Scientific publication

[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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-04617235] CowPILOT -Piloter la note d'état corporel pour optimiser la reproduction des vaches laitières

Le projet CowPILOT avait pour objectif d’évaluer la possibilité du pilotage individuel de la note d’état corporel (NEC) afin d’optimiser la reproduction des vaches laitières. Les enquêtes auprès d’éleveurs et techniciens ont indiqué que son utilisation en routine pour gérer la reproduction reste à construire. A partir de données issues de six fermes expérimentales, des profils d’évolution de l’état corporel au cours de la lactation ont pu être mis en évidence : 4 en race Holstein et 3 en race Normande. Les différences de performance de reproduction ont été de faible ampleur entre les profils. Éleveurs et conseillers ont échangé autour des leviers pour mieux piloter la NEC : ils y sont peu enclins au cours de la lactation. L’adaptation des durées de tarissement apparait comme un levier acceptable pour piloter la NEC lors de la lactation suivante ; l’approche par modélisation a confirmé son influence sur les performances de reproduction.

ano.nymous@ccsd.cnrs.fr.invalid (Fabrice Bidan) 19 Jun 2024

https://hal.inrae.fr/hal-04617235v1

[hal-04653317] Quels défis au développement de la production porcine en agriculture biologique en France ?

La production porcine française en AB est très diversifiée de par ses élevages, notamment en termes de taille avec de nombreux ateliers à faibles effectifs ; de par la commercialisation des produits, avec une filière longue bien implantée dans le grand ouest de la France, et des filières courtes plus territorialisées ; et de par la multiplicité de ses acteurs spécifiques à l’AB ou mixtes. Bien que le nombre de truies certifiées en AB ait doublé entre 2016 et 2021, il ne représente que 1,9 % du cheptel français. Face à ce constat, une étude a été réalisée par le consortium ORIGAMI (INRAE-Métabio) pour comprendre les freins et leviers au développement de cette production. Des entretiens de 21 porteurs de projets ont permis d’identifier 164 freins et 231 leviers. Des analyses en composantes multiples suivies d’une classification ont mis en évidence sept types de freins et six types de leviers en fonction de leur niveau d’organisation (de l’animal au territoire) et du maillon de la filière qu’ils concernent (de l’agrofourniture à la consommation). L’interprétation de ces typologies permet d’identifier des thèmes de recherche pour relever les principaux défis identifiés. Ces thèmes concernent l’acquisition de références techniques spécifiques pour l’AB, la meilleure articulation entre filières et territoires, la promotion des débouchés des produits, mais aussi la formation des acteurs actuels et futurs et la communication auprès du grand public. Ces sujets sont des pistes de réflexion pour la construction de projets transdisciplinaires de recherche ou recherche-action avec les acteurs des filières.

ano.nymous@ccsd.cnrs.fr.invalid (Lucile Montagne) 18 Jul 2024

https://hal.inrae.fr/hal-04653317v1

[hal-04309414] Assessment of beef sensory attributes and physicochemical characteristics: A comparative study of intermediate versus normal ultimate pH striploin cuts

The quality of beef, defined by key attributes such as the intrinsic sensory qualities texture, flavour, and juiciness, is shaped by various intrinsic and extrinsic factors. This study conducted a detailed examination of Nellore beef, focusing on two categories based on ultimate pH (pHu) levels: intermediate (pHu ≥ 5.8) and normal (pHu < 5.6) beef. A comprehensive approach was taken, involving twenty trained assessors who applied the Optimised Descriptive Profile (ODP) method to evaluate grilled striploin steak samples. In parallel, consumer preferences were measured through a hedonic test and a Check-all-that-apply (CATA) task, involving 135 participants. The ODP results revealed that the intermediate pHu samples were juicier (P < 0.05) compared to the normal pHu group. The CATA analysis highlighted differences in both intermediate and normal pHu beef, especially in juiciness, a crucial factor for consumer satisfaction. Notably, variations in deoxymyoglobin content linked to ageing were observed, with higher levels at the 3rd day compared to the 28th day, especially in the intermediate pHu samples (P < 0.05). Moreover, colour-related aspects such as L*, b*, chroma (C*), and oxymyoglobin were significantly influenced (P < 0.05) by both the pHu category and ageing time. Regarding consumer acceptance, the study found no significant difference in perception between the intermediate and normal pHu groups (P > 0.05). These findings revealed the complex interactions between pHu levels, sensory characteristics, and consumer preferences in beef quality, offering valuable insights for both the industry and research community.

ano.nymous@ccsd.cnrs.fr.invalid (Iliani Patinho) 04 Dec 2023

https://hal.inrae.fr/hal-04309414v1

[hal-04619014] From the biochemical pieces to the nutritional puzzle: using meta-reactions in teaching and research

We now live in an era where metabolic data are increasingly accessible and available. Analysis of this data can be done using novel techniques (e.g., machine learning and artificial intelligence) but this does not alleviate scientists to use “human intelligence”. The objective of this paper is to combine the information of a large database of biochemical reactions with a method and tool to make nutritional biochemistry more accessible to nutritionists. A script was developed to extract information from a database with more than 16 000 biochemical reactions so that it can be used for “biochemical bookkeeping”. A system of more than 300 meta-reactions (i.e., the outcome reaction of a series of connected individual reactions) was constructed covering a wide range of metabolic pathways for macro- and micronutrients. Meta-reactions were constructed by identifying metabolic nodes, which are inputs or outputs of a metabolic system or that serve as connection points between meta-reactions. Complete metabolic pathways can be constructed by combining and balancing the meta-reactions using a simple Excel tool. To illustrate the use of meta-reactions and the tool in the teaching of nutritional biochemistry, examples are given to illustrate how much ATP can be synthesized from glucose, either directly or indirectly (i.e., via storage and mobilization or via transfer of intermediate metabolites between tissues and generations). To illustrate how meta-reactions and the tool can be used in research, nutrient balance data of the mammary gland of a dairy cow were used to construct a plausible pathway of nutrient metabolism of the whole mammary gland. The balance data included 34 metabolites taken up or exported by the mammary gland and 39 meta-reactions were used to construct a metabolic pathway that accounted for the uptake and output of metabolites. The results highlighted the importance of the synthesis of proline from arginine and the concomitant synthesis of urea by the mammary gland. It also raised the question of whether the availability of metabolic pathways or glucose uptake would be the more limiting factor for the synthesis of NADPH required for fatty acid synthesis. The availability of an open database with biochemical reactions, the concept of meta-reactions, and the provision of a tool allow users to construct metabolic pathways, which helps acquiring a more comprehensive and integrated view of metabolism and may raise issues that may be difficult to identify otherwise.

ano.nymous@ccsd.cnrs.fr.invalid (Jaap J. van Milgen) 20 Jun 2024

https://hal.inrae.fr/hal-04619014v1

[hal-04773240] Impact of genome build on RNA-seq interpretation and diagnostics

Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.

ano.nymous@ccsd.cnrs.fr.invalid (Rachel Ungar) 08 Nov 2024

https://hal.inrae.fr/hal-04773240v1

[hal-04628706] Effects of parity and week after calving on the metabolic, redox and immune status of dairy cows

At the onset of lactation in dairy cows, inflammation and oxidative stress may occur and result in a risk of pathologies and lower milk yield. To propose an innovative management strategy for cows during this period, it is essential to better understand these physiological variations. Our objective was to evaluate the metabolic, redox and immune status of 7 primiparous and 8 multiparous Holstein cows during late gestation and the first months of lactation. Blood samples were collected between 3 weeks before calving until 12 weeks postpartum. Milk samples were also collected, but only at the time points after calving. The metabolic (nonesterified fatty acids (NEFA), BHB, glucose, urea, calcium) and redox (reactive oxygen metabolites (ROM), oxidative stress index (OSI), glutathione peroxidase activity, vitamin E) statuses were analyzed in plasma or erythrocytes. The expression of genes related to antioxidant functions was determined in leukocytes collected from milk. For immune status, plasma cytokine levels and the production of reactive oxygen species (ROS) in classical and regulatory neutrophils were measured in 2 whole blood ex vivo challenges. The data were analyzed using a mixed model that included the fixed effects of parity and week and their interaction. Milk yield, plasma NEFA and BHB in wk 2 and 4 after calving were higher in multiparous cows than in primiparous cows, whereas glucose and calcium tended to be lower. Plasma ROM and OSI levels in wk 8 were higher in multiparous than in primiparous cows. Multiparous cows also displayed higher glutathione peroxidase activity in erythrocytes, and antioxidant transcription factor and superoxide dismutase-1 expression levels in milk leukocytes. Moreover, multiparous cows had higher plasma concentrations of vitamin E but lower plasma levels of cytokines CXCL10, CCL2, IL1Ralpha and IFNgamma. Following ex vivo whole blood stimulation with Escherichia coli, lower IL1alpha and TNFalpha levels were measured in multiparous than in primiparous cows. Intracellular ROS production by neutrophils was lower in multiparous than in primiparous cows. These results thus indicated marked physiological changes in wk 8 compared with wk 2 and 4 of lactation. These differences in the physiological status of primiparous and multiparous cows offer interesting perspectives for potential dietary strategies to prevent pathologies which take account of parity and week relative to calving.

ano.nymous@ccsd.cnrs.fr.invalid (Angélique Corset) 02 Oct 2024

https://hal.inrae.fr/hal-04628706v1

[hal-04448073] Bioaccessibility and associated concepts: Need for a consensus

Background: The definition of the term 'bioaccessibility' is not clear. In the fields of Nutrition and Food Sciences, the term bioaccessibility was introduced in the context of micronutrients, which can lead to some confusion when applied to macronutrients, the latter requiring hydrolysis (sometimes included in the definition of bioaccessibility). Scope: In the context of macronutrient digestion, particularly in plant-based food where cell walls play a significant role, it seems coherent to differentiate between the release of nutrients from the food matrix, hydrolysis and absorption. Key findings and Conclusions: We concluded that the terms bioaccessibility, digestibility and bioavailability have been misused over time and have lost some of their meaning. Therefore, in this study, we suggest a definition for “bioaccessibility” and related vocabulary, as well as a possible classification of the biochemical events occurring during food or feed digestion. It is critical to use precise, specific vocabulary to describe the mechanisms involved while food transits through the different compartments of the gastro-intestinal tract. This goes hand in hand with a recent realisation of the importance of the food matrix, which has an impact on the breakdown of food in the digestive tract and thus on human and animal health.

ano.nymous@ccsd.cnrs.fr.invalid (Myriam M.L. Grundy) 09 Feb 2024

https://hal.inrae.fr/hal-04448073v1

[hal-04703322] Interaction between drinker density and cow social dominance affects drinking behavior

Dairy cow welfare and milk production levels can be negatively affected when animals lack access to sufficient amounts of good-quality drinking water. Farms vary greatly in how well they meet this standard. Here, we explored how the interaction between drinker density and social dominance level influenced the drinking behaviors of a group of 40 mid-lactation cows. We recorded cow drinking behavior and competitive outcomes (i.e., number of replacements) at the drinkers during the final 5 d of 2 drinker density treatments, applied successively (12 drinkers, then 4 drinkers available). Four social dominance categories were defined by applying the quartile classification method to the normalized David's score obtained from the low-density treatment data (NormDS values). The high- and low-density treatments used approximately 56 (±16) versus 119 (±31) replacements per drinker per day. Subordinate cows were lighter and younger than dominant cows. Dominant cows drank around 5 L more per day in the low- versus high-density treatment. Furthermore, both drinking rate and daily drinking frequency were higher in the low-density treatment, with the most pronounced differences seen for subordinate cows. In the low-density treatment, mid-subordinate cows shifted their drinking times, visiting the drinkers 1 to 2 h after peak water consumption by the group. The results for the low-density treatment thus indicate that the cows were experiencing more intense competition for water, leading to behavioral responses that were related to social dominance. Our findings underscore the need to more broadly explore the effects of increasing drinker numbers under a variety of rearing conditions to provide farmers with better technical recommendations.

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 20 Sep 2024

https://hal.inrae.fr/hal-04703322v1

[hal-04549544] Porcine ear necrosis is associated with social behaviours in weaned piglets

Background: Porcine ear necrosis (PEN) is a worldwide health issue and its aetiology is still unclear. The aim of this study was to describe the prevalence and the severity of PEN in a commercial farm, associated with pig behaviour and health biomarkers measures. On two consecutive batches, PEN prevalence was determined at the pen level. PEN scores, blood haptoglobin concentration and oxidative status were measured on two pigs per pen ( n = 48 pens) 9, 30 and 50 days (D) after arrival to the post-weaning unit. Social nosing, oral manipulation and aggression of pen mates and exploration of enrichment materials were observed on two to three pigs per pen twice a week from D9 to D50. Results: At the pen level, the higher the time spent nosing pen mates, the lower the percentage of pigs affected by PEN during both the early and the late post-weaning periods ( P < 0.002) and, in the opposite, the higher the time spent orally manipulating pen mates during the late post-weaning period, the higher the percentage of affected pigs ( P = 0.03). At the pig level, the higher the increase in hydroperoxides and haptoglobin during the early post-weaning period, the higher the PEN scores on D30 ( P < 0.001). Conclusions: This study suggests that a high incidence of social nosing, which can be an indicator of good social cohesion in a group, was significantly associated with less frequent lesions of PEN. In opposite, high incidence of oral manipulation of pen mates may increase the percentage of PEN-affected pigs. According to these observations, PEN is a multifactorial condition which may have social causes among others.

ano.nymous@ccsd.cnrs.fr.invalid (Gwenaël Boulbria) 17 Apr 2024

https://hal.inrae.fr/hal-04549544v1

[hal-04283002] Nitrogen offset potential in a multi-year farmlet-scale study; milk and herbage production from grazed perennial ryegrass/white clover swards

The objective of this study was to quantify the farm gate nitrogen (N) off-set potential of perennial ryegrass (Lolium perenne L.; PRG) white clover (Trifolium repens L.; WC) swards by comparing the herbage and milk production from dairy farmlets that were simulations of full farming systems. A study was established where 120 cows were randomly assigned to 4 farmlets of 10.9 ha (stocking rate: 2.75 cow/ha), comprised of 20 paddocks each. Cows were fed 526 kg DM of concentrate on average each year. The 4 grazing treatments were PRG-only at 150 or 250 kg N/ha and PRG-WC at 150 or 250 kg N/ha. Cows remained in their treatment group for an entire grazing season and were re-randomized as they calved across treatments each year. As cows calved in the Spring as standard practice in Ireland, they were rotationally grazed from early-February both day and night (weather permitting) to mid-November, to a target post-grazing sward height of 4.0 cm. Mean sward WC content was 18.1 and 15.4% for the 150 and 250 kg N/ha WC treatments, respectively over the 3 year period. When WC was included, lowering the N rate did not reduce pre-grazing yield, pre-grazing height or herbage removed but did so significantly when WC was absent. Total annual herbage DM production was 13,771, 15,242, 14,721 and 15,667 kg DM/ha, for the 4 treatments; PRG-only swards receiving 150 kg N/ha or 250 kg N/ha and a PRG-WC sward receiving 150 kg N/ha or 250 kg N/ha respectively. In addition, when WC was present, compressed post-grazing sward heights were lower (4.10 vs. 4.21 cm) and herbage allowance (approximately 17 kg/cow feed allocation per cow per day) higher than the high N control (+ 0.7 kg of DM/cow per day). There was a significant increase in milk production, both per cow and per ha (P > 0.001), when WC was included into PRG swards. Over the 3-year study, cows grazing PRG-WC had greater milk (+ 304 kg) and milk solids (MSo; + 31 kg fat + protein) yields than cows grazing PRG-only swards. This significant increase in milk production suggests the inclusion of WC in grazing systems can be effectively used to increase milk production per cow and per ha and help offset nitrogen use. This result offers potential to increase farm gate NUE, and reduce the N surplus compared with PRG-dominant sward grazing systems receiving 250 kg N/ha without negatively impacting on MSo yield or herbage production and increasing farm profit by €478/ha.

ano.nymous@ccsd.cnrs.fr.invalid (Á. Murray) 13 Nov 2023

https://hal.inrae.fr/hal-04283002v1

[hal-04586224] Strategies of maize silage supplementation of grazing dairy cows: Effects on milk production, pasture intake, grazing behaviour and methane emissions

Supplementation strategy and grazing management can strongly influence dairy cow feeding behaviour, herbage intake, milk production and methane emissions. Two studies were conducted to investigate (1) the level of supplementation with partial mixed rations (PMR) and (2) the timing of maize silage feeding (morning vs. evening) for cows that have access to pasture either only during the day or day and night. A dataset was built that includes all individual cow measurements from both studies. It consists of 18 Microsoft (R) Excel files that correspond to several scales of information. The main file, "GrASTech_04_CowMeasurements", contains individual weekly measurements of milk production and composition, body weight, supplement and herbage dry matter intake measured using the n -alkane method and grazing behaviour measured using Lifecorder Plus, for a total of 168 cow x week datapoints. Five Excel files provide supplementary information at larger scales: periods, experimental treatments, feeds offered and their chemical composition, pasture characteristics and grazing management, and cow characteristics. The remaining 12 Excel files provide information at the daily scale on weather (1 file), methane concentrations and emissions (1 file), the grazing schedule (1 file) and grazing behaviour (9 files). The files related to grazing behaviour include the daily pattern of grazing time every 2 min as determined by Lifecorder Plus, as well as the daily pattern of grazing time, rumination, overactivity, other activity, rest and standing every 5 min as determined by Feed'Live. This dataset can be used to better understand and investigate relations among and the influence of animal characteristics, grazing management, the supplementation strategy and weather conditions on daily herbage intake, grazing behaviour, milk production and methane emissions at a weekly scale. The detailed information on feeding and grazing behaviour can also be used to study between -cow and between -day variability in daily cow activities.

ano.nymous@ccsd.cnrs.fr.invalid (Rémy Delagarde) 24 May 2024

https://hal.inrae.fr/hal-04586224v1

[hal-04568409] Data-independent acquisition-based SWATH-MS proteomics profiling to decipher the impact of farming system and chicken strain and discovery of biomarkers of authenticity in organic versus antibiotic-free chicken meat

In the literature, there is a paucity of methods and tools that allow the identification of biomarkers of authenticity to discriminate organic and non-organic chicken meat products. Shotgun proteomics is a powerful tool that allows the investigation of the entire proteome of a muscle and/or meat sample. In this study, a shotgun proteomics approach using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) has been applied for the first time to characterize and identify candidate protein biomarkers of authenticity in post-mortem chicken Pectoralis major muscles produced under organic and non-organic farming systems (antibiotic-free). The proteomics characterization was further performed within two chicken strains, these being Ross 308 and Ranger Classic, which differ in their growth rate. From the candidate protein biomarkers, the bioinformatics enrichment analyses revealed significant differences in the muscle proteome between the two chicken strains, which may be related to their genetic background and rearing conditions. The results further provided novel insights on the potential interconnected pathways at interplay that are associated with the differences as a consequence of farming system of chicken strain, such as muscle contraction and energy metabolism. This study could pave the way to more in-depth investigations in proteomics applications to assess chicken meat authenticity and better understand the impact of farming systems on the chicken muscle and meat quality.

ano.nymous@ccsd.cnrs.fr.invalid (Laura Alessandroni) 04 May 2024

https://hal.inrae.fr/hal-04568409v1

[hal-04415987] Meat Omics: Trends and applications of Omics strategies in meat research

In this thematic issue, the potential of Omics methods currently applied to meat research have been demonstrated through seventeen papers that grouped seven reviews and ten original research papers. Overall, the papers described cutting-edge Omics methods to study several key aspects of meat quality, which were mainly dominated using proteomics (both traditional and label-free shotgun approaches), followed by metabolomics, lipidomics and new emerging approaches such as Rapid Evaporative Ionization Mass Spectrometry (REIMS) fingerprinting.

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 26 Jan 2024

https://hal.inrae.fr/hal-04415987v1

[hal-04664474] Effects of natural oral alternatives to parental iron supplementation on haematological and health-related blood parameters of organic piglets

The most common and efficient iron supply to prevent neonatal anaemia in piglets is the injection of iron dextran or gleptoferron. This treatment is problematic in organic farms because organic specifications strictly limit the use of chemically-synthesized allopathic drugs. Based on the observation that piglets raised outdoors rarely develop anaemia, we hypothesized that piglets satisfy their iron needs by ingesting soil from their environment. Therefore, we compared the efficacy of a 100-g intramuscular iron dextran injection (Iron, 8 litters, n=98 piglets) at 4 days (d) of age (d4), to a daily ad libitum supply of dried soil (Soil, 8 litters, n=101) or dried eat-like river silt (Peat, 8 litters, n=102) from d4 to weaning (at 49 days of age, d49). Pigs were raised according to organic farming rules. Blood was collected on 3 males and 3 females per litter on d4, 20, 41, 50 and 69. BW was similar in the 3 groups on d4, 20, 41, 50 and 69 (P &gt; 0.1). During the experiment, piglets were affected by a severe digestive E. coli episode but litter mortality rate between d4 and d69 did not differ between groups (P &gt; 0.1). Blood haemoglobin concentration (Hb) was similar in all groups on d4, 50 and 69. However, on d20, Hb was higher in Peat and Iron groups than in the Soil group (P &lt; 0.001), and on d41 and d50, Hb was higher in the Peat group than in Iron and Soil groups (P &lt; 0.001). Mean red blood cell volume (RBCV) remained stable over time in the Peat group. In comparison, RBCV dropped in the Soil group on d20 and d41 (P &lt; 0.001), and in the Iron group on d41 (P &lt; 0.001). Soil and Iron group RBCV returned to values similar to the Peat group by d69 (P &gt; 0.1). In conclusion, soil supply in the pen was not sufficient to ensure a satisfactory iron intake in piglets, unlike peat-like river silt, which enable to reach haemoglobin concentrations above 80 mg/mL for over 90% of the piglets from d20 and, over 100% of piglets at weaning. The daily supply of the silt proved more efficient than the 100-mg iron injection beyond 20 days.

ano.nymous@ccsd.cnrs.fr.invalid (Elodie Merlot) 30 Jul 2024

https://hal.inrae.fr/hal-04664474v1

[hal-04677211] Organic rearing of non-castrated male pigs: welfare indicators, carcass traits, pork quality and boar taint in Duroc and Pietrain crossbreds

The main principles of organic farming as presented by the European organisation for organic food and farming are health, ecology, fairness and care, but intrinsic quality of products is also important for consumers. Pig genotype was tested as a lever to improve animal welfare and pork quality (meat tenderness, processing ability) of organic, non-castrated males while controlling the risk for boar taint. Non-castrated Large White × Duroc (D, n = 47) or Large White × Pietrain NN (P, n = 34) males were involved in two batches, each including one group of pigs per genotype. Each group was reared in a pen from the same building on deep straw bedding (1.3 m²/pig), with a feeding zone (0.2 m²/pig) and an outdoor area (1.0 m²/pig), from 28 kg BW until slaughter at ca. 125 kg BW. All pigs received ad libitum the same growing and finishing diets, and hay. Overall, health and welfare indicators showed few problems, but the proportions of pigs with skin scratches, and tail lesions at the end of the finishing period, were lower in D than P pigs (P &lt; 0.05). Growth rate and final BW did not differ between genotypes. The D pigs had lower carcass lean meat content (P &lt; 0.001) and relative proportions of ham and loin (P ≤ 0.01), and higher proportions of belly and backfat (P ≤ 0.001) than P pigs. Compared to P, loin (Longissimus muscle) of D pigs was less light and exudative and had higher chroma (P &lt; 0.05), but pH 24 h and glycolytic potential did not differ. Loin meat of D pigs had higher intramuscular fat content (P &lt; 0.001) and tended to have a lower shear force (P = 0.09), but cooking loss did not differ. In the ham muscles, D pigs had higher chroma than P pigs in the Gluteus medius, whereas pH 24 h did not differ in the Gluteus medius and Semimembranosus. D pigs had higher backfat concentrations of androstenone (P &lt; 0.001), and skatole and indole (P &lt; 0.05) than P pigs, suggesting a higher risk of rejection by consumers due to boar taint. However, only one D carcass was detected as tainted by human nose test. Altogether, organic farming of non-castrated Duroc crossbred males appears to be favourable for animal welfare, technological and several sensory pork properties, provided that the risk of undesirable odours is limited through management practices.

ano.nymous@ccsd.cnrs.fr.invalid (Bénédicte Lebret) 25 Aug 2024

https://hal.inrae.fr/hal-04677211v1

[hal-04998084] Pourrait-on parvenir à une alimentation saine dans le monde en 2050 sans expansion des terres agricoles ?

Sera-t-il possible de fournir une alimentation plus saine à la population mondiale en 2050 sans étendre les terres agricoles ? Pour répondre à cette question, nous avons estimé grâce au modèle de bilan GlobAgri-AE2050, les besoins en terres cultivées et en pâtures en 2050 pour 21 régions du monde, induits par l’adoption de régimes plus sains, sur la base de projections des variables exogènes d’offre et de demande de produits agricoles, en prenant en compte l’impact du changement climatique sur les rendements des cultures, les intensités de pâturage et les surfaces maximales cultivables, et en tenant compte des échanges inter-régionaux. Les résultats des simulations pour deux projections des rendements (croissance « modérée » et « forte ») montrent que plusieurs régions (Afrique du Nord, Proche et Moyen Orient, Inde et reste de l’Asie) seraient contraintes par leurs disponibilités en terres cultivables, et que les besoins additionnels en pâtures en Afrique subsaharienne deviendraient extrêmes.

ano.nymous@ccsd.cnrs.fr.invalid (Agneta Forslund) 20 Mar 2025

https://hal.inrae.fr/hal-04998084v1

[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-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-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-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-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-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-04510660] Sensitivity analysis of the INRA 2018 feeding system for ruminants by a one-at-a-time approach: Effects of dietary input variables on predictions of multiple responses of dairy cattle

In the INRA 2018 feeding system for ruminants, the prediction of multiple animal responses is based on the integration of the characteristics of the animal and the available feedstuff characteristics, as well as the rationing objectives. In this framework, the characterization of feedstuffs in terms of net energy, digestible protein, and fill units requirs information on their chemical composition, digestibility, and degradability. Despite the importance of these feed characteristics, a comprehensive assessment of their impact on the responses predicted by the INRA 2018 feeding system has not been carried out. Thus, our study investigated how variables predicted by the INRA feeding system (i.e., outputs) for dairy cows are affected by variation in feed characterization (i.e., inputs). Five input variables were selected for the sensitivity analysis (SA): CP, OM apparent digestibility (OMd), GE, effective degradability of nitrogen assuming a passage rate of 6%/h (ED6_N) and true intestinal digestibility (dr_N) of nitrogen. A one-at-a-time SA was performed on predicted digestive, productive and environmental output variables for dairy cows with 6 contrasted diets. These 6 diets were formulated to meet 95% of the potential daily milk production (37.5 kg) of a multiparous cow at wk 14 of lactation. Then, the values of the 5 key input variables of each feedstuff were randomly sampled around the INRA 2018 feed table values (reference point). The response of the output variable to the variation of the input variable was quantified and compared using the tangent value at the reference point and the normalized sensitivity coefficient. Among the major final output variables, CP and dr_N had the greatest impact on nitrogen (N) excretion in urine (as a proportion of total fecal and urinary N excretion, UN/TN), OMd and GE had the greatest impact on N utilization efficiency (N in milk as proportion of intake N, NUE), and ED6_N had the greatest impact on milk protein yield (MPY). Additionally, CP, GE, and dr_N had the least effect on methane emission, OMd had the least effect on UN/TN, and ED6_N had the least effect on NUE. The responses of most output variables to ED6_N and dr_N variations were highly dependent on diet, and were related to the ratio between PDI (i.e., metabolizable protein) and UFL (i.e., NEL) at the reference point of each diet. In conclusion, we were able to analyze the response of output variables to the variations of the input variables, using the tangent and its normalized value at the reference point. The predicted final outputs were more impacted by variations in CP, GE, and OMd. The other 2 input variables, ED6_N and dr_N, had a smaller effect on the final output variables, but the responses varied between the diets according to their PDI/UFL ratio. Among the final output variables affected by ED6_N, MPY was the most impacted, but when quantified this impact was at an acceptable level. Our present study was conducted using 6 representative diets for dairy cattle fed at their potential, but should be completed by the analysis of more diverse conditions.

ano.nymous@ccsd.cnrs.fr.invalid (Seoyoung Jeon) 19 Mar 2024

https://hal.science/hal-04510660v1

[hal-04582488] Evidence of stable preferential affiliative relationships in the domestic pig

Affiliative relationships are well documented in a wide range of wild animals. However, there is limited evidence of their existence in social farm animals, despite potential significant animal welfare implications. We aimed to determinewhether pigs have preferential partners for affiliative interactions and associations andwhether these preferences remain stable over time or are influenced by sex, dominance rank or litter of origin (i.e. kinship or familiarity). Two pens of 12 domestic pigs, Sus scrofa, twomales and two females from three litters, were weaned at 28 days of age and observed from 42 to 57 days (postweaning phase) and from 70 to 85 days (finishing phase) following a change of housing at 62 days. Sociopositive behaviours, including nose-to-nose and nose-to-body contacts, allogrooming and associations while lying were scored on video observations over 6 days per phase. Using social network analysis methods, we found nonrandom social preferences for allogrooming in both pens of pigs, which remained stable between the postweaning and finishing phases.We also observed nonrandom associations for proximities while lying, although these patterns were not found in both pens of pigs and did not systematically persist between phases. In contrast, nose-to-nose interactions were expressed randomly in both pens and phases. Depending on the housing conditions, social preferences for grooming interactions or proximity while lying were only weakly influenced by sex, dominance rank or litter of origin. We did not find any correlation between social networks for grooming interactions and associations while lying. In summary, our study highlights the existence of durable affiliative relationships based on grooming interactions and proximity while lying within stable pig groups. These relationships appear to be minimally affected by sex, dominance, kinship or familiarity. Taking these relationships into account, particularly from a young age, could be pivotal in improving the welfare of pigs on farms.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Clouard) 22 May 2024

https://hal.inrae.fr/hal-04582488v1

[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-04603561] Intake profile, milk production and energy balance of early lactation spring calving Holstein Friesian and Jersey x Holstein Friesian dairy cows in high utilisation pasture-based systems

Early lactation is a critical period for dairy cows as energy requirements rapidly increase with the onset of lactation, however, early lactation dry matter intakes (DMI) in pasture-based systems are under-measured. The objectives of this study were 1) to measure and profile total DMI (TDMI) and animal performance of dairy cows during early lactation in a pasture-based system 2) to investigate early lactation energy balance in pasture-based systems and 3) to examine production efficiencies including TDMI and milk solids production per 100 kg bodyweight. Eighty spring-calving dairy cows were allocated to a grazing group as they calved over a 2 year period (2021 and 2022). Cows were offered a daily herbage allowance to achieve a post-grazing sward height of 4 cm with silage supplementation when necessary due to inclement weather. Total DMI was measured using the n-alkane technique over a 12 week period from 1st of February to the 23rd of April. Total DMI and daily milk yield were significantly affected by parity with both variables being greatest for third parity animals (17.7 kg DM and 26.3 kg/cow/day, respectively), lowest for first parity (13.2 kg DM and 19.6 kg/cow/day, respectively) and intermediate for second parity animals (16.8 kg DM and 24.1 kg/cow/day, respectively). Peak TDMI was reached on wk 10 for first parity animals (14.6 kg DM), wk 11 for second parity animals (19.3 kg DM) and wk 12 for third parity animals (19.9 kg DM). Parity also had a significant effect on UFL (feed units for milk) feed balance as first parity animals experienced a greater degree of negative energy balance (−3.2 UFL) compared with second and third parity animals (−2.3 UFL). Breed and parity had an effect on production efficiencies during the first 12 weeks of lactation as Jersey x Holstein Friesian cows had greater TDMI/100 kg bodyweight and milk solids/100 kg bodyweight compared with Holstein Friesian cows.

ano.nymous@ccsd.cnrs.fr.invalid (S. Walsh) 06 Jun 2024

https://hal.inrae.fr/hal-04603561v1

[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-04636071] Yaks are dependent on gut microbiota for survival in the environment of the Qinghai Tibet plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai–Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai–Tibetan plateau.

ano.nymous@ccsd.cnrs.fr.invalid (Runze Wang) 05 Jul 2024

https://hal.inrae.fr/hal-04636071v1

[hal-04802821] BIOMARQ'LAIT -Identification of biomarkers in milk to monitor the nutritional status of dairy cows

The aim of the BIOMARQ'LAIT project was to identify molecules that could be measured in milk, in order to use a non-invasive approach to determine the capacity of dairy cows to cope with an energy deficit. In this project, numerous milk components have been studied in whole milk, fat globules, extracellular vesicles and mammary epithelial cells. A panel of candidate biomarkers consisting of metabolites, proteins and microRNAs was built up. The project then led to the development of equations to predict the concentrations of three metabolites of interest based on the mid-infrared spectra of milk. The new references acquired during the project were then disseminated to stakeholders in the dairy sector through institutional, technical and scientific communications. An educational kit was also produced to provide farmers and students with a better understanding of the energy deficit in dairy cows.

ano.nymous@ccsd.cnrs.fr.invalid (Marine Gele) 25 Nov 2024

https://hal.inrae.fr/hal-04802821v1

[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

[hal-04687408] Eco-friendly diet: nutrient digestibility, nitrogen and energy balances and growth performance of growing pigs

The traditional approach to formulating pig diets is based only on minimizing cost while meeting nutritional requirements and thus does not consider the environmental impacts associated with producing feed ingredients. To reduce the overall environmental impact of pork production, feed ingredients can be considered to formulate environmentally friendly diets. However, their potential effects on pig performance could decrease environmental benefits at the farm gate. The objective of this study was to quantify the effects of such eco-friendly pig diets on nitrogen (N) and energy (E) balances, the components of heat production (HP), and the performance of growing pigs. Digestibility coefficients of dry matter (84.5% vs. 88.2%, P &lt; 0.01) and N (80.4% vs. 86.3%, P &lt; 0.01) were significantly lower for the eco-friendly diet than the Control-diet (a commercial diet used in France). N excretion in feces was significantly higher for the group of pigs fed the eco-friendly diet than for the group fed the Control-diet (9.8 vs. 6.9 g/d, respectively, P = 0.01), while the N retention tended to be lower (27.8 vs. 30.3 g/d, respectively; P = 0.06). The metabolizable E:digestible E ratio did not differ between diets, but total HP was significantly lower for the eco-friendly diet group than for the Control-diet group (1,340 vs. 1,388 kJ/kg body weight0.60/d, respectively, P = 0.03). Using feed ingredients with lower environmental impacts, such as locally produced protein or co-products from wheat processing, is an effective way to decrease the environmental impacts of pig production. However, the nutritional composition of these eco-friendly ingredients could be overestimated, in particular the true digestibility of amino acids. This indicates the need to better estimate and consider the true digestibility of eco-friendly diets to decrease environmental impacts of livestock production without decreasing animal performance.

ano.nymous@ccsd.cnrs.fr.invalid (Francine de Quelen) 04 Sep 2024

https://hal.inrae.fr/hal-04687408v1

[hal-04675026] Exposure to natural stray currents of low voltage affects the behaviour and some stress biomarkers of weaned piglets

With the modernisation of pig breeding facilities, pigs may be exposed to both on-farm and off-farm sources of stray voltages. Data from ruminant species suggest that exposition to stray voltages may be a source of stress and impair animal welfare, but data are scarce for pigs. The aim of this study was to evaluate the impact of stray currents of voltages under 0.5 Volts in pig housing on piglet behaviours and some biomarkers after weaning. Two replicates of 820 piglets were reared in a farm naturally exposed to stray voltage for seven weeks. The difference in electrical potential between the floor and each drinker and feeder was measured every two weeks. Piglets exposed to high-voltage drinkers (HVD &gt; 125 mV) spent more time orally manipulating pen mates (P = 0.0031). They also spent more time lying inactive with open eyes (P = 0.0027) and less time nosing pen mates (P = 0.043), but these effects were influenced by the voltage in feeders (P = 0.0021 and P = 0.024, respectively). Piglets exposed to high-voltage feeders (HVF &gt; 50 mV) spent less time lying with their eyes closed (P = 0.024) and more time aggressing pen mates (P = 0.0081). Fifty days after entering the farm, blood hydroperoxide concentration was higher in piglets exposed to HVD (P = 0.039). The increase in socio-negative behaviours and oxidative stress in pigs exposed to stray voltages in pig housing suggested that stray voltages might have moderate detrimental consequences for piglets in post-weaning facilities.

ano.nymous@ccsd.cnrs.fr.invalid (Théo Nicolazo) 22 Aug 2024

https://hal.inrae.fr/hal-04675026v1

[hal-04618232] Association between body condition profiles, milk production and reproduction performance in Holstein and Normande cows

Body-condition dynamics are known to affect the different steps of reproduction in cattle (cyclicity, estrus expression, fertilization, embryo development). This has led to a widespread idea that there is an ideal-target optimal body condition, but no clear profile has yet been identified. Here we investigated the relationships between body condition score (BCS) profiles and reproductive performance in dairy cows. Data were from Holstein or Normande herds in 6 French experimental farms. In the Holstein breed, we discriminated 4 BCS profiles based on combining BCS at calving (Low: around 2.6 points, or High: around 3.3 points) with BCS loss after calving (Moderate (M): ≤ 1.0 points, or Severe (S): &gt; 1.0 points). The Low-M profile mostly included multiparous cows with higher milk yield and lower reproductive performance than cows in the 3 other profiles. Low-M cows that experienced abnormal ovarian activity had lower reproductive performance than their profile-mates. Moreover, 67% of Low-M cows kept the same profile at the following lactation. The High-S profile mostly included primiparous cows with lower milk yield and higher reproductive performance than cows in other profiles. In High-S cows, higher milk yields correlated to higher risk of failure to calf on first insemination. Moreover, 38% of High-S cows kept the same profile at the following lactation, and none changed to Low-M. The other 2 BCS profiles (Low-S and High-M) were intermediate in terms of milk yield and reproductive performance. In Normande, we discriminated 3 BCS profiles based on combining BCS at calving (Low: around 2.6 points, or High: around 3.5 points) with BCS loss after calving (Flat (F): flat with no loss, Moderate (M): around 0.5 points, or Severe (S): around 1.0 point). The Low-M and High-S profiles included cows with similar performance, even though High-S-profile cows showed better but not significantly different milk yield and reproduction performance. The High-F profile included cows that were more likely to experience abnormal ovarian activity and fail at first insemination than cows in other profiles. More than 50% of Normande cows with 2 successive lactations kept in the same BCS profile at the next lactation. Even though a low BCS at calving combined with severe BCS loss (more than 1 point) after calving was found to increase reproductive failure, there was no evidence of an optimal BCS profile for reproduction in dairy cows, and reproductive success or failure is multifactorial.

ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Dezetter) 20 Jun 2024

https://hal.inrae.fr/hal-04618232v1

[hal-04533050] Genetic background of body reserves in laying hens through backfat thickness phenotyping

In this study, we pursued three primary objectives: firstly to test and validate the phenotyping of backfat thickness as an indicator of the overall fatness of laying hens; secondly, to estimate genetic parameters for this trait; thirdly, to study the phenotypic and genetic relationships between this trait and other traits related to production and body composition. To address these questions, hens from two lines under divergent selection for residual feed intake, were phenotyped for body weight, body composition traits (backfat, total fat volume, and blood adipokines levels), and egg number. Linear mixed models enabled to estimate variance components and calculate genetic parameters. The two lines largely differed in body fatness: the efficient line had larger backfat and lower chemerin levels compared to the inefficient line. However, there were no significantly differences between the two lines concerning body weight, total fat volume, other blood adipokines levels (adiponectin, ghrelin, and visfatin), and egg production. The genetic parameter estimation revealed moderate heritability (0.38 and 0.42) for backfat and body weight, high heritability (higher than 0.80) for blood adipokines levels and low heritability (0.24 and 0.27) for egg production and total fat volume. The backfat and total fat volume were genetically highly and positively correlated (0.91). The body weight and total fat volume were also highly positively correlated (0.67). However, backfat and body weight were moderately positively correlated (0.39). The genetic correlation between backfat and egg number was moderate and negative. In conclusion, backfat could provide additional genetic information to that of the body weight as a selection criterion for body reserves. However, its correlation with laying performance should be taken into account to avoid undesired responses to selection

ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Bédère) 30 Apr 2024

https://hal.inrae.fr/hal-04533050v1

[hal-04878611] Sward species diversity impacts on pasture productivity and botanical composition under grazing systems

This research investigated the effect of intensive grazing on the annual and seasonal yield and botanical composition of three sward types: (1) Lolium perenne monoculture sward receiving 250 kg nitrogen (N) ha −1 year −1 (PRG 250 N); (2) Lolium perenne — Trifolium repens sward receiving 125 kg N ha −1 year −1 (PRGWC 125 N) and (3) a multispecies sward comprising eight species receiving 125 kg N ha −1 year −1 (MSS 125 N). Each sward type had its own farmlet of 20 paddocks and comprising 47 cows on 18.7 ha with each group of cows remaining on the same farmlet for the 2‐year study. Total yield (13,015 kg ha −1 year −1 of dry matter forage) did not differ among the three sward types, despite a substantial difference in chemical N fertiliser between PRG 250 N and both PRGWC 125 N and MSS 125 N. Average botanical composition of PRG 250 N comprised 994 g kg −1 grasses and 6 g kg −1 weeds. The PRGWC 125 N sward had 864, 134 and 2 g kg −1 of grasses, white clover and weeds, respectively, while the MSS 125 N had 671, 144, 180 and 5 g kg −1 of grasses, legumes, forbs and weeds, respectively. Despite considerable variation in the component species, nutritive values were relatively unaffected by sward type. Lower organic matter digestibility was observed on MSS 125 N compared to PRG 250 N and PRGWC 125 N (788, 801 and 799 g kg −1 , respectively). These results suggest that increasing sward diversity and reducing the use of chemical N fertiliser can maintain grass yield and nutritive value.

ano.nymous@ccsd.cnrs.fr.invalid (A. Jezequel) 10 Jan 2025

https://hal.inrae.fr/hal-04878611v1

[hal-04557071] Synthesis of milk components involves different mammary metabolism adaptations in response to net energy and protein supplies in dairy cows

Net energy for lactation (NEL) and metabolizable protein (MP) are the 2 main nutritional forces that drive synthesis of milk components. This study investigated mammary-gland metabolism in dairy cows in response to variations in the supply of NE L and MP. Four Holstein dairy cows were randomly assigned to a 4 × 4 Latin square design, in which each experimental period consisted of 14 d of dietary treatment. The diets provided 2 levels of NEL (low energy, 25.0 Mcal/d vs. high energy, 32.5 Mcal/d) and 2 levels of MP (low protein, 1,266 g/d vs. high protein, 2,254 g/d of protein digestible in the intestine) in a 2 × 2 factorial arrangement. Performance and dry matter intake (DMI) were measured during the last 5 d of each period, and the mammary net balance was measured on d 13 by collecting 6 sets of blood samples from the left carotid artery and left mammary vein. Mammary plasma flow was measured according to the Fick principle for Phe and Tyr. The mammary net balance of carbon equaled the uptake of nutrients expressed as carbon minus the output of lactose, fatty acids (FA) synthesized in the mammary gland, AA of milk protein, and glycerol-3P from triglyceride on d 13. Milk, lactose, fat, and protein yields increased when NE L and MP supplies increased. However, increasing the NEL supply increased FA synthesis more than increasing the protein supply did. In addition, FA secretion increased more than lactose secretion when the NE L supply increased. Increasing the NEL supply increased the left half-udder uptake of all major energy-yielding nutrients by increasing mammary plasma flow. However, nutrient uptake increased more than milk output did, which in turn increased carbon dioxide output. This increase in nutrient oxidation by the mammary gland decreased the mammary efficiency of nutrients utilization when the NE L supply increased. Increasing MP supply tended to increase glucose up-take through mammary clearance and increased mammary AA uptake with no change in mammary plasma flow. In addition, the protein supply did not change the mammary uptake of acetate or β-hydroxybutyrate. The increase in milk-component secretions in response to either NE L or MP supplies occurred through different metabolic adaptations (increase in mammary plasma flow vs. clearances, respectively). These results suggest that the nutrient use by the mammary gland is highly flexible, which helps in maintaining milk and milk-component yields even with limiting nutrient supplies.

ano.nymous@ccsd.cnrs.fr.invalid (Jean-Charles Anger) 24 Apr 2024

https://hal.inrae.fr/hal-04557071v1

[hal-04915076] Impliquer et former les apprenants à la valorisation de l'Herbe : exemple des actions menées en filière Caprine au Campus Terre et Paysages en Deux-Sèvres et à l’institut agro

La part d’herbe dans l’alimentation des chèvres est de l’ordre de 65 % dans la ration. C’est pourquoi il semble essentiel de former les futures générations à l’utilisation de celle-ci dans les élevages. Les apprenants du Campus Terres et Paysages Sud Deux-Sèvres, du lycée au BTS (Melle, 79) et les étudiants agronomes de niveau Master 2, spécialisés en sciences et productions animales de l’Institut Agro et du Master Sciences Animales pour l’Elevage de Demain (Rennes, 35) sont régulièrement sensibilisés à la valorisation de l’herbe dans les systèmes caprins du Grand-Ouest, lors d’enseignements de formats divers et adaptés au niveau de formation. Ces derniers s’appuient fortement sur les travaux et les collaborations avec le réseau REDCap et l’UMT SC3D. Ainsi, les lycéens s’initient régulièrement à la reconnaissance de plantes fourragères. Des séances sont également destinées sur l’étude des espèces les plus appréciées par les caprins. Un temps fort a été réalisé au sein de l’établissement au travers d’un partenariat pour identifier les adaptations techniques à mettre en œuvre au sein de l’exploitation caprine, support des travaux pratiques des lycéens. Pour les BTS agricoles en productions animales, la valorisation de l’herbe est traitée à l’échelle d’une exploitation agricole, prenant en considération le maximum de leviers pouvant être mis en place pour garantir la durabilité de l’entreprise. Quelque soit le public (lycéen – étudiant), l’objectif pédagogique vise à les former au vocabulaire herbager et à les sensibiliser aux diverses pratiques et conduites à mettre en œuvre dans les systèmes fourragers caprins pour faire face aux changements. Enfin, les étudiants de niveau Master ont étudié l’intérêt de l’herbe dans les systèmes caprins pour la transition agroécologique, et les freins et leviers d’action à une meilleure valorisation à l’échelle de la filière et de l’ensemble de ses acteurs.

ano.nymous@ccsd.cnrs.fr.invalid (Emilie Wimmer-Bonneau) 27 Jan 2025

https://hal.inrae.fr/hal-04915076v1

[hal-04536587] The fate of Cu and Zn along the feed-animal-excreta-effluent continuum in swine systems according to feed and effluent treatment strategies

Copper (Cu) and zinc (Zn) have negative environmental impacts as they accumulate in the soil after pig manure is spread. Cu and Zn are essential elements in pig nutrition but due to their low retention rate, more than 90% of ingested Cu and Zn are excreted. A better understanding of the behaviour of these elements throughout the animal-manure-soil continuum according to feed composition and manure management chain is thus required to propose alternative ways to reduce these environmental impacts. The aim of this study was to determine the fate of Cu and Zn throughout this continuum by studying the effect of Cu and Zn contents in animal feed and in the manure management chain based on anaerobic digestion and composting. Faeces were collected from 24 finishing pigs fed with 4 different Cu and Zn dietary levels and sources of supplementation. Samples of faeces were exposed to mesophilic anaerobic digestion or to 5-week composting with straw. Concentrations of Cu and Zn in the faeces were highly dependent on dietary supplies and ranged from 38 to 188 mg Cu/kg DM and from 191 to 728 mg Zn/kg DM. Degradation of a significant fraction of organic matter during treatment led to a significant increase in Cu and Zn concentration relative to the product's dry matter (DM) content, which. Cu and Zn concentrations relative to DM content were twice as high after treatment whatever the content and the form of Cu and Zn dietary supplementation. Otherwise, effluent treatment tended to reduce the possible availability of Cu and Zn in final organic products according to water-extractible contents. This study clearly shows that feed management is the main lever for reducing the amount of Cu and Zn amount in pig effluents and hence in the soil. Appropriate treatment could also facilitate the supply of organic fertilisers to areas with soil deficiency, but feed strategies need to be adapted to the treatment chain to enable the production of good quality organic products that respect EU regulations.

ano.nymous@ccsd.cnrs.fr.invalid (Emma Gourlez) 08 Apr 2024

https://hal.inrae.fr/hal-04536587v1

[hal-04741493] Qualité et authentification des produits animaux issus de l’agriculture biologique vs conventionnelle

Cette synthèse fait le point des connaissances sur les différentes dimensions de la qualité des produits issus d’élevages en agriculture biologique (AB) vs conventionnelle et sur les méthodes développées pour les authentifier. Les pratiques d’élevage étant variables, en AB comme en agriculture conventionnelle (AC), les résultats sont hétérogènes. Nous soulignons les pratiques à l’origine des différences observées, ce qui permet d’éclairer les conséquences des possibles trajectoires de l’agriculture biologique. De manière générale, la qualité est plus variable pour les produits AB, en lien avec un moindre niveau d’intrants et/ou une plus grande variabilité des conditions d’élevage, ainsi qu’une moindre sélection génétique pour le poulet de chair. Les propriétés améliorées sont la teneur en acides gras polyinsaturés, notamment oméga 3, plus élevée pour le lait de vache et les viandes AB, une réduction du risque de résidus de médicaments et d’apparition de résistances bactériennes aux antimicrobiens. Mais l’accès au plein air et la période d’élevage souvent plus longue augmentent la probabilité et la durée d’exposition des animaux aux éventuels contaminants environnementaux et le risque de leur bioaccumulation dans les produits. Nous identifions des antagonismes entre différentes dimensions de la qualité, notamment pour les viandes ovine et porcine. Les implications de la plus grande variabilité de la qualité des produits AB sur leur acceptabilité par les consommateurs et l’adaptation des procédés de transformation restent peu étudiées. La fiabilité des méthodes d’authentification se heurte à la variabilité des pratiques d’élevage, car elles se fondent sur les différences dans l’alimentation des animaux.

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Prache) 17 Oct 2024

https://hal.inrae.fr/hal-04741493v1

[hal-04850550] Utilisation de la semence sexée en production bovine

Le sexage de la semence de taureau (également validé chez diverses espèces de mammifères) est un procédé permettant de séparer les spermatozoïdes porteurs du chromosome X de ceux porteurs du Y. Le procédé actuel diffusé depuis 20 ans par l’entreprise Sexing Technologies repose sur le tri cellulaire, basé sur le contenu en ADN plus élevé pour les porteurs du X que du Y. La précision du sexage est d’environ 91 %. La part de marché de la semence sexée (femelle) atteint actuellement 12,5 % des premières inséminations. Son utilisation est très majoritairement en races laitières et plutôt sur génisses. Elle est la plus élevée en races jersiaise, montbéliarde et brune. Par rapport à la semence conventionnelle, elle s’accompagne d’une baisse de fertilité de l’ordre de 6 à 8 points de réussite, baisse qui tend à se réduire avec le temps. Aucun autre effet défavorable n’est observé. Le produit né ne présente pas d’augmentation du taux de néomutation dans son génome, ni de perte de performance significative sur aucun des caractères analysés. L’intérêt principal de la semence sexée se concrétise dans l’utilisation conjointe avec deux autres outils : tandis que la semence sexée est réservée à la part du troupeau assurant le renouvellement, dont le choix est bien plus précis avec génotypage et évaluation génomique, le croisement avec un taureau de race à viande assure une meilleure valorisation des produits non conservés pour le renouvellement. Ces trois techniques devraient donc continuer à se développer, surtout si la perte de fertilité liée au sexage est limitée.

ano.nymous@ccsd.cnrs.fr.invalid (Didier Boichard) 20 Dec 2024

https://hal.inrae.fr/hal-04850550v1

[hal-04661694] The use of computed tomography for in vivo estimation of reticulo-rumen and omasum contents in Alpine goats

Precise in vivo measurement of reticulo-rumen content (volume and mass) is required for the study of digestive processes. Rumen-cannulated animals have been classically used for this purpose, and less invasive alternatives are currently investigated to meet the replacement, reduction, and refinement (3Rs) ethical considerations in animal science. The objective was to compare in vivo reticulo-rumen and omasum volumes assessed by computed tomography (CT) scan with postmortem measurement of their respective digesta masses in dairy goats. Twenty Alpine dairy goats were scanned by CT, and the volumes of the reticulo-rumen and omasum were measured by CT image postprocessing. Goats were slaughtered immediately after CT scan and the masses of reticulo-rumen and omasum digesta were measured. Simple linear regressions were performed between volumes measured in vivo by CT and the corresponding digesta wet masses measured postmortem. Reticulo-rumen and omasum volumes determined by CT were significantly and linearly regressed against the corresponding digesta masses measured postmortem (R2 = 0.72 and 0.87, residual standard deviation = 1.18 and 0.06 kg, and residual coefficient of variation = 11% and 12%, n = 20 and 19, respectively). The use of CT is a promising noninvasive method to measure volume and estimate digesta masses of reticulo-rumen and omasum in small ruminants.

ano.nymous@ccsd.cnrs.fr.invalid (J.A.A. Pires) 25 Jul 2024

https://hal.inrae.fr/hal-04661694v1

[hal-04666195] Sequential window acquisition of all theoretical mass spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers

Recent advances in “omics” technologies have enabled the identification of new beef quality biomarkers and have also allowed for the early detection of quality defects such as dark-cutting beef, also known as DFD (dark, firm, and dry) beef. However, most of the studies conducted were carried out on a small number of animals and mostly applied gel-based proteomics. The present study proposes for the first time a Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomics approach to characterize and comprehensively quantify the post-mortem muscle proteome of DFD (pH24 ≥ 6.2) and CONTROL (5.4 ≤ pH24 ≤ 5.6) beef samples within the largest database of DFD/CONTROL beef samples to date (26 pairs of the Longissimus thoracis muscle samples of young bulls from Asturiana de los Valles breed, n = 52). The pairwise comparison yielded 35 proteins that significantly differed in their abundances between the DFD and CONTROL samples. Chemometrics methods using both PLS-DA and OPLS-DA revealed 31 and 36 proteins with VIP &gt; 2.0, respectively. The combination of different statistical methods these being Volcano plot, PLS-DA and OPLS-DA allowed us to propose 16 proteins as good candidate biomarkers of DFD beef. These proteins are associated with interconnected biochemical pathways related to energy metabolism (DHRS7B and CYB5R3), binding and signaling (RABGGTA, MIA3, BPIFA2B, CAP2, APOBEC2, UBE2V1, KIR2DL1), muscle contraction, structure and associated proteins (DMD, PFN2), proteolysis, hydrolases, and activity regulation (AGT, C4A, GLB1, CAND2), and calcium homeostasis (ANXA6). These results evidenced the potential of SWATH-MS and chemometrics to accurately identify novel biomarkers for meat quality defects, providing a deeper understanding of the molecular mechanisms underlying dark-cutting beef condition.

ano.nymous@ccsd.cnrs.fr.invalid (Laura González-Blanco) 01 Aug 2024

https://hal.inrae.fr/hal-04666195v1

[hal-04299155] Challenges and future perspectives for the European grading of pig carcasses – A quality view

This study sought to evaluate pig carcass grading, describing the existing approaches and definitions, and highlighting the vision for overall quality grading. In particular, the current state of pig carcass grading in the European Union (SEUROP system), its weaknesses, and the challenges to achieve more uniformity and harmonization across member states were described, and a broader understanding of pig carcass value, which includes a vision for the inclusion of meat quality aspects in the grading, was discussed. Finally, the noninvasive methods for the on-line evaluation of pig carcass and meat quality (hereafter referred to as pork quality), and the conditions for their application were discussed. As the way pigs are raised (especially in terms of animal welfare and environmental impact), and more importantly, their perception of pork quality, is becoming increasingly important to consumers, the ideal grading of pigs should comprise pork quality aspects. As a result, a forwardlooking "overall quality" approach to pork grading was proposed herein, in which grading systems would be based on the shared vision for pork quality (carcass and meat quality) among stakeholders in the pig industry and driven by consumer expectations with respect to the product. Emerging new technologies provide the technical foundation for such perspective; however, integrating all knowledge and technologies for their practical application to an "overall quality" grading approach is a major challenge. Nonetheless, such approach aligns with the recent vision of Industry 5.0, i.e. a model for the next level of industrialization that is human-centric, resilient, and sustainable.

ano.nymous@ccsd.cnrs.fr.invalid (Marjeta Čandek-Potokar) 22 Nov 2023

https://hal.inrae.fr/hal-04299155v1

[hal-04456512] Biopreservation of pre-processed fresh fish by bio-based coatings

The demand for pre-processed fresh fishery products is growing due to their convenience for subsequent processing and cooking. However, when improperly stored, the combined impacts of microbial deterioration and chemical reactions render them inedible, leading to significant food waste. To tackle this issue, several approaches have been proposed, among which bio-based edible coating provides a promising solution with a green approach. Edible coatings are formed of bio-based polymers, particularly using macromolecules such as proteins and polysaccharides that are biodegradable, edible, and can serve as carriers for naturally sourced active agents. Coatings made from a variety of proteins and polysaccharides with the main focus on gelatin and chitosan to preserve pre-processed fish products are discussed in this review along with their properties from the microbial, physicochemical, and sensory perspectives. Coating carriers and composite natural preservatives as well as formula optimization and investigation of coating mechanisms, challenges, and potential research prospects have been further reviewed. Overall, edible coatings with active substances can be used to efficiently preserve freshly pre-processed fish. The underlying mechanisms are multiple, and the applications were mainly for preventing or reducing moisture loss and purge accumulation, postponing microbial spoilage, and restricting the growth of pathogenic microorganisms, slowing and/or inhibiting lipid, protein, and pigment oxidation, and extending the shelf-life along with improving sensory properties. Edible coatings are viewed as ecologically friendly and sustainable packaging alternatives for the preservation of pre-processed fish products.

ano.nymous@ccsd.cnrs.fr.invalid (Don Hettiarachchige Udana Eranda) 19 Feb 2024

https://hal.inrae.fr/hal-04456512v1

[hal-04495509] Quel modèle pour couvrir ses besoins dans le cadre d’une alimentation durable ? Focus sur les protéines et le calcium

La société se trouve confrontée à de nouveaux enjeux planétaires rendant nécessaires des modifications de nos systèmes alimentaires. La SFN, avec le soutien financier de Bel, a organisé un webinaire sur les modèles de régimes alimentaires permettant de couvrir les besoins nutritionnels dans le cadre d’une alimentation durable, avec un focus sur les protéines et le calcium. Cette session s’est tenue en digital le 21 juin 2023.

ano.nymous@ccsd.cnrs.fr.invalid (Bernard Guy-Grand) 08 Mar 2024

https://hal.inrae.fr/hal-04495509v1

[hal-04604803] In-depth exploration of the high and normal pH beef proteome: First insights emphasizing the dynamic protein changes in longissimus thoracis muscle from pasture-finished Nellore bulls over different postmortem times

This study aimed to evaluate for the first time the temporal dynamic changes in early postmortem proteome of normal and high ultimate pH (pHu) beef samples from the same cattle using a shotgun proteomics approach. Ten selected carcasses classified as normal (pHu &lt; 5.8; n = 5) or high (pHu ≥ 6.2; n = 5) pHu beef from pasture finished Nellore (Bos taurus indicus) bulls were sampled from Longissimus thoracis muscle at 30 min, 9 h and 44 h postmortem for proteome comparison. The temporal proteomics profiling quantified 863 proteins, from which 251 were differentially abundant (DAPs) between high and normal pHu at 30 min (n = 33), 9 h (n = 181) and 44 h (n = 37). Among the myriad interconnected pathways regulating pH decline during postmortem metabolism, this study revealed the pivotal role of energy metabolism, cellular response to stress, oxidoreductase activity and muscle system process pathways throughout the early postmortem. Twenty-three proteins overlap among postmortem times and may be suggested as candidate biomarkers to the dark-cutting condition development. The study further evidenced for the first time the central role of ribosomal proteins and histones in the first minutes after animal bleeding. Moreover, this study revealed the disparity in the mechanisms underpinning the development of dark-cutting beef condition among postmortem times, emphasizing multiple dynamic changes in the muscle proteome. Therefore, this study revealed important insights regarding the temporal dynamic changes that occur in early postmortem of high and normal muscle pHu beef, proposing specific pathways to determine the biological mechanisms behind dark-cutting determination.

ano.nymous@ccsd.cnrs.fr.invalid (Iliani Patinho) 07 Jun 2024

https://hal.inrae.fr/hal-04604803v1

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HAL : Dernières publications

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[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

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

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

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

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

[hal-04617235] CowPILOT -Piloter la note d'état corporel pour optimiser la reproduction des vaches laitières

[hal-04653317] Quels défis au développement de la production porcine en agriculture biologique en France ?

[hal-04309414] Assessment of beef sensory attributes and physicochemical characteristics: A comparative study of intermediate versus normal ultimate pH striploin cuts

[hal-04619014] From the biochemical pieces to the nutritional puzzle: using meta-reactions in teaching and research

[hal-04773240] Impact of genome build on RNA-seq interpretation and diagnostics

[hal-04628706] Effects of parity and week after calving on the metabolic, redox and immune status of dairy cows

[hal-04448073] Bioaccessibility and associated concepts: Need for a consensus

[hal-04703322] Interaction between drinker density and cow social dominance affects drinking behavior

[hal-04549544] Porcine ear necrosis is associated with social behaviours in weaned piglets

[hal-04283002] Nitrogen offset potential in a multi-year farmlet-scale study; milk and herbage production from grazed perennial ryegrass/white clover swards

[hal-04586224] Strategies of maize silage supplementation of grazing dairy cows: Effects on milk production, pasture intake, grazing behaviour and methane emissions

[hal-04568409] Data-independent acquisition-based SWATH-MS proteomics profiling to decipher the impact of farming system and chicken strain and discovery of biomarkers of authenticity in organic versus antibiotic-free chicken meat

[hal-04415987] Meat Omics: Trends and applications of Omics strategies in meat research

[hal-04664474] Effects of natural oral alternatives to parental iron supplementation on haematological and health-related blood parameters of organic piglets

[hal-04677211] Organic rearing of non-castrated male pigs: welfare indicators, carcass traits, pork quality and boar taint in Duroc and Pietrain crossbreds

[hal-04998084] Pourrait-on parvenir à une alimentation saine dans le monde en 2050 sans expansion des terres agricoles ?

[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

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

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

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

[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

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

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

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

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

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

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

[hal-04510660] Sensitivity analysis of the INRA 2018 feeding system for ruminants by a one-at-a-time approach: Effects of dietary input variables on predictions of multiple responses of dairy cattle

[hal-04582488] Evidence of stable preferential affiliative relationships in the domestic pig

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