de la filière de production comme du territoire, les stratégies pour améliorer la santé et le bien-être des animaux tout en préservant la viabilité économique sont à étudier, comme la possibilité d’étiquetage et de labellisation des produits, le consentement à payer des consommateurs, les conséquences de l'hétérogénéité phénotypique des animaux pour la transformation des produits et la répartition spatiale des exploitations. Au niveau des citoyens, un défi consiste à mieux relier leurs préoccupations en matière de bien-être des animaux et de santé. Ces nombreuses questions plaident en faveur d'une approche interdisciplinaire et transdisciplinaire sur de nombreux sujets, associant l’ensemble des acteurs, y compris les décideurs publics, dans une démarche de recherche participative.

ano.nymous@ccsd.cnrs.fr.invalid (Christian Ducrot) 05 Dec 2024

https://hal.inrae.fr/hal-04820215v1

[hal-04764494] Effect of using germinated and fermented lupin and oats as a dietary protein source on laying hen performance and egg quality

Soybean meal is the dominant protein source for poultry nutrition. However, soybean is not widely grown in Europe, necessitating importation from other countries. To reduce dependency on imported soybean meal, an alternative feed material is needed. Fermentation and/or germination of grains are known to increase the value of the protein content of a diet. This study aimed to determine if they could substitute partly soybean meal in a diet. Germinated or fermented or germinated and fermented grains of lupin and oats were used in laying hen's diet (a mix of 6.50% lupin and 3.50% oat grains). Oats were dehulled or not dehulled. The hens' weight loss and the downgraded eggs rate were the lowest when using fermented grains. All trial diets reduced the egg cholesterol content. Dehulling had only a slight effect on performance. Diets containing germinated grains led to a decrease in laying performance and an increase in body weight loss. Diets containing fermented grains gave the best results in terms of quantity of amino acids, hen weight maintenance, laying performance, and egg quality. In conclusion, fermented lupin and oats can be used in laying hen diets to partly substitute sources of protein such as soya, but germinated grains cannot.

ano.nymous@ccsd.cnrs.fr.invalid (Koffigan Kponouglo) 04 Nov 2024

https://hal.science/hal-04764494v1

[hal-04675948] Partitioning of energy intake in broiler breeders from 27 to 63 weeks old

Describing the energy partition during the production phase of broiler breeders helps to define the energy requirements of breeders. This study aimed to determine the energy intake partition for maintenance, tissue growth, and egg production in broiler breeders during the laying phase. An energy and nitrogen balance study was carried out in a respirometry chambers with fifty Cobb 500 broiler breeders from 27 to 63 weeks old. Every four weeks, 5 birds were individually housed in a respirometry chamber and fed according to the guidelines. Feed intake (FI), excreta, and egg output were recorded daily. O2 consumption (VO2) and CO2 production (VCO2) were measured under feeding and fasting conditions to calculate total and fasting heat production (THP and FHP, respectively). The collected data were used to calculate the retained energy (RE) in the egg and body as protein or fat by using energy balance calculations. Linear regressions were used to fit the collected data as a function of age. The measured apparent metabolizable energy corrected for zero-nitrogen retention (AMEn, kJ/kg feed) was higher than formulated. The FI and apparent metabolizable energy intake (AMEi) showed the highest values at 31 and 35 weeks (P &gt; 0.05). Linear regression was not significant (P &gt; 0.05) for FHP, THP, heat increment (HI), egg mass, and RE in the egg as fat and as protein, suggesting that these parameters remained constant as the bird aged. The RE in the body as protein increased (P &lt; 0.005), while the RE in the body as fat decreased (P &lt; 0.0001) as the birds aged. Variation in the AMEi influenced RE in the body (P &lt; 0.05) but not in the egg (P = 0.109). It can be concluded that net energy for maintenance does not change during the laying phase and represents an expenditure of 267.1 kJ/kg0.75 per day in broiler breeders under a feed-controlled program. As expected, energy is primarily used for maintenance and egg production in the net energy system, with excess energy stored preferentially as fat rather than protein.

ano.nymous@ccsd.cnrs.fr.invalid (Guilherme Ferreira da Silva Teofilo) 23 Aug 2024

https://hal.inrae.fr/hal-04675948v1

[hal-04685713] GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations

GEGA is a user-friendly tool designed to navigate through various genomic and functional information related to an enriched gene atlas in chicken that integrates the gene catalogues from the two reference databases, NCBI-RefSeq and EMBL-Ensembl/GENCODE, along with four additional rich resources such as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA encompasses a total of 78 323 genes, including 24 102 protein-coding genes (PCGs) and 44 428 long non-coding RNAs (lncRNAs), significantly increasing the number of genes provided by each resource independently. However, GEGA is more than just a gene database. It offers a range of features that allow us to go deeper into the functional aspects of these genes. Users can explore gene expression and co-expression profiles across 47 tissues from 36 datasets and 1400 samples, discover tissue-specific variations and their expression as a function of sex or age and extract orthologous genes or their genomic configuration relative to the closest gene. For the communities interested in a specific gene, a list of genes or a quantitative trait locus region in chicken, GEGA’s user-friendly interface facilitates efficient gene analysis, easy downloading of results and a multitude of graphical representations, from genomic information to detailed visualization of expression levels.

ano.nymous@ccsd.cnrs.fr.invalid (Fabien Degalez) 03 Sep 2024

https://hal.inrae.fr/hal-04685713v1

[hal-04706111] Work: a barrier to reducing pesticide use in Breton dairy farms?

Implementing alternative practices to reduce pesticide use presents work-related challenges that can limit their adoption, especially on dairy farms, well-known for being heavily constrained on work, especially due to routine work. Changes in practices may disrupt work organization, requiring additional skills and knowledge, and increasing mental workload. Nine interviews with experts in Brittany (advisors, facilitators of farmers’ groups, experts of technical institutes) were conducted about the challenges of implementing alternative practices and their effectiveness in Breton dairy farms. Notably, the use of resistant varieties, mechanical weed control, and crop rotation extension were examined. In the case of dairy farmers, experts recognized work, as an issue for changing practices and highlighted challenges unique to dairy farms to reduce pesticide uses. They declare that the cropping system cannot be modified without integrating the livestock system into the considerations. Those three practices require varying levels of skill and knowledge. Accessing accurate information, in a proper time, is a challenge for implementing resistant crop varieties, while mechanical weed control management demands training, investment, or outsourcing. Extending crop rotations, perceived as a system redesign, necessitates resources, time, and autonomy to conceptualize new rotations. Addressing these work-related dimensions in both public policies and farm advisory strategies is essential for reducing pesticide use on dairy farms implementing alternative practices to reduce pesticide use presents work-related challenges that can limit their adoption, especially on dairy farms, well-known for being heavily constrained on work, especially due to routine work. Changes in practices may disrupt work organization, requiring additional skills and knowledge, and increasing mental workload.

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Lise Jacquot) 23 Sep 2024

https://hal.science/hal-04706111v1

[hal-04538081] Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions

The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed‑efficient and non‑efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat‑soybean based diet (CTR) or a lowenergy, high‑fibre corn‑sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet‑dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short‑chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.

ano.nymous@ccsd.cnrs.fr.invalid (Maria Bernard) 09 Apr 2024

https://hal.inrae.fr/hal-04538081v1

[hal-04495275] Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability

Highlights: • Improving jointly health and welfare of farm animals raises new research questions. • An integrated measure of animal health through their lifespan has to be developed. • Synergies and tensions between health, welfare and production need to be investigated. • Improving animal health and welfare challenges in industrial and territorial dimensions. • Livestock farmer and citizen expectations towards animal condition need consideration. Abstract: The need to integrate more clearly societal expectations on livestock farming has led the authors of this article to consider that livestock farming systems must be redesigned to position health and welfare at the heart of their objectives. This article proposes a vision of the advances in knowledge required at different scales to contribute to this transformation. After defining health and welfare of animals, the article emphasises the need to consider health in a broader perspective, to deepen the question of positive emotional experiences regarding welfare, and raises the question of how to assess these two elements on farms. The positive interactions between health and welfare are presented. Some possible tensions between them are also discussed, in particular when improving welfare by providing a more stimulating and richer environment such as access to outdoor increases the risk of infectious diseases. Jointly improving health and welfare of animals poses a number of questions at various scales, from the animal level to the production chain. At the animal level, the authors highlight the need to explore: the long-term links between better welfare and physiological balance, the role of microbiota, the psycho-neuro-endocrine mechanisms linking positive mental state and health, and the trade-off between the physiological functions of production, reproduction and immunity. At the farm level, in addition to studying the relationships at the group level between welfare, health and production, the paper supports the idea of co-constructing innovative systems with livestock farmers, as well as analysing the cost, acceptability and impact of improved systems on their working conditions and well-being. At the production chain or territory levels, various questions are raised. These include studying the best strategies to improve animal health and welfare while preserving economic viability, the labelling of products and the consumers’ willingness to pay, the consequences of heterogeneity in animal traits on the processing of animal products, and the spatial distribution of livestock farming and the organisation of the production and value chain. At the level of the citizen and consumer, one of the challenges is to better inter-relate sanitary and health perspectives on the one hand, and welfare concerns on the other hand. There is also a need to improve citizens’ knowledge on livestock farming, and to develop more intense and constructive exchanges between livestock farmers, the livestock industry and citizens. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research.

ano.nymous@ccsd.cnrs.fr.invalid (Christian Ducrot) 08 Mar 2024

https://hal.inrae.fr/hal-04495275v1

[hal-04696591] On farm precision feeding of gestating sows based on energy and amino acids on farrowing performances and feeding behavior over 3 consecutive gestations

Gestating sows are often fed a single diet throughout their gestation cycle, leading to situations of nutrients deficiency or excess at the individual level. The purpose of this study was to characterize, over 3 consecutive cycles, the impact of a precision feeding (PF), i.e., dietary supplies adjusted at individual level in terms of quantity (energy intake) and quality (standardized ileal digestible (SID) lysine (Lys) intake), on gestating sows’ productive performance, feeding behavior, environmental outputs, and health status compared with sows fed a conventional feeding (CF, i.e., fixed SID Lys intake). At the start of the trial, 2 batches of 20 Landrace × Large White gestating sows were allocated to one of the 2 feeding strategies (PF vs. CF), based on their parity (1, 2, or 3 and more), body weight, and backfat thickness (BT) 3 days after insemination. The PF strategy consisted in mixing with automatic feeders 2 iso-energetic diets (9.8 MJ/kg of net energy with 3.3 and 8.5 g SID Lys/kg, respectively) in variable proportions at individual and daily levels, whereas for the CF strategy these proportions remained constant throughout gestation (73% and 27%, respectively, resulting in an SID Lys concentration of 4.7 g/kg). Sows were followed over 3 consecutive gestations and the sows remained allocated to the same strategy throughout the study. Some sows were culled before the end of the study and were replaced by other sows who therefore performed only 1 or 2 gestations during the study. Thus, 106 gestations and lactations from 51 sows were fully studied and their data analyzed. The PF strategy allowed the sows to reach more closely the expected BT values at farrowing across cycles than the CF strategy (P &lt; 0.001). The PF sows consumed 16% less SID Lys per gestation than the CF sows (P &lt; 0.001), resulting in a 4% improvement in N efficiency (P &lt; 0.001), with no impact on performance at farrowing (P &gt; 0.10). The sows consumed their daily ration in a single visit whatever the feeding strategy (P = 0.41), but CF sows spent more time in the feeder in cycles 2 and 3 (P &lt; 0.001). Thus, compared to the CF strategy implemented by farmers, the individual and daily nutritional supplies implemented with the PF strategy were more efficient in enabling sows to achieve body condition objectives at farrowing over the long term, also with a reduced SID Lys intake and an improved N efficiency without negative impact on farrowing performances.

ano.nymous@ccsd.cnrs.fr.invalid (Clément Ribas) 13 Sep 2024

https://hal.inrae.fr/hal-04696591v1

[hal-04603863] Three-dimensional imaging to estimate in vivo body and carcass chemical composition of growing beef-on-dairy crossbred bulls

The dynamics of cattle body chemical composition during growth and fattening periods determine animal performance and beef carcass quality. The aim of this study was to estimate the empty body (EB) and carcass chemical composition of growing beef-on-dairy crossbred bulls (Brown Swiss breed as dam with Angus, Limousin or Simmental as sire) using three-dimensional (3D) imaging. The 3D images of the cattle’s external body shape were recorded in vivo on 48 bulls along growth trajectory (75–520 kg BW and 34–306 kg hot carcass weight [HCW]; set 1) and on 70 bulls at target market slaughter weight, including 18 animals from set 1 (average 517 ± 10 kg BW and 289 ± 10 kg HCW; set 2). The linear, circumference, curve, surface and volume measurements on the 3D body shape were determined. Those predictive variables were used in partial least square regressions, together with the effect of the sire breed whenever significant (P &lt; 0.05), with leave-one-out cross-validation to estimate water, lipid, protein, mineral and energy mass or proportions in the EB and carcass. Mass and proportions were determined directly from postmortem grinding and chemical analyses (set 1) or indirectly using the 11th rib dissection method (set 2). In set 1, bulls’ BW and HCW were estimated via 3D imaging, with root mean square error of prediction (RMSEP) of 12 kg and 6 kg, respectively. The EB and carcass chemical component proportions were estimated with RMSEP from 0.2% for EB minerals (observed mean 3.7 ± 0.2%) to 1.8% for EB lipid (11.6 ± 4.2%), close to the RMSEP found for the carcass. In set 2, the RMSEP for estimation via 3D imaging was 9 kg for BW and 6 kg for HCW. The EB energy and protein proportions were estimated, with RMSEP of 0.5 MJ/kg fresh matter (10.1 ± 0.8 MJ/DM) and 0.2% (18.7 ± 0.7%), respectively. Overall, the estimations of chemical component proportions from 3D imaging were slightly less precise for both sets than the mass estimations. The morphological traits from the 3D images appeared to be precise estimators of BW, HCW as well as EB and carcass chemical component masses and proportions.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Xavier) 06 Jun 2024

https://hal.inrae.fr/hal-04603863v1

[hal-04808292] Impact of milking interval and time on milk spontaneous lipolysis and composition in dairy cows

Milk lipolysis is defined as the hydrolysis of triglycerides, the major component of milk fat, resulting in the release of short-chain fatty acids (FA) responsible for rancid flavor and partial glycerides that impair functional properties such as foaming and creaming abilities. Milk lipolysis is a complex phenomenon that depends on both animal parameters and breeding factors. Milk spontaneous lipolysis is known to be higher in milk from evening milkings than from morning milkings. This may be related to the longer length of overnight milking intervals or to the nycthemeral cycle. In this experiment, our objective was thus to study the impact of both milking intervals and time of day on milk spontaneous lipolysis in twice-daily-milking systems with one of 3 milking intervals: Short Day - Long Night (SD-LN, 6.30 a.m. and 4.30 p.m.,); Long Day - Short Night (LD-SN, 6:30 a.m. and 8:30 p.m.,); and Balanced Day and Night (BDN, 6:30 a.m. and 6:30 p.m.,). To achieve this goal, 21 multiparous dairy cows in mid-lactation were used in a 3 * 3 Latin square design over 3 periods. The experiment lasted 5 weeks, corresponding to 3 experimental periods of 6 d alternating with 8 d of milking with conventional hours (morning-evening gap of 10 h). We confirmed that milk spontaneous lipolysis was influenced by milking interval, but not the milking time. Indeed, we observed more lipolysis in SD-LN evening milk (+0.20 mEq/100 g fat) and LD-SN morning milk (+0.22 mEq/100 g fat), both of which corresponded to a 10 h interval between successive milkings. High lipolysis milk came from cows that produced less milk with a higher milk fat content. No significant difference between milkings was observed for BDN. Milk protein, total P and citrate contents increased according to the duration of mammary gland storage of milk (from 10 to 14 h). There was no effect of milking intervals on milk fat globule diameter. The milk Na+/K+ ratio, indicating an opening of tight junctions in the mammary gland, increased only in evening milkings with BDN and LD-SN. In conclusion, we found that the effect of milking intervals on lipolysis is stronger than that of the nycthemeral cycle.

ano.nymous@ccsd.cnrs.fr.invalid (Catherine Hurtaud) 28 Nov 2024

https://hal.inrae.fr/hal-04808292v1

[hal-04575157] Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org

ano.nymous@ccsd.cnrs.fr.invalid (Fabien Degalez) 15 May 2024

https://hal.inrae.fr/hal-04575157v1

[hal-04364631] Pea cell wall polysaccharides and their structural integrity influence protein bioaccessibility and hydrolysis

Pea cell walls have been shown to encapsulate nutrients inside cells, thereby limiting their hydrolysis by digestive enzymes. However, it is unknown how the cell wall performs this barrier function. In particular, this could be due to the presence of specific polysaccharides or, most probably, the organisation of the components within the cell wall. This study aimed to investigate how cell walls prevented protein hydrolysis. To address this objective, isolated cells were obtained using different treatments thought to affect cell walls differently (incubations in water, salt or EDTA solutions) and digested in vitro using a three-phase (oral, gastric and intestinal) model. Purified polysaccharides (cellulose, rhamnogalacturonan I and xyloglucan) and solutions obtained from the incubation of pea fibres and flour were also used in our digestion experiments. We found that protein bioaccessibility (here defined as the amount of protein released from the pea cells) and hydrolysis was lower after the gastric phase for the isolated cells prepared with the salt solution compared to the other treatments. Regardless of the treatment, between 47% and 93% of proteins were released from the cells (bioaccessible) and hydrolysed, respectively. Therefore, after prolonged incubation time proteases seem to be able to penetrate the cells during digestion. In terms of purified polysaccharides, rhamnogalacturonan I had the greatest effect on protein hydrolysis. Incubation solutions made from the pea fibres reduced proteolysis to a greater extent than the pea flour. The present study showed that pea cell walls delay protein digestion mainly via its structural organisation within the cell wall, with purified polysaccharides having a more limited effect.

ano.nymous@ccsd.cnrs.fr.invalid (Maxence Noel) 27 Dec 2023

https://hal.science/hal-04364631v1

[hal-04709369] Assessing the contribution of French dairy ruminant farms to the production of food for human consumption

French dairy systems (cow, goat and ewe) have a wide variety of feeding systems. The feed consumed may compete with human food (cereals, grain legumes, silage maize) or not (grassland, rangeland). Gross and net energy and protein efficiencies were assessed. The net approach takes better account of feed-food-fuel competition. Dairy systems are net consumers of energy and net producers of protein for humans, with the best results from grassland systems. At a national scale, net protein efficiency is 1.16 for ewes, 1.12 for goats and 1.88 for cows. Edible energy feed consersion efficiencyis 0.63, 0.54 and 1.00 respectively. There is room for technical improvement in all three sectors, although the variability is sometimes considerable. In order to disseminate these results, innovation groups made up of members of the sectors and livestock farmers have made it possible to better target the methods of communicating the main results of the ERADAL project. In addition, a range of media was created and made available to everyone throughout the ERADAL project.

ano.nymous@ccsd.cnrs.fr.invalid (Benoit Rouille) 25 Sep 2024

https://hal.inrae.fr/hal-04709369v1

[hal-04609533] Effects of replacing corn silage and soybean meal with an increasing percentage of fresh herbage on dairy cow nitrogen use efficiency and flows

To improve sustainability, dairy farms can reduce protein‐rich concentrate in the cows' diet providing fresh herbage produced on‐farm. This study aimed to quantify effects of increasing the percentage of fresh herbage (0%, 25%, 50%, and 75%, on a dry matter [DM] basis) in a partial mixed ration‐based diet on cow N use efficiency and excretion. The study was performed with five lactating cows, in a 4 × 4 Latin square design for four 3 week periods. Individual DM intake, milk yield, feces and urine excretions, and their N concentrations were measured daily. Dietary crude protein concentrations varied little among treatments (127 to 134 g/kg DM). DM intake and milk yield decreased linearly by 5.2 and 3.7 kg/day, respectively, while N use efficiency increased by 4.1 percentage points from 0% to 75% DM of fresh herbage in the diet. Urinary N was not influenced by the treatments, while fecal N decreased as the percentage of fresh herbage increased. This study highlights that replacing partial mixed ration with an increasing percentage of fresh herbage with slight changes in dietary N concentration increases N use efficiency and the percentage of urinary N in excreted N.

ano.nymous@ccsd.cnrs.fr.invalid (Manon Ferreira) 12 Jun 2024

https://hal.inrae.fr/hal-04609533v1

[hal-04437975] Potential applications of biosurfactants in animal production and meat research

Muscle foods are perishable products that are subject to several contaminations such as microbial and/or chemical (lipid and protein oxidation) alterations, which result in their deterioration and quality loss. Several processing strategies are used to preserve and improve the stability, shelf-life and quality of meat and meat products, from which natural preservative agents are gaining interest from both industrials and consumers as green and eco-friendly strategies. Among these natural preservatives, biosurfactants are emerging molecules. Their natural origin and biodegradability make them appealing for use in the food industry. In meat research, biosurfactants are of great interest as antimicrobial and antioxidant agents to reduce meat spoilage and wastage as well as for improving the shelf-life of the products. We aimed to discuss the potential applications of biosurfactants with a focus on their antimicrobial and antioxidant activity within the objectives of reducing meat quality deterioration and improving the image quality (acceptability by consumers) of meat and meat products. Additionally, further perspectives under the context of practical applications of biosurfactants in meat emulsification have been discussed, serving as a reference to feed knowledge gaps in this emerging topic of research. Further studies and evaluations of biosurfactants in meat research are needed to establish more evidence of their potential benefits, applicability and feasibility at a larger scale.

ano.nymous@ccsd.cnrs.fr.invalid (Cerine Yasmine Boulahlib) 05 Feb 2024

https://hal.inrae.fr/hal-04437975v1

[hal-04527102] The genetics of resilience and its relationships with egg production traits and antibody traits in chickens

Background Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have been suggested, but they need further evaluation to determine whether they are indeed predictive of improved resilience, such as disease resilience. This study investigated different resilience indicators based on deviations between expected and observed egg production (EP) by exploring their genetic parameters, their possible trade-offs with production traits, and their relationships with antibody traits in chickens. Methods Egg production in a nucleus breeding herd environment based on 1-week-, 2-week-, or 3-week-intervals of two purebred chicken lines, a white egg-laying (33,825 chickens) and a brown egg-laying line (34,397 chickens), were used to determine deviations between observed EP and expected average batch EP, and between observed EP and expected individual EP. These deviations were used to calculate three types of resilience indicators for two life periods of each individual: natural logarithm-transformed variance (ln(variance)), skewness, and lag-one autocorrelation (autocorrelation) of deviations from 25 to 83 weeks of age and from 83 weeks of age to end of life. Then, we estimated their genetic correlations with EP traits and with two antibody traits. Results The most promising resilience indicators were those based on 1-week-intervals, as they had the highest heritability estimates (0.02–0.12) and high genetic correlations (above 0.60) with the same resilience indicators based on longer intervals. The three types of resilience indicators differed genetically from each other, which indicates that they possibly capture different aspects of resilience. Genetic correlations of the resilience indicator traits based on 1-week-intervals with EP traits were favorable or zero, which means that trade-off effects were marginal. The resilience indicator traits based on 1-week-intervals also showed no genetic correlations with the antibody traits, which suggests that they are not informative for improved immunity or vice versa in the nucleus environment. Conclusions This paper gives direction towards the evaluation and implementation of resilience indicators, i.e. to further investigate resilience indicator traits based on 1-week-intervals, in breeding programs for selecting genetically more resilient layer chickens.

ano.nymous@ccsd.cnrs.fr.invalid (Tom Berghof) 04 Apr 2024

https://hal.inrae.fr/hal-04527102v1

[hal-04283061] Genetic covariance components for measures of nitrogen utilization in grazing dairy cows

Improved nitrogen utilization of dairy production systems should improve not only the economic output of the systems but also the environmental metrics. One strategy to improve efficiency is through breeding programs. Improving a trait through breeding is conditional on the presence of exploitable genetic variability. Using a database of 1,291 deeply phenotyped grazing dairy cows, the genetic variability for 2 definitions of nitrogen utilization was studied: nitrogen use efficiency (i.e., nitrogen output in milk and meat divided by nitrogen available) and nitrogen balance (i.e., nitrogen available less nitrogen output in milk and meat). Variance components for both variables were estimated using animal repeatability linear mixed models. Genetic variability was detected for both nitrogen utilization metrics, even though their heritability estimates were low (<0.10). Validation of genetic evaluations revealed that animals divergent for nitrogen use efficiency or nitrogen balance indeed differed phenotypically, further demonstrating that breeding for improved nitrogen efficiency should result in a shift in the population mean toward better efficiency. Nitrogen use efficiency and nitrogen balance were not genetically correlated with each other (<|0.28|), and neither metric was correlated with milk urea nitrogen (<|0.12|). Nitrogen balance was unfavorably correlated to milk yield, showing the importance of including the nitrogen utilization metrics in a breeding index to improve nitrogen utilization without negatively impacting milk yield. In conclusion, improvement of nitrogen utilization through breeding is possible, even if more nitrogen utilization phenotypic data need to be collected to improve the selection accuracy considering the low heritability estimates.

ano.nymous@ccsd.cnrs.fr.invalid (E. Tavernier) 13 Nov 2023

https://hal.inrae.fr/hal-04283061v1

[hal-04746222] Sorted stem/progenitor epithelial cells of pubertal bovine mammary gland present limited potential to reconstitute an organised mammary epithelium after transplantation

The development and maintenance of mammary gland tissue depend on the proliferation and differentiation of mammary stem and progenitor cells. Here, we investigated populations of mammary epithelial cells that are potential candidates for bovine mammary gland development using xenotransplantation into mice cleared mammary fat pad. Transplanted mammary explants from 17-month-old Holstein heifers developed outgrowths exhibiting the archetypal morphology and molecular marker distributions of the bovine gland. Xenotransplantation of sorted mammary epithelial cells (CD49 f pos ) into bovinised fat pads using inactivated bovine fibroblasts resulted in outgrowth developments with 50% take rate, but these lacked the ductal or alveolar epithelial structures of the normal mammary gland. Similar results were obtained with xenografts of candidate bovine mammary epithelial stem cells (CD49 f high CD24 pos ) or epithelial cells of the basal lineage (CD49 f high CD24 neg ) which also developed as clumps of cells surrounded by stromal stretches within the mouse adipose tissue. In conclusion, sorted cells showed compromised regenerative potential for epithelial morphogenesis. Further work is therefore needed to identify mammary stem/progenitor cells with full regenerative capabilities for biogenesis of normal mammary gland structure, with milk-secreting function.

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Finot) 21 Oct 2024

https://hal.inrae.fr/hal-04746222v1

[hal-04666242] Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers

Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens. Until now, breeding companies have been using or developing SNP chips. Nevertheless, alternatives methods based on sequencing have been developed. Among these, reduced representation sequencing approaches can offer sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability of double digested Restriction site Associated DNA sequencing (ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CR SNP ) and mean depth of sequencing per SNP (DP SNP ) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CR SNP of 0.55, a DP SNP of 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CR SNP and DP SNP values were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CR SNP (0.25) and DP SNP (1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CR SNP , DP SNP , genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a minimum of 40% of the SNPs with a CcR of 98%. Then, ddRAD-seq was defined as a suitable method for variant calling and genotyping in layers.

ano.nymous@ccsd.cnrs.fr.invalid (Mathilde Doublet) 01 Aug 2024

https://hal.inrae.fr/hal-04666242v1

[hal-04865452] Le comportement du porc domestique (Sus scrofa domesticus)

L’étude du comportement animal, ou éthologie, apporte des connaissances sur les animaux d’élevage depuis les années 1950. Si les études se sont focalisées dans un premier temps sur les comportements d’intérêt pour la production (reproduction), elles permettent aujourd’hui de mieux connaître de nombreux autres comportements inhérents à la vie des animaux d’élevage. Le porc domestique a ainsi fait l’objet de nombreuses études, dont il est important de faire la synthèse. Cet article a donc pour objectif de faire le bilan des connaissances sur les différentes catégories de comportement du porc domestique : exploratoire, alimentaire, social, sexuel et parental, et de jeu. Chaque catégorie de comportement est décrite, ainsi que les facteurs l’influençant. Au travers de ce bilan, il ressort que certaines conditions et pratiques d’élevage permettent de favoriser l’expression des comportements des porcs. La connaissance et la mise en place de celles-ci peuvent permettre de répondre à certains besoins comportementaux pour un meilleur bien-être animal (réduction de la contention, enrichissement du milieu…). Cependant, favoriser l’expression des comportements naturels n’est pas toujours bénéfique pour les animaux, et comprendre leur expression est un moyen de trouver des solutions pour pallier les effets indésirables. Même si les recherches sur le comportement des porcs domestiques sont en expansion, elles doivent maintenant s’étendre à des sujets peu explorés à ce jour comme les comportements sociaux non hiérarchiques et le comportement maternel.

ano.nymous@ccsd.cnrs.fr.invalid (Céline Tallet) 06 Jan 2025

https://hal.inrae.fr/hal-04865452v1

[hal-04634569] Sows and piglets adjust their use of an outdoor paddock with season and piglet age during the first weeks of life in an organic farm

Few studies have examined sows and piglets' use of outdoor access during their first weeks of life, when reared with access to a hut and a pasture as in the organic system. We studied whether the age of the piglets and the season of the year influenced the use of an outdoor area by piglets and the sow, and the use of indoor spaces. For this, the localisation of sows and their piglets inside and outside the hut was analysed on 16 sows and their litters during the summer and 16 others during the winter, by scan sampling, on days 2, 7 and 13 after parturition in an organic herd in Denmark. When inside the hut, the number of piglets in the creep area, next to the sow or other piglets was noted. All parameters were analysed by linear mixed-effects ANOVA models. Sows were less often observed outside the hut in the wintertime and during the mornings compared to later times of the day (P&lt;0.001). Furthermore, the sows increased their outdoor use with the age of their litter (P&lt;0.001). The season also influenced the piglet use of outdoor areas (winter &lt; summer; P&lt;0.001). Piglets that were observed outside for the first time were older (8.9±0.9 d) during winter than during summer (3.5±0.5 d). The proportion of piglets observed outside increased with age, with a significant Season x Age interaction (P&lt;0.001). The proportion of observations where the sows and piglets were outdoors together increased with the piglets’ age (P &lt; 0.001). Sows’ outing was correlated with summer (R=0.3) and winter (R=0.2) temperatures, unlike piglets, where outings were correlated only with summer temperatures (R=0.3, P&lt;0.001). The proportion of piglets observed in the creep area was significantly affected by the age with a Season x Age interaction effect (P&lt;0.001). Piglets were rarely observed lying alone inside the hut. The proportion of piglets in contact with the sow and other piglets inside the pen was influenced by a significant Age x Season interaction effect (P&lt;0.001). We showed that piglets given access to an outside paddock gradually increase their use with age and don’t go outside right away. Their first exit and the proportion of piglets outside depended also on the season. In general, a higher proportion of sows and piglets were observed indoor during the wintertime. Thus, sows and piglets adjust their use of outdoor paddock with season and piglet age during the first weeks of life.

ano.nymous@ccsd.cnrs.fr.invalid (Anissa Jahoui) 04 Jul 2024

https://hal.inrae.fr/hal-04634569v1

[hal-04575196] Face au changement climatique, quelles stratégies d’atténuation et d’adaptation pour les productions avicoles ?

La viande de volaille et les œufs sont des sources principales de protéines animales pour l’alimentation humaine dans le monde. Leur pro-duction a augmenté rapidement au cours des dernières décennies. Cependant, les productions avicoles sont vulnérables au changement climatique, en particulier au réchauffement de la planète et à ses conséquences directes et indirectes. Pour y faire face, il est nécessaire de mettre en place des stratégies d’adaptation des animaux, en particulier en améliorant leur résilience. Ces stratégies nécessitent d’une part de mieux comprendre la physiologie des oiseaux (thermorégulation, efficacité pour la production de viande et d’œufs...) et d’autre part de rechercher des innovations en lien avec la nutrition, la santé, la reprogrammation précoce ou encore la génétique (intégration de nouveaux caractères adaptatifs dans les stratégies de sélection). Il faut également trouver des solutions au niveau des systèmes de production, par exemple en prenant en compte les aires de répartition géographique des maladies liées au changement climatique et en introduisant des pratiques d’atténuation pour réduire les consommations d’énergie et les émissions de gaz à effet de serre. Des recherches interdiscipli-naires axées sur la génétique, les méthodes techniques (telles que la programmation thermique précoce), les solutions d’ingénierie, des innovations nutritionnelles et de nouvelles stratégies d’élevage agroécologiques sont ainsi développées. Ces stratégies tiennent compte de la demande sociale croissante en faveur de productions animales éthiques dans les perspectives d’une seule santé (« One Health ») et d’un seul bien-être (« One Welfare ») et visent à limiter la concurrence entre l’homme et les animaux pour les ressources alimentaires. Cette revue illustre par quelques exemples les leviers d’amélioration et de stratégies adaptatives envisageables pour rendre les animaux et les systèmes de production avicole plus résilients dans le contexte du changement climatique.

ano.nymous@ccsd.cnrs.fr.invalid (Anne Collin) 15 May 2024

https://hal.inrae.fr/hal-04575196v1

[hal-04703177] Quelles génétiques pour les systèmes d’élevages certifiés en agriculture biologique ?

Dans les systèmes d’élevage sous cahier des charges agriculture biologique (AB), les animaux peuvent être plus vulnérables car ils sont élevés dans des environnements moins contrôlés. Élever des animaux issus de programmes de sélection conçus pour les systèmes conventionnels dans des systèmes moins intensifs peut s’avérer inadéquat s’ils ne savent pas composer avec les fluctuations de la disponibilité et de la qualité des ressources alimentaires. Les cahiers des charges en AB font peu mention de races ou de lignées et les productions animales AB actuelles peuvent souffrir d’un manque de ressources génétiques adaptées. Les éleveurs AB tendent à formuler des besoins génétiques spécifiques à leurs systèmes d’élevage avec un intérêt majeur pour la robustesse, ce qui suppose pour les généticiens et les sélectionneurs d’être en mesure de fournir une offre somme toute différente et plus diversifiée. Peu de travaux portent sur les objectifs de sélection spécifiques au cahier des charges AB, et l’offre génétique attendue par les éleveurs concernés est souvent réfléchie en rupture avec les systèmes conventionnels. Il est nécessaire de repenser l’utilisation des méthodes de sélection animale dans le cadre de l’AB. Cet article présente l’état des connaissances et les moyens génétiques qui sont mobilisables pour adapter les animaux issus de populations sélectionnées aux systèmes biologiques.

ano.nymous@ccsd.cnrs.fr.invalid (Laurianne Canario) 19 Sep 2024

https://hal.inrae.fr/hal-04703177v1

[hal-04536609] Decreased lactose percentage in milk associated with quarter health disorder and hyperketolactia, a proxy for negative energy balance, in dairy cows

Several studies have described variations in lactose content (LC) in dairy cows during udder quarter health disorder or negative energy balance (NEB). However, their joint effects on LC have never been described. This was the aim of a longitudinal observational study performed on 5 Quebec dairy farms using automatic milking systems. Quarter milk samples were collected every 14 d from 5 to 300 DIM. Quarter health status was described by combining SCC level (SCC- or SCC+: &lt; or ≥100,000 cells/mL) and infectious status (Patho- or Patho+: presence or absence of pathogens on a milk culture). Cows with NEB in early lactation (DIM &lt;70) were identified using milk β-hydroxybutyrate (BHB) content: 0.15 mM = BHB-; 0.15 - 0.19 mM = BHB+; &gt; 0.19 mM = BHB++. A total of 14,505 quarter cisternal milk samples were collected from 380 lactating cows. The quarter LC was analyzed using a mixed linear regression model with the following fixed effects: quarter health status, parity, time interval between last milking and sampling, quarter milk yield (in kg/d), DIM, and herd. A random quarter intercept with a repeated measures correlation structure and a cow random intercept were also specified. The LC of SCC+ quarters was lower (-0.17 ± 0.013% pts) compared with LC of SCC- quarters for both primiparous and multiparous cows. Over the 162 bacterial species identified, only 8 species had a prevalence greater than 4.0%, and just 5 of them were associated with a reduction in LC: Staphylococcus aureus, Staph. chromogenes, Streptococcus dysgalactiae, Staph. epidermidis, and Staph. simulans. Cows identified as BHB+ and BHB++ in early lactation had a lower LC (-0.05 ± 0.019% and -0.13 ± 0.020% pts, respectively) compared with BHB- cows. For BHB++ cows, in both parity groups the decrease in LC (-0.20 ± 0.025% pts) was higher in SCC+ quarters compared with SCC- quarters. Moreover, the additive effect of the quarter health status and NEB on milk LC was greater with larger increases in BHB. Our findings highlight the necessity to jointly take into consideration both quarter health status and milk BHB concentration when using LC as a biomarker for NEB.

ano.nymous@ccsd.cnrs.fr.invalid (Auxane Hamon) 08 Apr 2024

https://hal.inrae.fr/hal-04536609v1

[hal-04693509] Dataset describing the effects of housing environment, dominance status and parity on the PBMC transcriptome of sows during gestation and lactation

Blood immune cells transcriptome can be used as a tool to investigate molecular mechanisms or identify biomarkers of several physiological processes. Factors such as reproductive status, age, or physical and mental states resulting from social and non-social environmental aspects can influence the activation and phenotype of immune cells. This data paper describes the gene expression levels in peripheral blood mononuclear cells (PBMC) of multiparous sows, using RNA sequencing. Sows of various parity ranks were housed during gestation in a stable social group either in a conventional environment on a slatted concrete floor (C) or in an enriched environment with deep straw litter and a bigger space allowance (E). Videos were recorded between days 99 and 104 of gestation (G99 and G104) to determine the sows’ dominance status. Blood samples were collected at 98 days of gestation (G98) and 12 days of lactation (L12) and the PBMC fraction was isolated. Then, total RNA was extracted from PBMC and submitted to next-generation sequencing using the Illumina NextSeq 2000 system. Quality control, mapping, and annotation were performed using the Dragen RNA v3.8.4 software. The differential analysis was performed using the R package DESeq2. Differentially expressed genes (DEGs) were identified using a criterion of Padj cut-off &lt; 0.1 and FC &gt; 1.2 or &lt; 0.83 to identify up-regulated and down-regulated genes. For each time point (G98 and L11), the following contrasts were used for the differential analysis: sows housed in the enriched environment compared to the conventional environment [E vs C], dominant sows compared to subordinate sows [Dom vs Sub], and high parity sows (HP: 4th gestation or higher) compared to low parity sows (LP: 2nd and 3rd gestation) [HP vs LP]. The identified DEGs were used for functional analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) software. To our knowledge, this is the first dataset allowing the investigation of the simultaneous effects of housing environment, dominance status, and parity on the PBMC transcriptome of adult sows. These data could also be used to compare the transcriptome of pregnant and lactating females.

ano.nymous@ccsd.cnrs.fr.invalid (Mariana Mescouto Lopes) 10 Sep 2024

https://hal.science/hal-04693509v1

[hal-04586201] Monitoring individual drinking behaviour and the social hierarchy in dairy cows using electronic drinkers

Sufficient access to clean drinking water is essential for the production and welfare of dairy cows. However, dairy farms vary greatly in how they provide water to cows. Electronic drinkers are now available to monitor cows’ water intake on individual level and can be used to better define their water need. The objective of this study was to validate the detection of agonistic replacements when competing for water access with a new electronic drinker and to explore the ability of using these interactions to identify the social hierarchy within a group of cows. A group of 22 Holstein mid-lactating cows were housed in a free-stall barn equipped with 6 electronic drinkers, 22 individual feeders and 7 cameras. For 9 days over the 18 days of the trial, agonistic interactions were identified via video. We used an algorithm relying on visit start times of subsequent cows at the electronic drinkers to automatically detect agonistic replacements. We determined 4 social hierarchies using the normalized David's score (NormDS) based on 1) agonistic interactions video observed in areas outside the drinkers, 2) agonistic interactions video observed at the drinkers, 3) replacements at the drinkers obtained from video, and 4) replacements at the drinkers detected by the algorithm. We found a weak correlation between the hierarchy recorded outside the drinkers and the one based on agonistic interactions at the drinkers. The hierarchy based on agonistic interactions at the drinkers was strongly correlated with the one relying on video-based replacements but showed a weaker association with the hierarchy relying on replacements detected by the algorithm. To explore the influence of dominance on drinker use, we defined dominant (n = 6), mid-dominant (n = 6), mid-subordinate (n = 4) and subordinate (n = 6) cows according to NormDS quartiles in the video-based replacement hierarchy. Subordinate cows drank less than the other social groups at the peak consumption of the whole group at 1800 h but drank more than the most dominant cows 2 hours later. Subordinate cows preferentially used the most isolated drinker of the barn, furthest from the feeding area, and they drank less from drinkers in higher density areas. Detecting replacements at the drinker can be useful in studies aimed to analyze the effect of social groups on individual drinking behaviour. However, we suggest that for the automatic detection of replacements at the drinker, technology that allows for the recording of non-drinking visits is necessary.

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 24 May 2024

https://hal.inrae.fr/hal-04586201v1

Name of the cookie	Purpose	Shelf life
CAS and PHP session cookies	Login credentials, session security	Session
Tarteaucitron	Saving your cookie consent choices	12 months

Name of the cookie	Purpose	Shelf life
atid	Trace the visitor's route in order to establish visit statistics.	13 months
atuserid	Store the anonymous ID of the visitor who starts the first time he visits the site	13 months
atidvisitor	Identify the numbers (unique identifiers of a site) seen by the visitor and store the visitor's identifiers.	13 months

HAL : Dernières publications

[hal-05131958] Protein signatures of feed restriction and spontaneous lipolysis in skimmed ewe milk

[hal-05131572] Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression: a pilot study

[hal-05042762] Co-conception d’outils d’observation et d’évaluation du bien-être animal

[hal-05040032] PIGLOW, une application pour évaluer le bien-être animal en élevage porcin

[hal-05050868] Prise en compte du bien-être animal dans les développements du Cati SICPA

[hal-05003464] Le chantier « Agroécologie &amp; Marché » conduit par les groupes filières INRAE

[hal-05003526] Méthode d'analyse de la transition agroécologique à l'échelle des filières

[hal-04838897] In vitro evaluation of intestinal barrier function after exposure to digested pea ingredients -food matrix effect

[hal-05006836] Sauvegarde d'une race locale porcine par la filière Noir de Bigorre

[hal-04951257] Effect of temporal water restrictions on drinking behavior and time budget in lactating dairy cows according to their position in the social hierarchy within the herd

[hal-04951317] A conceptual mechanistic model of amino acid fluxes in the small intestine, taking the example of pig

[hal-04590313] Environmental trade-offs of meeting nutritional requirements with a lower share of animal protein for adult subpopulations

[hal-04874121] Sensitivity analysis of the INRA 2018 feeding system for ruminants by hybrid local and global approaches: Comparing the contribution of dietary input variables to multiple response prediction in dairy cattle

[hal-04802793] Comparative genomics and epigenomics of transcriptional regulation

[hal-05051425] Enrichir le milieu de vie des porcs

[hal-05122259] Early life reproductive investment affects longevity in ewes

[hal-05131593] Nitrogen and truly digestible protein efficiencies of dairy cows fed fresh herbage- or maize forage-based diets: a meta-analysis

[hal-04964242] Refining the soil and water component to improve the MoSt grass growth model

[hal-05109749] Myogenic and adipogenic potential of porcine muscle satellite cells isolated by flow cytometry

[hal-05042739] L'introduction d'animaux en vergers et en vignes : une solution agroécologique pour gérer les adventices ?

[hal-05051412] À l’écoute des cochons

[hal-04966411] ECL Method for the Determination of Skatole in Pig Plasma

[hal-04891786] CowComfort: A R-shiny app to visualize the evolution of thermal comfort of dairy cows under climate change and the associated uncertainty

[hal-05081949] The Denver call for action

[hal-04867271] Polar lipids and proteins in milk fat globule membranes as players in spontaneous lipolysis in cow’s milk

[hal-05045421] Genetic regulation of gene expression across multiple tissues in chickens

[hal-04998059] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

[hal-05104838] Chickens perceive humans as social buffers and may follow human-given cues: A pilot study

[hal-05128106] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

[hal-05057234] Towards a ‘One quality’ approach of pork: A perspective on the challenges and opportunities in the context of the farm-to-fork continuum – Invited review

[hal-04993749] The Changes in Grassland Animal Husbandry and Herdsmen’s Life in the Qinghai Pastoral Area of China Based on the Perspective of Changes in the Grassland Property Rights System

[hal-05087086] Ordre de distribution de deux fourrages chez la chèvre : effets sur l’ingestion, la production et le comportement alimentaire

[hal-05087066] Edito. Valorisation des fourrages en élevage caprin : des modalités de distribution à leurs impacts sur la qualité des produits

[hal-04880108] The Kerbernez long-term experiment: A dataset on crop yield and soil organic matter evolution in forage crop rotations and permanent grasslands in a temperate oceanic climate

[hal-04964254] Characterization of grazing Holstein-Friesian dairy cows based on a combination of nitrogen use efficiency and nitrogen balance

[hal-05122302] A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats

[hal-05100241] Oral-stomach sampling as an alternative to rumen canula for the inoculation of in vitro batch fermentation systems

[hal-05012247] Optimizing the MoSt GG model a sensitivity-driven calibration for better grass growth forecasting

[hal-04702523] Electrical stimulation to improve meat quality: Factors at interplay, underlying biochemical mechanisms and a second look into the molecular pathways using proteomics

[hal-04865671] Effects of intramuscular fat on the flavor of fresh sheep and goat meat: Recent insights into pre-mortem and post-mortem factors

[hal-05019793] Research note: double digest Restriction site Associated DNA sequencing is a suitable alternative to high density SNP chips for genomic selection of layers

[hal-05042837] The application of near‐infrared spectroscopy to predict composition, gross energy yield, and methane production of natural forages on the Qinghai–Tibet Plateau

[hal-05087203] Pâturage estival de mûrier blanc (Morus alba) par les chèvres laitières : effets sur les performances zootechniques, le lait et le fromage

[hal-05121191] Clarifying grazing management methods: a data-driven review

[hal-05114435] Efficient pigs do not always have less environmental impacts: insights from an individual-based model to assess environmental, economic and technical performances

[hal-05128077] Editorial: Values shared by journals of learned societies, associations, and scientific institutions in animal science

[hal-05079670] Dynamics of the lactose content and other osmotic agents in milk throughout lactation according to the cow's parity

[hal-05087116] Fréquence de distribution des fourrages chez la chèvre laitière : effets sur l’ingestion, la production et le comportement

[hal-05049047] Comportement social du porc domestique et son importance pour le bien-être animal en élevage

[hal-05003496] La transition agroécologique à l'échelle sectorielle : un long processus de convergence vers un nouveau paradigme

[hal-04829504] Work in agriculture: A blind spot in reducing pesticide use on dairy farms?

[hal-04998547] Editorial : Values shared by journals of learned societies, associations, and scientific institutions in animal science

[hal-04959534] A mass balance model to predict the fate of copper and zinc in pig farming systems to reduce environmental impacts: Application to French context

[hal-04986525] Editorial: Values shared by journals of learned societies, associations and scientific institutions in animal science

[hal-04757159] Mastitis has a cumulative and lasting effect on milk yield and lactose content in dairy cows

[hal-04832467] Impact of UV pre-treatment on the Longissimus thoracis et lumborum muscle proteomes of dry-aged beef cuts: A characterisation within two sampling locations

[hal-04999356] Transitioning to low chemical nitrogen perennial ryegrass white clover pastures on wetland grazing dairy systems

[hal-04821220] Postmortem proteolysis and its indicators vary within bovine muscles: Novel insights in muscles that differ in their contractile, metabolic, and connective tissue properties

[hal-04718511] Stocking density at feeders and drinkers and temporal feed restriction affects dairy cows’ drinking behavior

[hal-05051419] L’enrichissement du milieu de vie

[hal-05084798] A pilot study on alternative blood sampling methods in pigs

[hal-05109811] Replacing hexane with 2-methyloxolane for defatting soybean meal fed to dairy cows: Effects on dairy performance and nitrogen partitioning

[hal-05100159] How does feeding strategy affect the aromatic volatile compounds profile and sensory properties of organic fresh pork?

[hal-05077824] Application of machine learning for optimizing biomarker combinations and guiding decisions on meat authentication

[hal-05049982] Bioaccessibility and associated concepts: Terminology in the context of in vitro food digestion studies

[hal-05087181] Luzerne et/ou fétuque déshydratées chez la chèvre : effets sur l’ingestion, la production et les aptitudes fromagères

[hal-05087156] Prévision de la composition chimique du fourrage ingéré par des chèvres laitières selon sa nature et le taux de refus

[hal-05079463] Dry matter intake and production efficiencies of dairy cows rotationally grazing a perennial ryegrass monoculture, a perennial ryegrass-white clover sward, or a multispecies sward

[hal-04998536] Oxidative stress‐induced changes in wooden breast and mitigation strategies: A review

[hal-05109827] Corrigendum to “Association between body condition profiles, milk production, and reproduction performance in Holstein and Normande cows” (J. Dairy Sci. 107:11621–11638)

[hal-05010133] Analyse transversale de 28 démarches de filières agrialimentaires : des dynamiques d'innovation variables au travers de leur engagement dans l'agroécologie

[hal-05109774] Integrated multi-omic analyses of bovine milk identify biomarkers of negative energy balance

[hal-04925986] Grazing time of dairy cows recorded using two devices based on accelerometers

[hal-04843455] Révéler et valoriser vos données avec le thésaurus INRAE

[hal-04820215] Améliorer conjointement la santé et le bien-être des animaux dans la transition des systèmes d’élevage vers la durabilité

[hal-04764494] Effect of using germinated and fermented lupin and oats as a dietary protein source on laying hen performance and egg quality

[hal-04675948] Partitioning of energy intake in broiler breeders from 27 to 63 weeks old

[hal-04685713] GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations

[hal-05003464] Le chantier « Agroécologie & Marché » conduit par les groupes filières INRAE