Scientific publication

[hal-05494620] Designing and evaluating livestock farming systems that promote biodiversity: example of a student project

The article presents a project carried out at Institut Agro Rennes Angers for agronomy engineering students and second-year master's students specialising in animal production. The 24-hour pedagogical framework aimed at designing resilient and acceptable livestock systems that promote biodiversity. The objective was to develop skills in systemic analysis and multi-criteria assessment through collaborative work. The students used LEGO® to model livestock systems and evaluate transformation scenarios for a mixed farming operation in the Rennes region. Two scenarios were proposed and assessed using a grid created by the students. The results show that the scenarios strengthen the connection between society and biodiversity. Feedback from teachers highlights the importance of project-based learning and the need to adapt teaching to students' profiles.

ano.nymous@ccsd.cnrs.fr.invalid (Justine Faure) 05 Feb 2026

https://hal.inrae.fr/hal-05494620v1

[hal-05496839] Effects of Different Feeding Methods on Growth Performance, Enzyme Activity, Rumen Microbial Diversity and Metabolomic Profiles in Yak Calves

Yaks are important for the ecology and economy of the Qinghai-Tibetan Plateau. The growth of the yak industry depends on sustainable and accelerated growth of calves, sustaining herd reproduction and production systems. Yak calves born in the summer months of June and July are faced with a heightened risk of winter mortality. Exclusive traditional, natural feeding prolongs the suckling period, and this leads to a series of problems due to the harsh high-altitude environment, such as inadequate nutrition leading to retarded growth and an imbalanced herd structure. To enhance growth performance and breeding efficiency, 12 male calves of similar weights (68.53 ± 6.41 kg) were randomly assigned to a control group (suckle the dam (SU)) or an experimental group (early weaning with full feeding, concentrate and oat hay at a 7:3 ratio (CO)). The results showed that compared with suckling, early weaning with full feeding significantly improved the growth performance, volatile fatty acids and digestive enzyme activity. The abundance of the Firmicutes was reduced, but there was an increased abundance of Bacteroidetes, which affected the rumen metabolome. In conclusion, early weaning with full feeding improves growth performance, promotes rumen fermentation and carbohydrate degradation, reduces the diversity and richness of rumen microbial flora and alters the content and pathways of metabolites in yak calves. These factors contribute to the growth and market readiness of yak calves born in June and July, accelerate herd turnover and enhance the production efficiency of grazing yaks.

ano.nymous@ccsd.cnrs.fr.invalid (Hongli Wang) 06 Feb 2026

https://hal.inrae.fr/hal-05496839v1

[hal-05479184] The proteome of goat meat exudate: Temporal proteomics as a new way to uncover the underlying mechanisms of meat tenderization

This study applied shotgun proteomics to investigate the temporal changes in goat meat exudate and elucidate the biochemical mechanisms underlying postmortem aging. Exudates were collected from vacuum packaged goat Longissimus thoracis muscles at 24, 48 and 72 h postmortem. A total of 823 proteins were identified and quantified, of which 188 were differentially abundant: n = 60 between 24 h vs. 48 h, n = 56 between 48 h vs. 72 h and n = 168 between 24 h vs. 72 h. Comparative analyses revealed distinct temporal release patterns, with catalytic and ATP-metabolic proteins predominating early postmortem (17%), structural and contraction-related proteins peaking between 48 h and 72 h (39%), and binding, transport, and calcium homeostasis proteins (27%), as well as extracellular matrix (ECM) and matrisome components (14%), accumulating later. Chaperones including heat shock proteins and proteolytic and related enzymes were consistently released from 24 h to 72 h, but in lower percentages (5% and 4%, respectively). Overlap analysis identified 14 core proteins including FLNC, TNNI2, TNNC2, PDLIM7, TMOD4, MYOZ1, MYBPC1, MYOM2 (muscle contraction and structure), DYSF, EIF4G2, PPARGC1A (binding, transport and calcium homeostasis), DCN, OGN, and IGFALS (matrisome and ECM associated proteins), shared across all time points, which mapped to five significantly enriched pathways, primarily myofibril assembly and muscle system processes. These findings provide the first comprehensive proteomic profile of goat meat exudate, demonstrating its potential as a non-invasive source for monitoring postmortem biochemical changes and meat tenderization dynamics, ultimately offering insights to improve meat quality.

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 27 Jan 2026

https://hal.inrae.fr/hal-05479184v1

[hal-05487060] IPEC-J2 as a cellular model for studying intestinal mucus

Mucus in the proximal small intestine serves critical protective and transport functions, regulating nutrient absorption to enterocytes. The porcine jejunal epithelial cell line IPEC-J2 is widely used to study epithelial barrier function, yet its capacity to express mucins remains inconsistently described. This study aimed to investigate the ability of IPEC-J2 cells to express mucins under various culture conditions: 5% or 10% porcine serum (5PS, 10PS), with agitation (5PSAg and 10PSAg) and air-liquid interface (ALI). Mucus production was assessed using functional and structural approaches. Expression of secreted mucin MUC2 and goblet cell marker TFF3 was limited under most conditions but markedly enhanced in ALI and 5PSAg cultures. Immunohistochemistry revealed membrane-associated mucins (MUC3, MUC13) although MUC13 localisation differed between IPEC-J2 and jejunal tissue. Flow cytometry revealed that ~8% of IPEC-J2 cells expressed MUC2 in 5PSAg, comparable to the proportion of jejunum’s goblet cells in vivo (~5%). This study demonstrated that IPEC-J2 cells can differentiate into mucus-secreting cells under specific culture conditions, and they are a suitable in vitro model for investigating interactions between mucus and food components, providing a valuable tool for nutritional research.

ano.nymous@ccsd.cnrs.fr.invalid (Frédéric Dessauge) 31 Jan 2026

https://hal.science/hal-05487060v1

[hal-05441629] Macronutrient and energy metabolism changes in domestic cats when fed cornstarch, whey protein, and, poultry fat

There is a lack of knowledge available on how cats adjust their macronutrient partitioning due to the consumption of single-macronutrient meals. The objective of this study was to evaluate consumption of a single meal of ingredients that contained foods of strictly carbohydrates (CHO), fat (FAT) or protein (PRO), on energy expenditure (EE) and macronutrient metabolism in cats. Ten domestic shorthair adult cats (1·9 years; 4·12 kg) were fed 22–24 g of chicken fat (FAT), 56–62 g of whey protein solution (PRO) or 54–56 g of cornstarch solution (CHO) for a single day in a randomised complete block design. Indirect calorimetry was conducted for 24 h post-feeding. Mean average EE over 24 h was highest in cats fed PRO (44 kcal/kg BW) and FAT (43 kcal/kg BW) compared with that in cats fed CHO (42 kcal/kg BW; P &lt; 0·01). During 0 to 4 h, cats fed FAT had greater EE (49 kcal/kg BW), suggesting that cats respond to oxidising more dietary fat over protein in the early postprandial stage. Mean 24 h respiratory quotient (RQ) was greatest for cats fed CHO (0·76) followed by PRO (0·75) and FAT (0·74; P &lt; 0·05). During 4 to 8 h, the RQ of cats fed PRO was the greatest (0·77), suggesting that cats initially increase gluconeogenesis from amino acids for subsequent glucose oxidation. In comparison to omnivores and herbivores, obligate carnivores have unique responses to single macronutrient intake, where they apparently generate energy from carbohydrate metabolism and rely more on gluconeogenic precursors.

ano.nymous@ccsd.cnrs.fr.invalid (Sophia Jantzi) 05 Jan 2026

https://hal.inrae.fr/hal-05441629v1

[hal-05497134] Comparative yak and Simmental rumen microbiome-metabolome across lactation stages: Implications for milk nutritional superiority

Both yaks and Simmental are dual-purpose highland varieties, but the mechanisms behind the differences in their milk production are not yet fully understood. This study compared milk composition, rumen microbial communities, and metabolomes across a range of lactation stages for both breeds. Yak milk yields were lower and it had higher levels of fat, protein, long-chain and polyunsaturated fatty acids, key amino acids, and essential minerals than Simmental milk. The microbial community of yak rumen exhibited unique characteristics, with the Family_XIII_AD3011_group persistently enriched and positively correlated with rumen fermentation parameters and milk quality, and the content of glutamate and glutamine in yak rumen was higher than in Simmental and positively correlated with milk quality. Therefore, key microorganisms and metabolites in yak rumen are crucial factors for high-yield dairy production, providing new insights to enhance milk production in ruminant dairy cattle.

ano.nymous@ccsd.cnrs.fr.invalid (Peng Jiao) 06 Feb 2026

https://hal.inrae.fr/hal-05497134v1

[hal-05440749] Effects of fermented total mixed diets on growth performance, nutrient digestibility, serum indicators, rumen fermentation and rumen microbiota in Tibetan sheep

The aim of this paper was to investigate the effects of unfermented and fermented total mixed ration (FTMR) on growth performance, nutrient digestibility, serum indices, rumen fermentation and rumen flora structure of Tibetan lambs. Twenty healthy male Tibetan lambs randomly divided into 2 treatment groups with 10 lambs/treatment. The TMR group was fed a non-fermented total mixed ration and the FTMR group was fed a fermented total mixed ration. The average daily gain was not statistically significant (P = 0.487). The total tract digestibility of neutral detergent fiber (NDF) was significantly higher (P = 0.005) in FTMR as compared TMR. The serum levels of total cholesterol (TC) (P= 0.001), low-density lipoprotein cholesterol (LDL-C) (P= 0.002), high-density lipoprotein cholesterol (HDL-C) (P= 0.019), creatinine (CR) (P= 0.047) and blood urea nitrogen (BUN) (P= 0.041) were significantly lower in FTMR group as compared to TMR. There were no significant differences (P &gt; 0.05) in Ace index, Chao1 index, Simpson index and Shannon index of Tibetan sheep in FTMR group compared to TMR group. The relative abundance of Firmicutes and Euryarchaeota was significantly higher in FTMR group than in the TMR group (P &lt; 0.05). The relative abundance of Prevotella was significantly higher, Methanobrevibacter was significantly lower in the FTMR group. In conclusion the FTMR can be fed to lambs without any adverse effects on serum chemistry, additionally FTMR improves average daily gain by 12 %, increase in Prevotella abundance and decrease in Methanobrevibacter.

ano.nymous@ccsd.cnrs.fr.invalid (Xinjian Lou) 05 Jan 2026

https://hal.inrae.fr/hal-05440749v1

[hal-05364836] Green extraction of undenatured type II collagen from goat cartilage by deep eutectic solvents: An integrated in silico and experimental study

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ano.nymous@ccsd.cnrs.fr.invalid (Wei Wu) 14 Nov 2025

https://hal.inrae.fr/hal-05364836v1

[hal-05410799] Data Paper: HotPig, a behavioural dataset of pigs under heat stress

The widespread use of videos in modern indoor livestock facilities coupled with the availability of efficient and low-cost computer vision algorithms provides strong incentives for continuously monitoring farm animal behaviour. Deciphering how pigs behave when experiencing prolonged heat stress is particularly important for animal welfare, as it helps us to better understand how animals use various thermoregulation and heat dissipation mechanisms. Data were collected on 24 pigs that were video-monitored day and night under two contrasted conditions: thermoneutral (TN, 22 °C) and heat stress (HS, 32 °C). All pigs were housed individually and had free access to an automatic feeder delivering pellets four times a day, and to water. After acquisition, videos were processed using YOLOv11, a real-time object detection algorithm that uses a convolutional neural network (CNN), to extract the following behavioural traits: drinking, willingness to eat, lying down, standing up, moving around, curiosity towards the littermate housed in the neighbouring pen, and contact between the two animals (cuddling). A minute frequency sampling rate was applied (each minute corresponds to 150 frames processed) for a continuous period of 16 days, spanning the two different thermal conditions (9 days on TN, 6 days on HS, 1 day back to TN). Consistency with the automatic electronic feeder’s data (also provided) was thoroughly checked. The dataset allows quantitative criterion to be analysed to decipher inter-individual differences in animal behaviour and their dynamic adaptation to heat stress. This dataset can be used to train any machine learning methods for behaviour prediction from videos in conventional growing pigs.

ano.nymous@ccsd.cnrs.fr.invalid (Louis Bonneau de Beaufort) 11 Dec 2025

https://hal.inrae.fr/hal-05410799v1

[hal-05441091] Clustering of the dynamics of milk lactose content throughout lactation and identification of variation factors

Interest in milk lactose content (LC) has grown due to its potential as an indicator of udder health and metabolic disorders in dairy cattle. However, the variability of LC dynamics during lactation remains poorly described, and a better characterization of these dynamics could clarify our understanding of LC variations among cows, and potentially those due to udder health and metabolismrelated variations. The aim of this study was to identify distinct patterns of LC dynamics and assess their environmental and genetic determinants, as well as their phenotypic and genetic associations with milk yield, Na, K, SCC, and their phenotypic associations with fat-toprotein ratio (FPR) and BHB. A total of 1,980,693 testday records were analyzed from 183,150 Holstein cows in 2,239 herds across France. At least 2 records in the first 90 d and 4 records between 7 and 300 DIM were available for each cow, averaging 7.3 records per cow. Functional principal component analysis was used to describe LC dynamics throughout lactation. This approach involved smoothing the LC curves for each cow and then summarizing their overall shape using 3 principal components: average LC throughout lactation, LC slope and LC at mid lactation. Dynamics of LC were grouped into 6 clusters. Three clusters (3, 4, and 5) represented 86% of the data and shared similar dynamics with a flat trend after an initial rise in LC at early lactation and different average LC levels (cluster 3: 4.68%, cluster 4: 5.10%, cluster 5: 4.86%). Environmental and intrinsic animal factors explained 69% of the variability in average LC among clusters 3, 4, and 5, with cow parity and LC EBV identified as the main intrinsic contributors. The remaining clusters (1, 2, and 6) showed LC levels similar to the mean of the dataset (LC: 4.88% ± 0.19%) until 150 DIM. Thereafter, 2 clusters displayed negative LC slopes (cluster 1: -0.13% and cluster 6: -0.07% per month of lactation) and one a positive slope (cluster 2: +0.05% per month). Fifteen percent of the variations in the LC slopes of clusters 1, 2, and 6 was explained by environmental factors, mainly calving season: winter calving was associated with clusters 1 and 6, and summer calving with cluster 2. The remaining unexplained negative slope variation from mid lactation onward appears to be related to distinct patterns characterized by higher FPR and milk BHB concentrations preceding the decline in LC, followed by increased SCC after 150 DIM. The lactosebased clusters also corresponded to distinct curves for milk sodium contents, and there were slight correlations for potassium levels, indicating different equilibria between the 3 main osmotic agents (lactose, sodium, and potassium), probably to maintain milk osmolarity. As a result, LC clustering uncovered meaningful physiological profiles: average LC levels were primarily driven by parity and genetics, whereas LC slope variations appeared to be more sensitive to environmental and health-related factors. These findings support the potential of LC dynamics, accessible via mid-infrared spectra, to serve as functional biomarkers for udder health and, potentially, of metabolic status.

ano.nymous@ccsd.cnrs.fr.invalid (Auxane Hamon) 05 Jan 2026

https://hal.inrae.fr/hal-05441091v1

[hal-05455359] Method: Modelling resource acquisition and allocation – extension and calibration of a cow model to a sheep

Simulation models are suitable to investigate how complex systems respond to changes. This is of particular interest regarding animal feed efficiency as this trait must be evaluated throughout the entire lifetime and thus is affected by trade-offs between physiological functions. The aim was to extend and calibrate the dynamic, mechanistic simulation model “Acquisition and Allocation” (AQAL) from dairy cows to reproductive ewes. This model was originally developed for investigating the effects of resource acquisition and allocation potentials on feed efficiency but also allows investigation of trade-offs between life functions. The model represents an individual female from birth to death or herd exit and uses four input parameters to describe the resource acquisition ability and allocation potential. The obtained energy is split between life functions such as maintenance, growth, reproduction and lactation. By including reproductive management rules, it allows for shifts between physiological stages, which then feedback and affect the current acquisition ability and resource allocation. To adapt the model to a reproductive ewe, we have included a litter size effect, an acquisition capacity linked to gestation, and a seasonal conception probability. The litter size is influenced by the proportion of fat in empty body weight at conception, and it affects the acquisition linked to gestation, the allocation to gestation and the allocation to lactation. We also incorporated the energetic costs of the gravid uterus depending on litter size. We use three different acquisition-allocation profiles to test the consistency of the litter size effect. We show that the model simulates consistent lifetime trajectories of reproductive ewes and that the effect of litter size adequately reflects the demands of increased litter size within the different acquisition/allocation profiles.

ano.nymous@ccsd.cnrs.fr.invalid (L.S. Kierkegaard) 13 Jan 2026

https://hal.inrae.fr/hal-05455359v1

[hal-05422931] The effect of increasing sward species diversity on enteric methane emissions from Holstein-Friesian and Holstein-Friesian × Jersey crossbred dairy cows in a rotational grazing system

An experiment was conducted to investigate the effect of sward system and dairy cow breed on enteric methane emissions from spring-calving grazing dairy cows using GreenFeed technology (C-lock Inc.). The study comprised 3 sward systems: a perennial ryegrass (Lolium perenne L.) monoculture receiving 250 kg N/ha per year (PRG), a perennial ryegrass white clover (Trifolium repens L.) sward receiving 125 kg N/ha per year (PRGWC), and a multispecies sward sown with grasses, legumes and herbs receiving 125 kg N/ha/yr (MSS). Each sward system had its own herd of dairy cows on a total area of 18.7 ha divided into 20 paddocks. Each herd comprised Holstein-Friesian (HF) purebred and HF × Jersey crossbred (JFX) animals which were divided equally across each sward system. Milk production and methane emissions were measured from mid-May to mid-October, and DMI and rumen characteristics were measured in late-July and early-October (165 and 228 DIM, respectively). Milk solids (milk fat + protein; MSo) was greatest for cows grazing MSS due to an associated increase in DMI. The greatest average daily methane output across the study was observed for cows grazing PRGWC (311 g/d) while those grazing PRG and MSS were similar (294 and 297 g/d, respectively). Methane intensity (g methane/kg MSo) was reduced for the MSS cows compared with both the PRG and PRGWC cows (208, 217, and 219 g/kg MSo respectively). The lowest methane yield (methane per kg of DMI) was also observed for the MSS cows (15.5 g/kg), whereas there was no difference between the PRG and PRGWC cows (17.6 and 17.7 g/kg, respectively). Greater VFA concentrations were observed for both the MSS and PRG cows compared with the PRGWC cows, whereas the MSS cows had a greater butyrate proportion compared with the cows grazing both other sward systems. Breed also had a significant effect on both milk and methane production characteristics with JFX animals having increased fat and protein concentration and increased MSo production compared with HF. The JFX cows also had reduced BW. Breed had no effect on DMI or methane yield, but JFX also had improved feed efficiency, both per kilogram of DMI and per kilogram BW. The HF cows had an increased methane intensity (223 g/kg MSo) compared with JFX (207 g/kg MSo). Rumen ammonia concentration and acetate-to-propionate ratio were increased for JFX, whereas VFA propionate proportion was decreased, and butyrate proportions were increased compared with HF. The results of this study highlight the potential for more diverse swards and Holstein-Friesian × Jersey crossbreeding to reduce enteric methane emission intensity within pasture-based dairy systems.

ano.nymous@ccsd.cnrs.fr.invalid (C. Dwan) 18 Dec 2025

https://hal.inrae.fr/hal-05422931v1

[hal-05494387] An integrated in silico, in vitro, and machine learning pipeline for rapid discovery of antioxidant peptides and co-product lipids from goat liver

Goat liver abundant in high-quality protein is a by-product during meat processing, which is currently underutilized. Traditional enzymatic hydrolysis and screening methods suffer from low extraction efficiency and unstable yields. This study aims to develop an integrated pipeline for rapid discovery of antioxidant peptides co-product lipids from goat liver. Papain was selected as the optimal protease, with hydrolysis time of 5 h. Peptidomics and machine learning enabled identification and activity-based prediction of antioxidant peptides, leading to discovery of two novel antioxidant peptides (WGF and GPLF) with IC₅₀ values for DPPH radical scavenging activities of 1244 μM and 2534 μM, respectively. Molecular docking and dynamics simulations indicated the stable binding of both peptides to Keap1 via hydrogen bond, van der Waals force, and water-mediated interactions, suggesting potential antioxidant activity through Keap1-Nrf2 pathway. GC–MS analysis revealed that saturated and unsaturated fatty acids accounted for 25.33 ± 0.02% and 74.67 ± 0.04%, respectively. This study develops an integrated pipeline for extraction of antioxidant peptides and co-product lipids from goat liver, and contributes to the future development of bioactive peptide-based packaging systems.

ano.nymous@ccsd.cnrs.fr.invalid (Dongjing Wu) 05 Feb 2026

https://hal.inrae.fr/hal-05494387v1

[hal-05301879] Monitoring changes in body reserves in gestating dairy heifers with 3D imaging technology: a potential tool to prevent early culling?

The use of 3-dimensional (3D) imaging technology to monitor dairy cows enables the acquisition of morphological, surface, and volume data, which can then be employed to estimate body weight (BW) or body condition score (BCS). Accurate tracking of morphological changes in these animals could lead to better management of the gestation and parturition periods, which are especially critical for primiparous cows. Indeed, BCS values that are too low or too high are associated with reproductive disorder and/or early culling after calving. To assess the potential utility of precise and continuous recordings in gestating animals, we studied BW and morphological changes in 13 gestating Holstein heifers from 3 mo of gestation until the start of lactation. BCS was estimated using both 3D imaging technology (BCS3d) and manual scores determined by trained technicians (BCSm). From mid-April (start of experiment) until the end of August (start of calving season) in 2021, average BW increased from 515 (±standard deviation, 40.5) kg to 604 (±49.4) kg, while average BCS3d decreased slightly, from 2.50 (±0.19) to 2.32 (±0.30). A similar decrease was noted for BCSm, from 2.63 (±0.19) to 2.11 (±0.24). Linear regression between the 2 estimates of BCS indicated that the technicians usually gave a higher BCS value than the imaging device (BCS3d = 0.97 x BCSm; R 2 = 0.58). Because of the small number of observations and the fact that the experiment ended after the first calving, we are not able to draw any conclusions about the long-term effects of changes in BCS during gestation on the overall longevity of cows. Nevertheless, using our system it was possible to detect small changes in BCS during the first gestation of nulliparous cows. Such information could be employed to adapt the diet of heifers to avoid inadequate, insufficient, or excessive fatness at parturition, thus potentially ameliorating calving difficulties (dystocia) and poor starts to lactation. The precise evolution of BCS in the pregnant heifer is of great interest, and the next step will be to examine larger groups of animals to shed more light on the potential value of this technology.

ano.nymous@ccsd.cnrs.fr.invalid (Yannick Le Cozler) 07 Oct 2025

https://hal.science/hal-05301879v1

[hal-05384038] Feed restriction has no effect on milk lipolysis, although it results in a marked reduction in milk lipoprotein lipase activity in dairy goats

Climate change pressures livestock feeding systems by reducing the availability and nutritional quality of forages and pasture. Previous studies have shown that dietary restriction impacts milk lipolysis (i.e. the hydrolysis of milk fat by lipoprotein lipase (LPL)) in cows and ewes. However, data regarding the effects of feed restriction on milk lipolysis in goats are scarce. Therefore, the present study aims to investigate the impact of feed restriction on goat milk composition, with a specific focus on lipolysis, LPL activity and milk fat characteristics. For that purpose, two groups of 12 dairy goats (121 ± 7 days in milk) balanced with regard to the αs1-casein (CSN1S1) genotype (7 A/A goats, corresponding to strong CSN1S1 genotypes and 5 O/O goats, corresponding to null CSN1S1 genotypes) received either a control diet (100 % of the dry matter intake (DMI) ad libitum: non-restricted; NR) or the experimental diet (65 % of the DMI ad libitum: restricted; R) according to a 2 × 2 cross-over design. Dietary restriction did not significantly affect either lipolysis levels in milk or milk fat globule size, whereas a sharp decrease was observed in milk LPL activity within the short-term restriction window tested. A genotype effect was evidenced for milk lipolysis (copper soap method), milk fat content and milk fat yield. No genotype × diet effect was observed with regard to lipolysis or LPL activity under feed restriction. This work provides a solid framework for follow-up lipidomic and proteomic studies to gain a comprehensive understanding of the regulation of the lipolytic system in goats.

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Bernard) 26 Nov 2025

https://hal.inrae.fr/hal-05384038v1

[hal-05493038] OasYs, a dairy cattle system based on the diversity of forage resources

Since 2013, the OasYs system experiment has been setting up a low-input dairy cattle system in a drying zone. The main hypothesis is that the diversity of system components and their functions can be a means of reconciling the objectives of production, environmental performance and resilience to climatic hazards. Grasslands and crops were diversified in terms of species, mixtures and production periods, with three rotations distributed across the cropping plan according to their distance from the milking parlour, to give priority to grazing. The diversification of grasslands and the introduction of annual forage dedicated to the difficult seasons of summer, autumn and winter have extended the grazing period. The proportion of grazed forage in the dairy herd's annual diet (50%) is much higher than in conventional dairy systems.

ano.nymous@ccsd.cnrs.fr.invalid (Sandra Novak) 04 Feb 2026

https://hal.inrae.fr/hal-05493038v1

[hal-05520191] Values shared by journals of learned societies, associations and scientific institutions in animal science

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ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 20 Feb 2026

https://hal.inrae.fr/hal-05520191v1

[hal-05359970] Economic performance of 3 farm systems differing in sward species diversity and nitrogen fertilization level across a range of future economic scenarios

The objective of this study was to compare the economic performances of 3 pasture-based systems: a perennial ryegrass (Lolium perenne L.; PRG) receiving 250 kg N/ha (PRG-250N); a PRG-white clover (Trifolium repens L.; WC) receiving 125 kg N/ha (PRGWC-125N); and a multispecies (MSS) sward composed of grasses, legumes, and herbs receiving 125 kg N/ha (MSS-125N). Sward and animal performances were measured over 3 years in a system-scale study involving 3 farmlets at Teagasc Moorepark, Ireland. Subsequently, based on the physical data collected, an economic performance of each sward system was evaluated using current output prices and input costs in the Moorepark Dairy Systems Model. The economic results show similar net farm profitability for both PRG-250N and PRGWC-125N. The PRGWC-125N system had lower costs linked to fertilizer; however, more grass silage was purchased due to reduced grass production. The MSS-125N system outperformed both PRG-250N and PRGWC-125N in net farm profitability (+€167/ha and +€148/ha, respectively) due to increased milk output coupled with reduced N fertilizer use. Sensitivity analyses indicated that MSS-125N was the most profitable system under varying milk and fertilizer prices. Given the variability of clover and herb establishment between paddocks for PRGWC-125N and MSS-125N, an increase in the reseeding frequency and oversowing frequency was simulated and resulted in reductions in farm profitability for both systems (€-14.25/ha per year and €-28.25/ha per year, respectively). This study underscores the potential of increasing sward species diversity using clovers and herbs to sustain economic performances of pasture-based systems while reducing fertilizer N reliance and enhancing animal performance. Further long-term research is required to investigate persistence and economic viability of both PRGWC and MSS under varying climatic and management conditions to validate the longer-term results of the first 3 years of the study.

ano.nymous@ccsd.cnrs.fr.invalid (A. Jezequel) 12 Nov 2025

https://hal.inrae.fr/hal-05359970v1

[hal-05444004] Les technologies numériques en élevage : de la mesure à l’évaluation comportementale du bien-être de chaque animal

Le bien-être des animaux est une notion difficile à définir car se référant à un phénomène complexe, intrinsèquement liée à la perception qu’a l’individu de son environnement. Ne pouvant être mesuré directement, le bien-être est évalué à partir de la détermination et la quantification d’indicateurs spécifiques. Ces indicateurs, dont les variations sont associées à différents états de bien-être, doivent être combinés en fonction du contexte d’évaluation. Le comportement animal, reconnu comme une des clés pour l’évaluation du bien-être, peut changer face aux variations de l’environnement d’élevage, telles que l’accès au pâturage, influençant à la fois la routine et la dynamique de l’occupation de l’espace des animaux. L'analyse de ces changements comportementaux permet de définir de nouveaux indicateurs, facilitant l’évaluation de l’impact positif ou négatif de ces modifications environnementales sur le bien-être des animaux. L’intégration des technologies de capteurs, de modèles mathématiques et de l’intelligence artificielle ouvre de nouvelles perspectives pour un suivi longitudinal des activités, des dynamiques spatiales et d’autres paramètres d’intérêt tout au long du cycle de vie des animaux. Par exemple, les algorithmes de classification supervisée ont permis d’associer les données brutes fournies par des capteurs aux comportements d’intérêt, tandis que les algorithmes non supervisés devraient révéler de nouveaux indicateurs en lien avec le bien-être des animaux. Cet article met en lumière les opportunités offertes par les technologies numériques émergentes. Nous nous concentrons sur l’évaluation comportementale et son rôle crucial dans l’évaluation du bien-être, en présentant trois études de cas : 1) pour distinguer les problèmes liés à la santé, au stress thermique et à la reproduction chez les vaches laitières, 2) pour prévoir la boiterie chez la vache laitière et 3) pour étudier des émotions chez les porcs. Enfin, nous soulignons l’importance d’une collaboration interdisciplinaire étroite entre éthologistes, physiologistes, mathématicien(ne)s et informaticien(ne)s pour favoriser le développement de ce domaine émergent que nous désignons sous le terme d’« éthologie numérique ».

ano.nymous@ccsd.cnrs.fr.invalid (Masoomeh Taghipoor) 06 Jan 2026

https://hal.inrae.fr/hal-05444004v1

[hal-05449736] Apports et limites des démarches participatives et de coconception pour améliorer le bien-être de l’animal en élevage

L’amélioration du bien-être des animaux en élevage, essentielle pour la durabilité de l'élevage, suscite des questionnements et des débats, parfois vifs, notamment parmi les professionnels de l’élevage, la recherche, les pouvoirs publics et les citoyens. Les démarches participatives et de coconception qui visent à faire coopérer de multiples acteurs, aux positions parfois divergentes, permettent l’interconnaissance, interrogent le besoin de nouvelles connaissances et peuvent également permettre la production collective de nouvelles connaissances. Faire émerger des connaissances et des solutions innovantes est particulièrement pertinent dans le domaine du bien-être animal. L’émergence d’un consensus autour d’une problématique, définie et comprise par tous les acteurs, puis d’une solution, nécessite une coopération dans un cadre de confiance et d’écoute mutuelles, dont l’animateur du processus sera le garant et nécessite du temps. Au travers de six projets illustratifs, des bénéfices notables ont été recensés, qu’ils soient de l’ordre de la prise de conscience et de l’ouverture d’esprit ou bien de la proposition de solutions opérationnelles. Les enjeux résident dans l’évaluation des impacts des solutions coconstruites en matière d’amélioration réelle du bien-être des animaux, ainsi que dans la diffusion des solutions sur le terrain, en tenant compte des dimensions économiques et sociales dans lesquelles elles s’inscrivent.

ano.nymous@ccsd.cnrs.fr.invalid (Vanessa Lollivier) 09 Jan 2026

https://hal.science/hal-05449736v1

[hal-05462148] Effect of using Hevea seed meal at different levels on Isa brown laying hen performance and egg quality

Egg consumption remains high in developing countries, yet the cost of poultry feed poses a significant challenge for farmers, limiting their ability to use commercial options. To address this, alternative feed sources for egg-laying hens need to be explored. In Côte d'Ivoire, Hevea brasiliensis trees' seeds are abundant but largely underutilized. These seeds have potential as dietary supplements in layer feed. This study aimed to evaluate the impact of incorporating H. brasiliensis seed meal into a white corn-based diet on laying performance, egg quality, yolk color, and composition. A total of 300 hens, 32 weeks of age, were randomly assigned to 30 pens with 10 hens per pen, and distributed across six dietary treatments with 5 replicates each over a period of 13 weeks. Two control groups received diets based on either yellow corn (Ye) or white corn (Wh). The remaining groups were fed on white corn diets supplemented with H. brasiliensis seed meal at inclusion rates of 2.5% (He2.5), 5% (He5), 7.5% (He7.5), and 10% (He10). The He2.5 diet led to improved egg production. Additionally, increasing levels of Hevea seed meal were associated with a decrease in yolk total cholesterol. However, higher inclusion rates also led to progressively yellow yolk colour compared to white corn-based diets. But, it did not fully restore the deep yellow pigmentation typically achieved with yellow corn. In conclusion, incorporating H. brasiliensis seed meal into white corn-based diets may be a costeffective strategy to enhance egg production and reduce cholesterol content in eggs, though it may affect yolk pigmentation

ano.nymous@ccsd.cnrs.fr.invalid (Gningnini Alain Koné) 16 Jan 2026

https://hal.science/hal-05462148v1

[hal-05387056] Towards a balanced view of livestock: Benefits of grazing farming systems to produce meat

Debates about livestock and meat consumption are generally fragmented, and to date no study has simultaneously analyzed all the dimensions affected by livestock farming. The environmental impacts of livestock are well described and often emphasized in the media as the negative effects of methane emission from ruminants, but the associated benefits are poorly described in scientific literature thus giving an unbalanced picture of livestock farming. Based on various findings from research, this review aims to propose a multidimensional view on this topic. Firstly, most of the environmental or nutritional arguments generally put forward against meat are provided without enough nuances. Without ignoring the negative impact of livestock on the climate and the environment, we show they need to be better deciphered. We provide examples dealing with the competition between feed and food, the water footprint of livestock, and the carbon footprint of meat production and consumption. On the other hand, livestock farming produces several ecosystem services beyond human food production that are not well known. Indeed, livestock production is the basis of agricultural activities and rural vitality in many parts of the world. Herbivores contributes to valorize large grassland areas that are not suitable for crop production and are hotspot of biodiversity. Livestock, notably ruminants, plays a key role in maintaining soil carbon content and soil fertility, and manure from livestock is a source of organic matter, nitrogen and phosphorus. An original service-bundle methodology designed to capture European livestock production in a global manner highlights antagonism between certain services. Thus, it is not possible to summarize livestock effects and impacts in a single indicator, be it positive or negative. Finally, we show that different scenarios exist to reduce the negative impacts of livestock. More global actions are needed on all fronts: improving meat production and supply, reducing demand, losses and waste of food. Eating less meat on average in developed countries and lowering the proportion of animal protein in diets may also be part of a global solution. Improving livestock farming systems in favor of grassland-based systems, which rely on natural resources without competing with human food production and which provide environmental services is also an essential strategy. In any case, a world without meat–producing livestock is unlikely to be sustainable as suggested by several studies.

ano.nymous@ccsd.cnrs.fr.invalid (Jean-Louis Peyraud) 28 Nov 2025

https://hal.inrae.fr/hal-05387056v1

[hal-05364659] How different strategies affect intramuscular fat deposition and marbling in meat: a meta-analysis on beef cattle

Context Intramuscular fat (IMF) deposition in meat is a multifactorial physiological process that is influenced by different feeding strategies and rearing practices. Aim This meta-analysis investigated for the first time the effects of different strategies designed to increase and/or manage IMF deposition and marbling score (MS) in beef cattle. Methods The dataset comprised 313 peer-reviewed publications. Strategies were assessed by examining the weighted mean difference between control diets (without additives or specific strategies to increase MS or IMF) and treatments under different conditions, including feeding (nutritional) strategy, sex class, feeding system, management, and feed efficiency phenotype. Key results Sex class (heifers or steers vs bulls) and feeding system (feedlot vs pasture) were associated with consistent increases in IMF and MS. Among the nutritional strategies, the inclusion of lipids, distillers grains (DG), and crude glycerin increased IMF and improved the fatty acid profile of beef. Significant increases in IMF were observed when comparing steers vs bulls (33.65%; P &lt; 0.001), heifers vs bulls (79.30%; P &lt; 0.001), and heifers vs steers (51.33%; P &lt; 0.001). Feedlot finishing increased IMF by 33.67% compared to pasture (P &lt; 0.001). Additionally, dietary inclusion of lipid sources (4.08%; P = 0.001), DG (7.09%; P = 0.001), and crude glycerin (14.71%; P = 0.009), as well as vitamin A reduction (14.48%; P &lt; 0.001), further enhanced IMF content. However, strategies such as β-agonists (P &lt; 0.001) reduced IMF content, while the addition of vitamins D and E, zinc, selenium, exogenous enzymes, essential oils, or tannins had no significant effect. Analysis of residual feed intake (RFI) indicated that efficient animals (low RFI) did not differ from inefficient animals (medium/high RFI) in terms of IMF levels but had lower MS (P = 0.055). Conclusion Feedlot finishing compared to pasture increased IMF and MS but reduced the concentrations of beneficial fatty acids such as rumenic acid (CLA C18:2 cis9, trans11) and omega-3 in meat. Among the nutritional strategies, the inclusion of lipids or DG improved the fatty acid profile of beef by increasing rumenic acid and α-linolenic acid content. Implications The different feeding and rearing strategies do not only affect IMF deposition but also the fatty acid profile of beef.

ano.nymous@ccsd.cnrs.fr.invalid (Rodrigo de Nazaré Santos Torres) 14 Nov 2025

https://hal.inrae.fr/hal-05364659v1

[hal-05455368] Resilience and Robustness in the Service of Longevity and Sustainable Efficiency in Dairy Production

Dairy cattle industries navigating increasingly frequent climate disruptions and volatile input costs must maintain productivity while simultaneously minimizing environmental impacts. This article examines how resilience (ability to recover from short-term disturbances) and robustness (capacity for long-term adaptation to challenging environments) contribute to longevity and lifetime efficiency in farm animals. Resilience reduces aging costs by enhancing recovery from environmental perturbations, e.g., health challenges, whereas robustness involves resource allocation strategies that facilitate survival in constraining environments. Both traits exhibit moderate heritability, offering opportunities for genetic improvement. However, their expression varies significantly across environments, necessitating context-specific selection approaches. Simulation studies, using models that incorporate robustness and resilience mechanisms, demonstrate that genotype-by-environment interactions strongly influence the economic and environmental benefits of selecting for these traits. In conclusion, incorporating resilience and robustness into breeding objectives can improve lifetime efficiency, particularly in challenging environments, but their economic value must be evaluated carefully in relation to specific production systems and anticipated future conditions.

ano.nymous@ccsd.cnrs.fr.invalid (M. Ithurbide) 13 Jan 2026

https://hal.inrae.fr/hal-05455368v1

[hal-05192006] Effects of mixing disbudded and horned young bulls during rearing on the post-mortem Longissimus thoracis muscle proteome

Eighty-one young Swiss cross-bred bulls, half of which were disbudded at 7 weeks of age, were reared in 6 rearing groups. Using a balanced design, these groups contained only horned, or only disbudded bulls (unmixed groups), or both (mixed groups), with only half of the bulls disbudded. They were slaughtered using two protocols, one with limited, the other with supplementary stress. Longissimus thoracis (LT) muscle samples were collected 48 h after slaughter and subjected to individual shotgun proteomic analysis. Results show that horn status and slaughter conditions influenced only 16 (6.2 %) and 8 (3.1 %) proteins, respectively, which is not more than expected by random error. By contrast, rearing conditions influenced 40 (15.5 %) of the identified proteins, which is significantly more than expected by random error. Eighteen of these differentially abundant proteins were involved in energy metabolism, and 9 in muscle structure and contraction. Overall, these proteins indicated greater glycolytic capacity and greater proportions of fast twitch fibres in the LT of bulls in mixed groups. These results are coherent with the lower physical activity and different physiological stress reactivity of these same mixed groups of bulls as reported in previous companion studies.

ano.nymous@ccsd.cnrs.fr.invalid (Claudia Terlouw) 30 Jul 2025

https://hal.inrae.fr/hal-05192006v1

[hal-05353972] Comprehensive evaluation of a pea co-product for piglet nutrition: fibre content, protein digestion, and intestinal barrier function

In pig production, weaning is a critical period associated with digestive intestinal disorders, due to the diet and environmental changes. The incorporation of transitional diets with high fibre and protein content represents a promising nutritional strategy to support piglets during the weaning period. This study examined the in vitro protein digestion and physicochemical properties of a co-product of interest for piglet at weaning: pea cream. The main objectives were i) to characterise pea cream in detail, focusing on its dietary fibre content, ii) to investigate in vitro the hydrolysis of its proteins, and iii) to examine the effect of pea cream digesta on intestinal barrier function using intestinal porcine epithelial cell lines (IPEC-J2). The composition in polysaccharides and the degradation of the pea cell wall were evaluated using biochemical and biophysical methods. The pea proteins from the pea cream were digested using an in vitro model of digestion simulating the upper gastrointestinal tract of pigs (based on the INFOGEST protocol). The obtained digesta were detoxified and then applied to IPEC-J2 cells. The results showed that pea cream was rich in dietary fibres, mainly insoluble, and contained approximately 4.6% protein (on an as fed-basis - 76.9% moisture). The in vitro protein digestibility of pea cream was high, with a significant release of proteins into the aqueous phase of the digesta earlier on during the digestion process. Microscopy revealed that some proteins remained encapsulated within cell wall fragments even after 6 h of digestion. The exposure of IPEC-J2 cells to detoxified pea cream digesta did not compromise the intestinal barrier integrity, as assessed by the passage of labelled molecules (FD4 and lucifer yellow) and the analysis of tight junction proteins (ZO-1 and occludin). In conclusion, pea cream presents several characteristics that make it a promising candidate for improving piglet weaning. It is a potential source of easily hydrolysable proteins, and its dietary fibres appear to maintain intestinal barrier function in the small intestine.

ano.nymous@ccsd.cnrs.fr.invalid (Maurane Grondin) 07 Nov 2025

https://hal.inrae.fr/hal-05353972v1

[hal-05310805] Evaluation of esophageal tubing and buccal swabbing versus rumen cannula to characterize ruminal microbiota in cows fed contrasting diets

Rumen microorganisms are primarily essential for feed decomposition and nutrition of the host animal, playing a key role in the health and well-being of cattle as well as the efficiency of milk or meat production. However, they also generate pollutant emissions such as methane. Analysing this microbiota under different farming conditions is therefore essential for optimizing production while minimizing its environmental impact. In this study, with metataxonomic sequencing and qPCR, we analysed the composition of the cow rumen microbiota sampled through the cannula and via esophageal tubing before morning feeding under two contrasting diets, low- and high-starch contents. Buccal swabs were also collected at the same sampling times to assess their potential as a proxy for the rumen microbiota. The two rumen sampling methods resulted in similar taxonomic compositions of bacteria, Archaea, fungi and protozoa and showed similar changes after the diet shift, indicating that the use of esophageal tubing is a reliable method for capturing the microbiota structure and its potential shifts following dietary changes. In contrast, the buccal swabs did not accurately reflect the rumen microbiota under the low- and high-starch diets, even after specific stringent filtering of the buccal sequences. Furthermore, we identified microbial markers of acidogenic challenge, with Dialister spp. also detected in buccal swab samples as potential indicators

ano.nymous@ccsd.cnrs.fr.invalid (Lysiane Dunière) 13 Oct 2025

https://hal.inrae.fr/hal-05310805v1

[hal-05283796] Detection of genomic regions affecting thermotolerance traits in growing pigs during acute and chronic heat stress

This study aimed to identify genomic regions involved in animal responses to chronic and acute Heat challenges in 1149 pigs tested in three climatic environments (temperate, tropical, and temperate Heated to 30 °C for 3 weeks). Production (growth rate, feed intake and efficiency, backfat thicknesses) and thermoregulation (rectal and cutaneous temperatures) traits were recorded in a backcross between Large White and Créole pigs. Genome-wide association studies were applied to the full population assuming SNP effects to be the same in both environments or to depend on the environment (GxE), and to the population in each environment separately. The genetic models used linkage disequilibrium in all chromosomes (LD) or only in Large White chromosomes (LW), or breed-of-origin of F1 alleles through linkage analyses (LA). Results Fifty-two regions distributed on 16 autosomes were detected. Most were identified with the LW or LD analyses, indicating both a large variability of effects in Large White in response to Heat stress, and high variability among the 10 Créole genomes segregating in the design. However, for thermoregulation traits, the majority of QTLs were detected with the LW model, suggesting interesting segregation of susceptibility and resistance alleles within the Large White breed. Ten regions were detected with the GxE model, mainly corresponding to significant effects in the temperate environment and no effect in the tropical situation, except for two regions on chromosome 2, which affected backfat thickness and growth rate, respectively. Twenty-four regions were detected for thermoregulation traits, but none were significant for both rectal and cutaneous temperatures. Of the 13 QTL regions detected for traits recorded during acute stress, four were also detected for similar traits during chronic stress, suggesting some consistency of responses during both stresses, although nine QTL regions were only detected during acute heat stress. Conclusions Measuring direct indicators of responses to heat stress, such as thermoregulatory responses, is essential to detect QTL and propose candidate genes involved in these responses. Multiple QTL for thermoregulatory responses segregate in the Large White breed were detected, paving the way for opportunities to select for heat stress resilience in European pig breeds.

ano.nymous@ccsd.cnrs.fr.invalid (Hélène Gilbert) 09 Oct 2025

https://hal.inrae.fr/hal-05283796v1

[hal-05203752] Seasonal dynamics of the nutritive value of temperate forage trees differ among species

There is growing interest in using temperate forage trees to alleviate the effects of summer drought and heatwaves on herbaceous forage. However, forage trees remain understudied in temperate climates. We studied the seasonal variation of the nutritive value of 16 tree species commonly found in Western Europe. We collected 285 samples of tree leaves between spring and autumn (June, August and October) over three years at 14 sites across France. We measured seven nutritive characteristics: in vitro dry matter digestibility (IVDMD) and the contents of crude protein (CP), dry matter (DM), neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent lignin (ADL), and ash. We used linear mixed models to analyse their seasonal variation and then clustered the species based on CP and IVDMD. CP content and IVDMD generally decreased from spring to autumn (by 26% and 6 percentage points), while DM and ash contents increased (by 42 and 32%). Corylus avellana , Morus alba , and Robinia pseudoacacia had the greatest CP content (from 138 to 250 g.kg −1 ), and M. alba had the greatest IVDMD (84.7% on average). We observed a trade-off between CP and IVDMD among clusters. The order of clusters based on their nutritive value remained consistent across seasons. Our findings highlight the importance of carefully planning tree use, as their nutritive value varies substantially among species and across seasons. Results provide new opportunities for farmers to compensate for the lack of herbaceous forage in summer, even though yield and palatability aspects remain to be studied.

ano.nymous@ccsd.cnrs.fr.invalid (Geoffrey Mesbahi) 08 Aug 2025

https://hal.inrae.fr/hal-05203752v1

[hal-05182514] L’élevage de ruminants s’adaptera-t-il au changement climatique ? Impacts et leviers d’adaptation

Les conséquences du changement climatique sur l’élevage de ruminants sont nombreuses. Elles affectent autant les animaux que les fourrages. Le stress thermique a des conséquences sur la production, la reproduction, le bien-être et la santé des animaux. Pour les prairies et fourrages, les évolutions climatiques se traduisent notamment par des modifications des périodes de production et une accentuation de la variabilité interannuelle. Les voies d’adaptation pour répondre à cette problématique sont diverses et complémentaires : adapter l’animal en améliorant sa tolérance à la chaleur et de façon générale son efficience, sa robustesse et sa résilience ; améliorer ses conditions de vie au pâturage et en bâtiment ; et assurer l’équilibre du système fourrager en jouant sur l’offre via la diversification et la complémentarité des ressources fourragères, et la demande (les besoins des animaux) en ajustant le chargement et la conduite des troupeaux pour faire coïncider les besoins avec la saisonnalité des prairies. Des méthodes et outils existent pour aider les éleveurs à déterminer les leviers les plus adaptés à leur système, et pour les accompagner dans la construction d’une stratégie d’adaptation les combinant au mieux. Ces démarches d’adaptation nécessitent de l’anticipation et l’implication des filières dans leur ensemble.

ano.nymous@ccsd.cnrs.fr.invalid (Aurélie Madrid) 23 Jul 2025

https://hal.science/hal-05182514v1

[hal-05147310] Effects of a methionine deficiency on chicken tissue protein turnover: comparative analysis of methionine source

Methionine (Met) supply is critical for optimum growth rate, muscle development, antioxidant activity, one-carbon metabolism in liver, and feather production in birds. Met is the first limiting amino acid (AA) in chicken diets, yet little is known about how different Met levels and sources influence tissue protein metabolism. Growth performance and tissue protein metabolism were compared in broilers fed either deficient or sufficient in Met, supplemented with either DL-Met or DL-HMTBA (a Met analogue). Protein synthesis rates were quantified in vivo in the liver, in 2 muscle types, and in the jejunum of 3-week-old chickens using a flooding dose of [C-13]-Valine. Additionally, tissue proteolytic activities and the expression of genes involved in proteolysis and autophagy were measured. The deficient Met supply reduced chicken weight, Pectoralis major (PM) muscle weight and protein synthesis (P&lt;0.05), though liver weight and protein synthesis remained unaffected. When expressed as fractional synthesis rates (FSR, %/d), protein synthesis was never depressed by Met deficiency irrespective of the tissue studied, whereas the proteasome proteolytic activity was consistently greater (P&lt;0.01) in the Met-deficient birds. These results were supported by the expression of proteolysis-related genes in the PM. For most parameters, including FSR and proteolytic activities (with the exception of the liver), there were minimal differences between birds receiving DL-Met and DL-HMTBA, indicating that DL-HMTBA effectively supports muscle protein synthesis when adequately supplied, similar to DL-Met. In conclusion, Met deficiency profoundly impacts chicken growth, PM development, and tissue protein turnover, while the two Met sources exhibit similar effects.

ano.nymous@ccsd.cnrs.fr.invalid (José Alberto Conde-Aguilera) 23 Sep 2025

https://hal.inrae.fr/hal-05147310v1

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

[...]

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

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

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

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

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

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

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

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

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

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

[hal-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-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-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>RésuméLe 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.</div>

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

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

[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) 21 Nov 2025

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

[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-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-05372624] RenouVeau -Réinventer les modèles de production de veaux de boucherie alliant enjeux sociétaux, qualité des produits et viabilité économique

Le projet RenouVeau a visé à étudier différents modes de production de veaux de boucherie, innovants du point de vue du logement et des conduites alimentaires appliqués, afin de répondre aux nouvelles attentes sociétales. Des consommateurs, ONG impliquées pour le bien-être animal et étudiants en agriculture ont été interrogés sur leur vision de la production de veau dans le futur. L'attente principale pour ces différents publics est de permettre aux animaux d'avoir un accès à l'extérieur. Différents modes de production de veaux de boucherie avec accès extérieur ont ainsi été testés en ferme expérimentale. Il a été constaté que les veaux occupent ce nouvel espace et se déplacent davantage comparé à un élevage en bâtiment fermé. Les comportements stéréotypés restent néanmoins présents et la présence de litière paillée pour le couchage entraine une consommation importante de paille. Les carcasses et les viandes produites dans ces nouveaux systèmes ressortent plus colorées, générant des problèmes de valorisation de ces produits. L'ensemble des résultats obtenus dans le projet a fait l'objet de nombreuses diffusions, dont la réalisation d'un webinaire 1 final disponible sur https://idele.fr/renouveau/publications/.

ano.nymous@ccsd.cnrs.fr.invalid (Didier Bastien) 19 Nov 2025

https://hal.inrae.fr/hal-05372624v1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[hal-05314842] Cross-sectional analysis of 28 agrifood value chain initiatives: Various innovation dynamics related to their commitment to agroecology

Plant and animal supply chains may choose to reinforce or adopt agroecological principles in various ways. Twenty-eight case studies on initiatives claiming to differentiate themselves through practices related to agroecological principles have been analysed across different fields of production. The analytical framework used is based on the innovation functions implemented by value chains. The different actions taken within the value chains are analysed relatively to their capacity to feed into a process of collective learning in the transition towards agroecology. The presented results show a variable transformative capacity of the value chains, but we observed several regularities based on which the agroecological transition in France may take place. This article makes suggestions regarding collective actions that can support the agroecological transition in France.

ano.nymous@ccsd.cnrs.fr.invalid (Marie-Benoît Magrini) 14 Oct 2025

https://hal.inrae.fr/hal-05314842v1

[hal-05224445] Empowering bioinformatics communities with Nextflow and nf-core

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.

ano.nymous@ccsd.cnrs.fr.invalid (Björn E Langer) 26 Aug 2025

https://hal.science/hal-05224445v1

[hal-05413023] Milk composition changes and alterations in bacteria, serum, and gut metabolome over time in lactating yaks and Simmental cows

Objective: This study aimed to elucidate the mechanisms underlying milk composition divergence between naks (female yaks) and Simmental cows (S-cows) by integrating longitudinal multi-omics analyses of gut microbiota and metabolomes.Methods: We determined the gut microbiota and metabolites of both species over a 54-day period (day 26 to 80 of lactation) of ten naks and ten S-cows. Gut microbiota dynamics were assessed via 16S rRNA sequencing, while serum and fecal metabolomes were profiled using ultra-high performance liquid chromatography–tandem mass spectrometry. Statistical analyses included Wilcoxon rank-sum tests, linear discriminant analysis effect size (linear discriminant analysis&gt;2, p&lt;0.05), and Spearman correlations (r&gt;0.70).Results: Milk yield was lesser (0.53–0.91 vs. 2.07–3.88 kg/d) but concentrations of fat (5.63%–6.30% vs. 3.30%–3.74%), protein (5.66%–6.30% vs. 3.39%–3.74%), and conjugated linoleic acid (CLA) (1.74%–2.35% vs. 1.40%–1.75%) were greater (p&lt;0.001) in nak than Scow milk. Species-specific microbial signatures emerged. In naks, the g-Family-XIIIAD3011-group and g-norank-Ruminococcaceae were correlated with bile acid metabolism and CLA synthesis via 13-hydroxyoctadecadienoic acid transport. Additionally, the naks gut had a greater concentration of 13-hydroxyoctadecadienoic acid, a precursor of CLA, which may be transported to mammary cells via phosphatidylcholine and converted to CLA under the catalysis of fatty acid desaturase2. S-cows harbored g-Succinivibrio and g-Eubacterium-ruminantium-group, which are linked to galactose utilization and mTORmediated amino acid allocation. Metabolomics revealed naks-enriched steroid biosynthesis and taurine pathways (false discovery rate&lt;0.05), while S-cows exhibited a lactating network associated with greater milk yield.Conclusion: Host-specific gut microbiota mediated nutrient allocation trade-offs. Naks optimized lipid-rich milk through bile acid and CLA metabolic networks, whereas S-cows enhanced yield via microbial-galactose synergies. This research underscores the pivotal role of the gut microbiome in mediating milk composition and suggests that microbiome manipulation could be a promising strategy to enhance milk quality in ruminants.

ano.nymous@ccsd.cnrs.fr.invalid (Runze Wang) 12 Dec 2025

https://hal.inrae.fr/hal-05413023v1

[hal-05412946] Opinion paper: Improving experimental design in animal research − seven key principles

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ano.nymous@ccsd.cnrs.fr.invalid (Carolien de Cuyper) 12 Dec 2025

https://hal.inrae.fr/hal-05412946v1

[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-05081949] The Denver call for action

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

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

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

[hal-05051412] À l’écoute des cochons

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

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

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

[hal-05429896] Discrimination of autochthonous pig breeds from meat and fat samples by FT-NIR spectra

The combination of Fourier transform near-infrared spectroscopy (FT-NIRS) of meat and fat samples and principal component discriminant analysis (DAPC) has been proposed as a tool for discriminating the local production of autochthonous pig breeds. Spectral samples (n = 272) belonging to 11 local European pig breeds, Longissimus muscle, and subcutaneous fat (both intact and minced) are collected. Classification accuracy based on DAPC was applied on FT-NIRS to predict breed of origin in i) semi-external cross-validation, splitting the data into training (80 %) and testing (20 %) sets; ii) external validation, in which one breed at a time was excluded from model training and classified in one of the remaining breeds. The effect of varying sample sizes from 50 % to 100 % of the data was assessed. Almost all breeds’ spectra variability was summarised into two principal components for tissue and sample preparation. In cross-validation, intact fat yielded higher classification accuracies than intact meat, with less pronounced differences in minced samples. Success assignment rates of ~81–83 % were obtained for two breeds in intact meat samples and were higher than 83 % for five breeds in fat samples. For minced samples, correct assignments between 80 % and 100 % were possible for five breeds, both in meat and fat samples. Sample size marginally affected the results. External validation confirmed similarity among some breeds, with greater accuracy for fat samples. The assignments success provides encouraging results for discriminating local pig production, mainly based on fat, using a rapid, eco-friendly FT-NIRS method, which could serve as tool for quality assurance.

ano.nymous@ccsd.cnrs.fr.invalid (S Parrini) 23 Dec 2025

https://hal.inrae.fr/hal-05429896v1

[hal-05424565] ASAS-NANP SYMPOSIUM: MATHEMATICAL MODELING IN ANIMAL NUTRITION: Contributions of mathematical modeling to life cycle assessment to support environmental sustainability of animal production

Life cycle assessment (LCA) provides a standardized framework for evaluating the environmental impacts of animal production systems through its four key steps: (1) goal and scope definition, (2) inventory analysis, (3) impact assessment, and (4) interpretation. However, traditional approaches using surveys and experimental data face limitations in capturing complex interactions among biological processes and management practices. This paper reviews how mathematical modeling can enhance LCA methodology for animal production systems, overcoming these constraints and supporting more robust environmental impact assessments. Mathematical models contribute significantly to LCA methodology at multiple scales and stages. At the inventory analysis stage, models predict feed intake, growth, production, and excretion of nutrients in response to animal characteristics and management practices. These range from nutritional metabolic models of average animals to sophisticated individual-based models that account for variability among animals in a herd. A systematic workflow could be followed for developing stochastic, individual-based models that generate comprehensive life cycle inventories through a bottom-up approach. Process-based models also improve emission estimates from animals and manure, progressing from simple Tier 1 default emission factors to complex Tier 3 mechanistic approaches that capture interactions between management practices and environmental factors. However, significant challenges remain in modeling manure emissions due to complex data requirements and microbial dynamics. Beyond inventory development, mathematical modeling enhances LCA's utility for decision support through optimization models that identify mitigation strategies balancing environmental and economic objectives. Individual-based models enable environmental phenotyping for genetic selection by quantifying how individual animal traits affect system-level impacts. These approaches represent promising developments for sustainable livestock production. Mathematical modeling transforms LCA from a descriptive tool to a predictive framework capable of evaluating numerous scenarios across different production contexts. Further development should focus on integrating performance and emission models, implementing optimization approaches for mitigation strategy identification, and expanding applications to regional and national scales to support evidence-based policies.

ano.nymous@ccsd.cnrs.fr.invalid (Alice Cadéro) 18 Dec 2025

https://hal.inrae.fr/hal-05424565v1

[hal-05347595] Patterns of plasma sexual steroids in Duroc and Pietrain crossbred male pigs in organic farming and prediction of boar taint risk according to slaughter weight

Boar taint risk in pork highly depends on fat tissue concentrations of androstenone and skatole, and indole to a lower extent. During pubertal development, androstenone is increasingly produced by testes and accumulates in fat tissues. Skatole and indole are produced and absorbed along in the colon and also accumulate in fat tissues. Skatole and indole are catabolised in the liver, but sexual steroids (including androstenone) inhibit their liver degradation. Therefore, slaughtering pigs before the pubertal peak of steroid production should reduce boar taint risk and thus make it possible to raise male pigs without inflicting detrimental castration. In the present experiment, non-castrated male pigs from two genotypes differing in their propensity to accumulate androstenone and skatole in backfat were compared: Large White × Duroc (D; n = 47) and Large White × Pietrain crossbreds (P; n = 34). Blood samples were drawn from the jugular vein two times during growth (at around 85 kg BW and 133 days of age, and around 105 kg BW and 153 days of age) and the day before slaughter (around 125 kg BW and 174 days of age). Plasma testosterone and 17b-oestradiol, whose concentrations increase during sexual development, were measured in all samples and correlated with backfat concentrations of androstenone, skatole and indole measured at slaughter. Plasma concentrations of both hormones increased (P &lt; 0.05) from the first to the second, and from the second to the third sampling stage (P &lt;; 0.05). Plasma testosterone concentration did not differ between genotypes (P &lt; 0.1) whereas plasma 17b-oestradiol was more than twice higher in D than in P pigs (P &lt; 0.001) regardless of the age. Plasma 17b-oestradiol concentration measured the day before slaughter was highly correlated with backfat androstenone (r = 0.91, P &lt; 0.001). Estimating backfat androstenone concentration from that of plasma 17b-oestradiol allowed to predict that reducing slaughter BW from more than 125 kg to less than 110 kg would reduce the percentage of carcasses with androstenone concentration above 1.7 lg/g liquid fat (severe threshold limit for boar taint) from 42 to 29% in D pigs and from 10 to 0% in P pigs, and with androstenone concentration above 3 lg/g (less severe limit for boar taint) from 19 to 7% in D pigs, whereas none of the P pigs would be above this limit regardless of the age. In conclusion, pig genotype and reducing slaughter BW (and age) are strong levers to avoid boar taint.

ano.nymous@ccsd.cnrs.fr.invalid (A. Prunier) 04 Nov 2025

https://hal.inrae.fr/hal-05347595v1

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

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

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

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

[hal-05360009] What can we do to improve the contribution of european grassland to net food security?

Intensification of animal production systems over the last number of decades has increased the consumption of human edible protein by livestock, leading to increased competition for and cost of human edible protein. Grassland‐based agriculture supports ruminant production systems, which convert human inedible proteins (grassland) into human edible meat and dairy products with high nutrient density. Grassland‐based systems have a low reliance on human edible food for production, and therefore optimizing the use of grassland to produce animal protein contributes to food security. Grassland‐based systems have conversion efficiencies of 2.5 to 4 in terms of kg human edible protein produced for each 1 kg human edible protein consumed by livestock, greater than that of confinement systems (≤ 1 for each 1 kg human edible protein consumed). Managed grassland offers a range of other ecosystem services including supporting plant and animal biodiversity, water resource management (e.g., water retention, provision of flood plains, water filtration), carbon storage and sequestration, and cultural services. Grassland management, sward species selection, and supplementation are amongst the strategies that can be used to optimise grassland production and utilisation by ruminants for human edible‐food production to contribute to global net food security, as well as environmental conservation and management.

ano.nymous@ccsd.cnrs.fr.invalid (Deirdre Hennessy) 12 Nov 2025

https://hal.inrae.fr/hal-05360009v1

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

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

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

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

[hal-05249668] Agronomic variability in white clover varieties under differing nitrogen application rates

White clover (Trifolium repens, L.) incorporation into pasture based ruminant production systems has the potential to increase their economic and environmental sustainability. Varieties of white clover are evaluated in national recommended list evaluation trials to identify the best varieties to sow on commercial farms. This highlights the need for recommendations to have a broad applicability. In this study, 17 clover varieties were examined under different nitrogen (N) levels to determine whether varieties re-rank in their agronomic characteristics and how sensitive they are to the imposed management. The clover varieties were sown with perennial ryegrass (Lolium perenne L.; PRG) along with a PRG monoculture control in a factorial plot study with three different N rates (0 kg N/ha, 75 kg N/ha and 150 kg N/ha). The experiment was carried out for two years, following an establishment year, measuring sward herbage yield, clover content and nutritive quality. The expected inverse relationship between N rate and clover content in the sward (r = -0.55) and positive correlation between N rate and herbage production (r = 0.38), were both observed. There was, however, a significant variety x N interaction, with a re-ranking of varieties between N application rates for both traits. The re-ranking of these clover varieties between N management systems indicated that the current evaluation of varieties under a single rate of N is not optimal to identify elite varieties for different farm management systems. This study outlines the need to design more effective and widely applicable testing schemes under varying N management systems to accurately define the agronomic potential of individual varieties, across a wider range of farming conditions. The identification of elite white clover varieties under varying N application rates will assist farmers in selecting varieties to reach both environmental mitigation and herbage production targets under their specific grassland management system.

ano.nymous@ccsd.cnrs.fr.invalid (Ciara Carroll) 11 Sep 2025

https://hal.inrae.fr/hal-05249668v1

[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-05318953] Values shared by journals of learned societies, associations and scientific institutions in animal science

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Ortigues Marty) 17 Oct 2025

https://hal.inrae.fr/hal-05318953v1

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

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

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

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

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

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

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

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

[hal-05319008] Sprouted grains fermentation: a comprehensive review of current knowledge, benefits, challenges, and perspectives

Sprouted seeds are attracting growing interest because of their improved digestibility, high nutritional value, variety, low cost and ease of production. However, their microbiological fragility and elevated levels of certain anti-nutritional factors can sometimes pose problems for their use in both food and feed. Recent research has shown that combining fermentation with germination can effectively solve these problems. Fermentation not only improves nutritional value by lowering levels of anti-nutritional factors, but also improves microbiological safety, making it a promising approach to extending shelf life. Additionally, fermented sprouted seeds have beneficial properties may be of use in the formulation of functional foods, particularly for managing metabolic diseases such as diabetes. Despite these positive points, there is still room for improvement in the fermentation of sprouted seeds. This literature review explores current knowledge of seed germination, the advantages of fermenting sprouted seeds, and discusses the disadvantages and potential axes for improvement.

ano.nymous@ccsd.cnrs.fr.invalid (Koffigan Kponouglo) 17 Oct 2025

https://hal.inrae.fr/hal-05319008v1

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

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

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

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

[hal-05316260] The agroecological transition in the agri-food sector: A long process of convergence towards a new paradigm

Agroecology is a paradigm for transforming our agri-food system towards greater sustainability. Technical, organisational and commercial transformations require the convergence of new cognitive, normative and regulative rules. After outlining the institutionalisation of agroecology on an international scale and in French legislation, we present a heuristic framework for thinking about agroecological transition in the agri-food sector using the multilevel perspective from sociotechnical transition studies. This perspective conducts us to build an analytical framework at the level of the value chains to strengthen the understanding of the levers and brakes of the agroecological transition.

ano.nymous@ccsd.cnrs.fr.invalid (Magrini Marie-Benoît) 15 Oct 2025

https://hal.inrae.fr/hal-05316260v1

[hal-05261972] Introducing animals into orchards and vineyards: an agroecological solution for managing weeds

The aim of the REVE project was to explore the many aspects of interactions between livestock and crop production. In particular, these interactions provide numerous services, including the regulation of bioaggressors. This article focuses on the introduction of animals into vineyards and orchards to manage weeds. The aim of this study was to analyse, for different animal species, the services rendered in terms of weed management, versus the disservices in terms of damage caused to soils, vine plants and trees in orchards.

ano.nymous@ccsd.cnrs.fr.invalid (Gentiane Maillet) 15 Sep 2025

https://hal.inrae.fr/hal-05261972v1

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

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

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

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

[hal-05168351] Genotype and dietary inclusion of omega-3 fatty acids and fiber influence metabolism of subcutaneous adipose tissue and systemic metabolic outcomes in growing pigs

Adipose tissue properties are considered as determinants of meat quality, but also play roles in animal robustness. From 33 kg to 116 kg on average, a total of 60 Duroc (D) or Pietrain (P) crossbred female pigs were individually fed either a conventional (C) or an experimental (R) feeding strategy with a diet rich in omega 3 fatty acids and crude fibers (n = 15 pigs per group). The D pigs had a lower feed efficiency and a higher proportion of subcutaneous adipose tissue (SCAT) at slaughter than P pigs (P &lt; 0.01). SCAT in D pigs had lower levels of polyunsaturated fatty acids (PUFA; P &lt; 0.001) and higher levels of peroxidized lipids (P &lt; 0.05) than SCAT in P pigs. In plasma, reactive oxygen metabolites to total antioxidant capacity was higher (P &lt; 0.01) in D pigs than in P pigs. Compared to C, feeding the R diet resulted in a marked decrease in the n-6:n-3 PUFA ratio in SCAT, which was even more pronounced in D pigs than in P pigs (P &lt; 0.05). The R feeding strategy increased beta-hydroxyacyl-coenzyme A dehydrogenase activity (P &lt; 0.05) acting in fatty acid oxidation, and SCAT susceptibility to peroxidation. This also led to a reduction in plasma phospholipid concentrations and oxidative stress in the D pigs (P &lt; 0.05). Thus, the nutritional value of fat products for humans and the systemic metabolic outcomes for pigs could be improved with an appropriate feeding strategy.

ano.nymous@ccsd.cnrs.fr.invalid (Florence Gondret) 17 Jul 2025

https://hal.inrae.fr/hal-05168351v1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[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-05407120] Data paper: Contribution of lipids to the net carbon balance across the liver and associated measurement uncertainty in dairy cows

Livestock systems are becoming more efficient and require physiological data to better estimate the nutritional requirements of animals. The liver plays a central role in nutrient processing and metabolism. To better understand liver function, five lactating Jersey cows (78 ± 12 days in milk) were surgically fitted with blood catheters in the mesenteric vein (for para-aminohippuric acid (pAH) infusion), portal (PV) and hepatic veins (HV), and in the mesenteric artery (MA). They were fed four isoenergetic treatment diets [(starch vs fiber rich diets) x (low vs normal protein diets)] according to a 4x4 Latin Square design; each treatment lasted 28 days. The data reported in this study presents all the metabolite concentrations (albumin, amino acids, beta-hydroxybutyrate, carbon dioxide, glucose, insulin, lactate, non-esterified fatty acids (NEFA), oxygen, phospholipids, total cholesterol, total lipids, total proteins, triglycerides, triiodothyronine, thyroxine, urea and volatile fatty acids) measured in the PV, HV and MA per cow, treatment diet and period. Blood or plasma flow per blood vessel was determined using the Fick principle and the pAH measurements.The afferent (MA and PV) and efferent (HV) fluxes were calculated for most of the carbon-containing metabolites (excluding NEFA, hormones and proteins for which only the concentrations are reported). The net carbon balance across the liver was then calculated as the difference between afferent and efferent fluxes, per cow and treatment diet. Laboratory methods were evaluated by Quality Assurance procedures, which may be used to select the appropriate analytical method for a study. The expanded measurement uncertainty (MU) associated with the net carbon balance across the liver was then determined considering the individual MU of each parameter involved in the calculation. The latter were calculated from statistical distribution of quantity values derived from Quality Assurance procedures (Type A approach; for most of the metabolites) or from other kinds of information when this was not possible (Type B approach; for total lipids, total amino acids and carbon dioxide). The present data may be used to better understand the hepatic metabolism of dairy cows, the MU of nutrient fluxes and the net carbon balance across the liver, and to evaluate the accuracy of existing prediction models. The large expanded measurement uncertainty of the carbon balance values is useful to understand the limits of interpretation of the present net flux data.

ano.nymous@ccsd.cnrs.fr.invalid (José Miguel Rodríguez-López) 09 Dec 2025

https://hal.science/hal-05407120v1

[hal-05431424] The need to consider the "functional quality" dimension in the holistic evaluation of animal-sourced foods

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 24 Dec 2025

https://hal.inrae.fr/hal-05431424v1

[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-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) 23 Jul 2025

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

[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-05387230] Interfacing mechanistic and breeding scheme simulation to predict selection response on lactation efficiency in dairy cows under different nutritional environments

Background Predicting selection response for lactation efficiency in dairy cows is challenging, as the expression of this complex trait depends on dynamic interactions between the ability of cows to acquire nutrients and allocate them to different life functions. Moreover, the relative emphasis of these components may change due to energetic trade-offs between life functions when kept in limiting environments. The objective of this study is to present a new approach combining mechanistic and breeding scheme simulations to predict selection response on components of lactation efficiency of dairy cows under a non-limiting nutritional environment and when transferred to a limiting environment with a moderate feed restriction. These predictions were compared to the ones obtained with the conventional method used in quantitative genetics considering a typical dairy cattle breeding scheme and several breeding goals (BG) aiming at improving milk production, lactation efficiency and fertility. Results In the non-limiting environment, selection responses predicted by the two methods differed for both milk production and fertility. The sign and magnitude of differences depended on BGs. Selection response predictions were consistent only for BGs that did not change much the body reserve mobilization patterns of cows, and hence their conception probability. Indeed, pregnancy status impacted energy allocation of cows and consequently milk production, more energy being allocated to lactation in case of reproductive failure. Differences in selection response between modelling approaches were slightly increased when cows were reared in the limiting environment. Overall, the choice of prediction method led to substantial BG reranking with respect to selection response on milk production and fertility. Mechanistic-based predictions of selection response for lifetime efficiency were also sensitive to the nutritional environment and BG. Conclusions Combining mechanistic and genetic modelling is a promising approach to benchmark breeding strategies of dairy cow lactation efficiency and better anticipate the impact of changes in energetic trade-offs induced both by selection and changes in the nutritional environment. Moreover, the simulations of phenotypic trajectories over cow lifetime before and after selection enabled a better understanding of the mechanisms underlying genetic improvement.

ano.nymous@ccsd.cnrs.fr.invalid (Alban Bouquet) 28 Nov 2025

https://hal.inrae.fr/hal-05387230v1

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

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

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

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

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

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

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

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

[hal-05181410] Concevoir et évaluer des systèmes d'élevages favorables à la biodiversité : exemple d'un projet d'étudiant(e)s

L'article présente un projet réalisé à l'Institut Agro Rennes Angers pour des élèves ingénieurs agronomes et master 2 en productions animales. Le dispositif pédagogique réalisé sur 24h vise à concevoir des systèmes d'élevage résilients, acceptables et qui favorisent la biodiversité. L'objectif était de développer des compétences en analyse systémique et pour l'évaluation multicritères grâce à un projet collaboratif. Les étudiants ont utilisé des LEGO® pour modéliser des systèmes d'élevage et définir les transformations d'une ferme polyculture-élevage située dans le bassin rennais. Deux scénarios ont été proposés et évalués grâce à une grille créée par les étudiant(e)s. Les résultats montrent un renforcement des liens avec la société et de la biodiversité. Le retour d'expérience des enseignantes souligne l'importance de l'apprentissage par projet et la nécessité d'adapter l'enseignement aux profils des étudiants.

ano.nymous@ccsd.cnrs.fr.invalid (Justine Faure) 23 Jul 2025

https://hal.inrae.fr/hal-05181410v1

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

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

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

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

[hal-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-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-05307663] Design of Hydrogel Microneedle Arrays for Physiology Monitoring of Farm Animals

For monitoring animal adaptation when facing environmental challenges, and more specifically when addressing the impacts of global warming—particularly responses to heat stress and short-term fluctuations in osmotic regulations in the different organs influencing animal physiology—there is an increasing demand for digital tools to understand and monitor a range of biomarkers. Microneedle arrays (MNAs) have recently emerged as promising devices minimally invasively penetrating human skin to access dermal interstitial fluid (ISF) to monitor deviations in physiology and consequences on health. The ISF is a blood filtrate where the concentrations of ions, low molecular weight metabolites (&lt;70 kDa), hormones, and drugs, often closely correlate with those in blood. However, anatomical skin differences between human and farm animals, especially large animals, as well as divergent tolerances of such devices among species with behavior specificities, motivate new MNA designs. We addressed technological challenges to design higher microneedles for farm animal (pigs and cattle) measurements. We designed microneedle arrays composed of 37 microneedles, each 2.8 mm in height, using dextran-methacrylate, a photo-crosslinked biocompatible biopolymer-based hydrogel. The arrays were characterized geometrically and mechanically. Their abilities to perforate pig and cow skin were demonstrated through histological analysis. The MNAs successfully absorbed approximately 10 µL of fluid within 3 h of application.

ano.nymous@ccsd.cnrs.fr.invalid (Laurabelle Gautier) 10 Oct 2025

https://hal.inrae.fr/hal-05307663v1

[hal-05307558] Influence of precision feeding of sows over three consecutive gestations adjusted for energy, amino acids and minerals on sow performances and a marker of bone resorption

Supplying only one type of diet to gestating sows does not sufficiently cover the variability in individual and daily requirements of sows throughout gestation. A cumulative mineral imbalance decreases the overall performance of a sow herd. Mineral deficiency is particularly critical during lactation, when mobilisation of bones occurs, and during gestation, when it should recover. Excess minerals influence environmental impacts and economic outcomes. The objective of this study was to assess the influence of a precision feeding (PF) strategy adjusted for energy, amino acids and P over three consecutive reproductive experimental cycles on sow productive performances, nutrient balances, health and mineral status. The PF strategy involved adjusting daily dietary supplies at the individual level based on quantity (energy) and quality, including amino acids (standardised ileal digestible lysine, SID-Lys) and minerals (apparent total tract digestibility of P, ATTD-P). Seven days after insemination, two batches of 28 Landrace x Large White gestating sows were allocated to one of the two feeding strategies (PF vs a standard feeding strategy with a single diet adjusted on energy requirements (SF)) based on their parity, BW and backfat thickness. The PF strategy consisted of mixing two iso-net energy (NE) diets (9.0 MJ/kg, 2.6 g/ kg ATTD-P, with low: 3.3 g/kg or high: 8.5 g/kg SID-Lys content, respectively) in an automatic feeder on an individual and daily basis until day 80 of gestation. During the last month of gestation, an additional diet (4.0 g/kg ATTD-P) was supplied to ensure that the sows' increased P requirements were met. In contrast, SF sows were supplied only one diet throughout gestation (9.0 MJ/kg NE, 2.6 g/kg ATTD-P and 4.7 g/ kg SID-Lys). The SID-Lys intake over three consecutive gestations was 18% (P &lt;0.001) lower for PF than SF sows without decreasing farrowing performances (P &gt; 0.10). PF reduced feed cost up to 5 /tonne (P &lt; 0.001). Only during the last week of gestation, daily ATTD-P intake was 1.5 g greater for PF sows than for SF sows (P &lt; 0.001). The feeding strategy did not influence total ATTD-P intake or urinary concentration of C-terminal telopeptide of type I collagen, a bone resorption marker (P &gt; 0.10). Adjusting P supplies to the sows' P requirements only during the last month of gestation better met their nutritional needs, had no long-term effects on farrowing performances and did not decrease bone resorption compared to the SF strategy adjusted for energy.

ano.nymous@ccsd.cnrs.fr.invalid (Clément Ribas) 10 Oct 2025

https://hal.inrae.fr/hal-05307558v1

[hal-05224401] The effect of supplementary feed on live weight and meat quality of grazing yaks on the Qinghai-Tibetan Plateau

This study examined the effects of supplemental feeding on the weight and meat quality of grazing yaks on the Tibetan Plateau. Thirty male yaks (2.5-3 years old) with similar characteristics were randomly assigned to two groups: the traditional grazing group (G) and the supplemental feeding group (SF). The SF group received 1.5 kg of supplemental feed daily. After 120 days, slaughter performance and meat quality were compared. The results showed that the SF group had significantly higher live weight (137.2 kg vs 175.3 kg, P &lt; 0.001) , carcass weight (63.6 kg vs 89.5 kg, P &lt; 0.001) , and net meat yield (34.0 % vs 40.2 %, P &lt; 0.001) compared to the G group. Moreover, the SF group exhibited lower cooking loss, drip loss, and shear force, indicating improved meat quality (P &lt; 0.05) . Amino acid analysis revealed that the SF group had higher total amino acids (TAA, 13.25 g/100 g vs 14.14 g/100 g, P &lt; 0.001) and essential amino acids (EAA, 5.19 g/100 g vs 6.03 g/100 g, P &gt; 0.05) content, the ratios of EAA/TAA and EAA/NEAA increased by 4 % and 10 %, respectively. Additionally, compared to the G group, the SF group had lower saturated fatty acids (SFA, 43.25 vs 39.22, P &lt; 0.001) and higher polyunsaturated fatty acids (PUFA 11.49 % vs 13.74 %, P &lt; 0.001), particularly omega-3 fatty acids (2.81 % vs 5.31 %, P &lt; 0.001), with a lower n-6/n-3 (2.88 % vs 1.44, P &lt; 0.001) ratio. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) confirmed the effects of supplementation on amino acids and fatty acids. In conclusion, supplemental feeding significantly improved yak growth and meat quality, particularly in amino acid and fatty acid composition, providing valuable insights for grazing management on the Tibetan Plateau.

ano.nymous@ccsd.cnrs.fr.invalid (Meisong Wang) 26 Aug 2025

https://hal.inrae.fr/hal-05224401v1

[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-05250561] Toward the automatic detection of social interactions in gestating sows using image analysis data

The identification of social interactions for group-housed gestating sows is crucial in order to monitor their welfare. They are key for understanding the social structure of the group and ensuring that disturbances, such as an abnormal frequency of aggression, are promptly detected. Assessing social interactions can be done through direct observation, manually recording the number and valence of interactions (positive or negative). This approach requires substantial human and financial resources. The study assesses the feasibility of using data produced by an image analysis software identifying sows' postures and key points to automatically detect and classify social interactions. Two pens of 19 and 20 gestating sows each were video recorded from 00:00 to 02:00 on days 30 and 103 of two consecutive gestations. The videos were analysed manually using the annotation system of the software in development. In total, 120 moments of positive interactions and 120 moments of negative interactions were annotated, including images before, during, and after the interaction. In addition, 120 moments without interactions (two sows not in contact) were annotated. The valence of the interaction (i.e. positive or negative), and for each interacting sow the posture (i.e., standing, sitting, lying), and the coordinates of 3 key points (nose, neck, tail) were identified. Relative distances between sows, movement speeds and individual distances travelled were calculated. Decision trees were performed to assess the relevance of these variables to detect an interaction. The start and end of an interaction were reliably detected with 88% accuracy using distances and postures. Interactions were characterized by a convergence of key points, spatial proximity, and at least one sow adopting a standing posture. The valence was effectively determined using the movement speeds and individual movements of sows during and after the interaction (respectively 74 and 80% accuracy). Negative interactions were characterized by faster movements and avoidance behavior. The performance in detecting sows’ orientation during interaction varied across categories (nose-nose, nose-neck, nose-tail, from 33% to 100%), and were particularly good for nose-tail interactions (94% F-score). This study shows the potential of the automatic image analysis software under development to detect and classify social interactions through post-processing analysis of key points and posture data.

ano.nymous@ccsd.cnrs.fr.invalid (Anna Blanc) 11 Sep 2025

https://hal.inrae.fr/hal-05250561v1

[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

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