Scientific publication

[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-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-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-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-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-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-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-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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[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-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-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-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-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-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-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-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-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-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-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-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-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-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-05318953] 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) 17 Oct 2025

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

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

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

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

[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-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-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-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-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-05198687] Milking frequency and dairy cow susceptibility to lipolysis interact to alter milk lipolysis and composition

Lipolysis is an ongoing issue for the French dairy industry that must be minimized. Milk lipolysis is defined as the hydrolysis of triglycerides, the major component of milk fat, resulting in the release of short-chain fatty acids responsible for rancid flavor and partial glycerides that impair functional properties such as foaming and creaming abilities. Milk lipolysis is a complex phenomenon that depends on both animal parameters and farming factors. Milk spontaneous lipolysis is higher in milk from automatic milking systems, which could be due to the number and intervals of milking, as lipolysis is lower in the case of a single daily milking. In addition, considerable interindividual variability in milk lipolysis has been observed, with some dairy cows being highly susceptible or nonsusceptible to lipolysis. The objective of this study was therefore to evaluate the impact on spontaneous milk lipolysis of different milking frequencies (i.e., 1 [morning or evening], 2, or 3 milkings per day) with evenly spaced milking intervals while accounting for individual susceptibility to lipolysis. To achieve this goal, 32 primiparous and multiparous dairy cows in mid-lactation were conducted using a continuous design with milking frequency as the main factor for a period of 3 wk. Four treatments were applied on 4 groups of cows: 1 milking per day at 6:00 a.m. (1M6am), 1 milking per day at 6:00 p.m. (1M6pm), 2 milkings per day at 6:00 a.m. and 6:00 p.m. (2M), and 3 milkings per day at 6:00 a.m., 2:00 p.m., and 10:00 p.m. (3M). In each group, there were 4 susceptible (SUS) dairy cows (lipolysis of SUS &gt;0.70 mEq/100 g fat) and 4 nonsusceptible (NONSUS) dairy cows (lipolysis of NONSUS &lt;0.70 mEq/100 g fat). As expected, 2M and 3M milkings increased milk yield by up to 30% compared with once-a-day milking. We con-firmed that milk spontaneous lipolysis was influenced by increased milking frequency: compared with 2M, we observed more lipolysis with 3M and less with 1M. Regardless of the lipolysis susceptibility, the 1M6am and 1M6pm treatments caused a similar reduction in lipolysis. On the other hand, lipolysis was significantly higher in SUS cows with 2M and 3M treatments. In conclusion, although increased milking frequency results in greater milk yield, our results indicate that it can adversely impact milk quality with regard to free fatty acid concentrations. Conversely, although once-aday morning or evening milking lead to decreased milk yield, they significantly reduced milk lipolysis regardless of a cow's susceptibility to lipolysis.

ano.nymous@ccsd.cnrs.fr.invalid (Catherine Hurtaud) 04 Aug 2025

https://hal.inrae.fr/hal-05198687v1

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

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

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

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

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

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

ano.nymous@ccsd.cnrs.fr.invalid (Lucille Rey-Cadilhac) 03 Sep 2025

https://hal.inrae.fr/hal-05077824v2

[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-05315879] The "Agroecology & Markets" project led by the INRAE sector groups

The agrifood sector encountered increasing market segmentation, with the proliferation of public and private quality claims (i.e. labels), which commit the supply chains to the building of differentiated production, processing and distribution practices. We know very little about the way in which value chains move towards agroecology, particularly for value chains with quality labels other than organic farming. From 2022 to 2023, INRAE's Scientific Division for Agriculture conducted an exploratory project with 11 sector research groups of INRAE to analyse how differentiated supply chains are committing to agroecology. This project, entitled 'Agroecology and Market', was based on desk research and interviews with over 60 actors from the interbranch organisations and different stages in agrifood chains. This introductory article presents the rationale for the project, the mission of the INRAE sector research groups and the 28 case studies selected for illustrative purposes in order to conduct this exploratory analysis in a diverse range of production and supply chain contexts.

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

https://hal.inrae.fr/hal-05315879v1

[hal-05172558] Evaluating the effect of white clover inclusion and dairy cow genetic merit on enteric methane emissions within rotational grazing systems

This study aimed to quantify and compare the enteric methane emissions from dairy cows grazing either perennial ryegrass (Lolium perenne L.; PRG) or PRG with white clover (Trifolium repens L.; clover) in a farm systems experiment. A study was established with 2 sward treatments consisting of PRG receiving 225 kg of nitrogen (N) per ha per yr (grass-only) and PRG and clover receiving 150 kg of N per ha per yr (grass-clover). Two dairy cow genetic groups, high and low economic breeding index (EBI), were randomly assigned across the 2 sward treatments, which were managed as self-contained farmlets. Enteric methane emissions were measured throughout the study (late-March to late-October) using GreenFeed units. Both swards had similar total herbage production (11.8 tonne of DM/ha) during the study, and the average clover content of grass-clover was 23.0% (SD = 16.51). Cows in the grass-clover treatment had greater DMI and consequentially had greater daily methane emissions (341 g/d) compared with the cows in the grass-only treatment (308 g/d). However, there was no difference in methane yield (methane per kg DMI) between the 2 treatments. There was also no treatment effect when methane emissions were expressed per kilogram of milk solids (milk fat + protein; MlS), but methane per kilogram of fat and protein corrected milk (FPCM) tended to be greater from cows grazing grass-clover. There was no effect of EBI group on daily MlS production, methane emissions, methane yield, or methane per kilogram of MlS. Cows in the high EBI group had lower milk yield and greater milk fat and protein content compared with the cows in the low EBI group. The ability to reduce artificial N fertilizer inputs in a grass-clover system benefits nitrous oxide emissions and farm-gate N use efficiency. However, the greater enteric methane emissions from cows grazing grass-clover highlight the need for balanced consideration when implementing environmental measures on farms to avoid pollution swapping.

ano.nymous@ccsd.cnrs.fr.invalid (C. Dwan) 21 Jul 2025

https://hal.inrae.fr/hal-05172558v1

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

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

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

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

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

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

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

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

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

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

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

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

[hal-05268699] Grazed grass-based dairy systems in Western France: efficient and sustainable due to their lower dependence on inputs

Since the end of milk quotas in 2015, French dairy farmers have had to adapt to a liberalised market and decoupled CAP subsidies. Two strategies have emerged: increasing production per cow and per farm or reducing production costs. This article examines the economic, social and environmental impacts of these strategies using data from the Technical-Economic Observatory of Dairy Cattle Systems for the 2022 fiscal year. Farms of the Agricultural Accounting Information Network (RICA) are characterised by high milk production per cow and per farm but are more sensitive to fluctuations in milk and inputs prices. In contrast, farms of the "Sustainable Agriculture Network" (RAD) focus on self-sufficiency and cost reduction. They are thus more effective at generating richness and are more economically stable in the long term. Grass-based systems of the RAD offer environmental advantages, including reduced nitrogen balance and better carbon emission compensation through pastures and hedgerows, in the associated bocage. These farms are also more efficient at remunerating their breeders and emitting less CO2 per unit of income generated. In conclusion, grass-based systems, based on local resources and cost reduction, appear to be a sustainable and economically viable strategy, despite the ongoing challenges related to grass management and the new related climate change.

ano.nymous@ccsd.cnrs.fr.invalid (Alexine Woiltock) 19 Sep 2025

https://hal.inrae.fr/hal-05268699v1

[hal-05283425] SWATH-MS proteomics data on differentially abundant proteins between normal and dark-cutting beef

Dark, firm, and dry (DFD) beef, also known as dark-cutting beef, lead to economic losses, food waste, and potential consumer rejection due to its very dark color at the point of sale. This condition is associated with a high ultimate pH, a limited blooming capacity, a redder cooked color that appears undercooked, and increased spoilage rates. Although several pre-slaughter factors have been linked to high ultimate pH, the mechanisms underlying DFD beef remain complex, multifactorial and not yet fully understood [1]. Proteomic approaches on post-mortem muscles have increasingly been employed to unravel the molecular mechanism and biological pathways underlying this quality defect and to identify candidate protein biomarkers for its early prediction or better characterization. In this study, SWATH-MS proteomics, a data-independent acquisition strategy, was applied for the first time for an in-depth characterization and quantification of post-mortem muscle proteomes. The analysis was conducted using the most extensive dataset available to date on this quality defect conditions, which included 26 DFD beef samples (pH24 ≥ 6.2) and 26 CONTROL samples (5.4 ≤ pH24 ≤ 5.6). Muscle samples from the Longissimus thoracis et lumborum of Asturiana de los Valles yearling bulls were collected at 24h post-mortem to investigate protein expression differences associated with DFD beef condition. A total of 735 proteins were quantified, among which 35 exhibited a significant difference in their abundances between the DFD condition and CONTROL samples, suggesting their potential as putative biomarkers for DFD beef.

ano.nymous@ccsd.cnrs.fr.invalid (Laura González-Blanco) 04 Oct 2025

https://hal.inrae.fr/hal-05283425v2

[hal-05291477] Lactation-wide genetic insights into nitrogen utilization in grazing dairy cows

Societal and economic pressure to reduce nitrogen use in the dairy cow sector is increasing. One potential contributing solution is to breed more nitrogen-efficient dairy cows that excrete less nitrogen. Although genetic variability for nitrogen utilization has been documented in dairy cows, how the phenotypic variance is partitioned into its causal components across lactation has not been previously explored in dairy cows. The objective, therefore, of the present study was to use 4,600 nitrogen utilization phenotypes across 2,255 lactations from 1,296 grazing dairy cows to explore whether the genetic variation in nitrogen utilization changes throughout lactation. Nitrogen utilization in the present study was evaluated using 2 metrics: nitrogen use efficiency (NUE), the ratio of nitrogen used and stored relative to the nitrogen available, and nitrogen balance (Nbal), calculated as nitrogen available minus the nitrogen used and stored. A random regression model was used to explore the variability of each studied trait over the lactation as well as the within-trait covariances across the lactation. The genetic variability in both NUE and Nbal did indeed change throughout lactation. The genetic SD of NUE decreased rapidly from 0.018 (SE = 0.003) at 6 DIM to 0.007 (SE = 0.001) at 82 DIM, then remained relatively constant until 191 DIM before increasing thereafter to 0.016 (SE = 0.002) at 268 DIM. Mirroring the change in the genetic variability across the lactation, the heritability of NUE decreased from 0.35 (SE = 0.09) at 6 DIM to 0.07 (SE = 0.03) at 80 DIM, before it increased up to 0.48 (SE = 0.10) by the end of the lactation. The genetic SD of Nbal increased from 11.87 (SE = 0.05) g/d of N at 6 DIM to 29.92 (SE = 3.61) g/d of N at 268 DIM, which was reflected in a gradual increase in heritability from 0.05 (SE = 0.04) at 6 DIM to 0.23 (SE = 0.05) at 268 DIM. Moreover, the within-trait genetic correlations between different DIM for NUE ranged from strongly positive to −0.25 (SE = 0.16), which was between 6 and 148 DIM. The within-trait genetic correlations for Nbal between different DIM were all strongly positive, with the weakest value being 0.61 (SE = 0.19), which was between 6 and 268 DIM. This profile in genetic correlations, combined with the sign of the eigenfunctions of the genetic covariance matrix for both nitrogen efficiency traits across lactation, suggest a greater potential to modify the shape of the lactation profile for NUE through genetic selection compared with Nbal. Nevertheless, there is still a good opportunity to genetically modify the height of the Nbal profile throughout lactation. Finally, given the limited evidence of a nonzero genetic correlation between NUE and Nbal, should both traits be deemed important, then both should be considered in a breeding objective to improve the nitrogen utilization metrics of dairy cows.

ano.nymous@ccsd.cnrs.fr.invalid (E. Tavernier) 01 Oct 2025

https://hal.inrae.fr/hal-05291477v1

[hal-05295319] Longitudinal changes of stem-like cells in colostrum and milk of dairy cows

This study aimed to identify and quantify the various stem-like cell types in dairy cows’ colostrum and milk at the onset of lactation. Five second parity Holstein cows were monitored from calving until the seventh-day postpartum. Mammary secretions were collected immediately after calving, then every 3 h until 12 h during day (d) 0, and during morning milking on d 1, d 2, d 4 and d 7. Cells were prepared from mammary secretions and analysed by flow cytometry using relevant cellular markers. The highest total and viable cell concentrations were observed in colostrum collected at calving and up to 6 h, with these concentrations decreasing substantially in samples collected later at d 0. Then, the concentrations of both total and viable cell populations continued to slowly decrease until d 7, the kinetic curves reaching a baseline plateau. Flow cytometry showed that the CD49f pos CD24 pos population, which identifies mammary epithelial stem cells, represented about 0.9% of viable cells at calving and about 0.1% 12 h later, the mammary epithelial stem cell concentration therefore being at its highest level in the very first colostrum. In contrast, the percentage of mesenchymal stem-like cells, defined as the population of CD34 neg CD105 pos CD90 pos CD29 pos cells, was roughly constant (≈0.3%) during the first two milkings and decreased mainly during the first day to a basal level close to 0. Concerning haematopoietic stem-like cells, defined as the CD45 neg CD34 pos CD117 pos CD90 pos cell population, they were only observed in the colostrum collected at calving. All the types of stem cells studied here were therefore only present in substantial quantities in the colostrum of the very first hours after calving, a period during which the calf’s intestine is permeable, possibly allowing the transfer and integration of these cells in the tissues of the newborn calf.

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Finot) 03 Oct 2025

https://hal.inrae.fr/hal-05295319v1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[hal-05316296] Methods for analysing the agroecological transition at the sector level

This article proposes an analytical framework for the agroecological transition process at the level of agrifood sectors, drawing on approaches from sustainability transition research (STR) and the economics of innovation. The aim of this framework is to examine the way in which the various stages engaged in an agrifood chain can coordinate to build a collective learning process to support more sustainable agrifood systems. A number of key functions were considered, such as learnings and cocreation of knowledge, market formation and supply development through contracts. The relevance of this analytical framework to our understanding of value chain dynamics was emphasised through a study of 28 value chain cases claiming to have differentiated practices related to agroecological principles;

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

https://hal.inrae.fr/hal-05316296v1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[hal-05166806] The effect of rearing strategy on the dry matter intake of pasture-based dairy heifers

Although dry matter intake (DMI) is important in terms of achieving heifer weight-for-age targets and the utilization of pasture, the DMI of pasture-based heifers has not been widely researched. In order to quantify pasture-based heifer DMI and to determine the effect of different rearing strategies on DMI, data were collected from Holstein-Friesian (HF; n = 124), and Jersey (JE; n = 56) heifers weaned at either eight or 12 weeks and subsequently offered either a low or high post-weaning feeding regime. The n-alkane technique was used to measure the DMI of the heifers on nine occasions throughout the rearing period. Nutrition and management in the postweaning period had a greater effect on DMI than that of weaning age. Although HF heifers had a higher total DMI than JE, JE heifers had a higher DMI when expressed as a percentage of BW. The results from this study indicate that rearing strategy may be used to manipulate DMI, and thus optimize the attainment of weight-for-age targets in pasture-based heifers.

ano.nymous@ccsd.cnrs.fr.invalid (Hazel Costigan) 17 Jul 2025

https://hal.inrae.fr/hal-05166806v1

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

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

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

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

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

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

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

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

[hal-05314324] Safeguarding a local breed of pig through the Noir de Bigorre value chain

Although French pork production is considered to be relatively homogeneous, a range of products from alternative breeding systems including, among others, official quality labels, has been developed. The example of the Noir de Bigorre chain, based on the preservation and promotion of the Gascon pig breed, can shed light on the development of an initiative whose principles largely correspond with the elements of agroecology proposed by the Food and Agriculture Organization (FAO). When interviewed about their organisation, the representatives of this pork chain and a processing partner largely identified with these different dimensions of agroecology. The founding principle shared by all is that of human and social values and although based on the enhancement of ancestral practices, the success of this chain is based on numerous technical and organisational innovations.

ano.nymous@ccsd.cnrs.fr.invalid (Bénédicte Lebret) 14 Oct 2025

https://hal.inrae.fr/hal-05314324v1

[hal-05385764] Aerodynamic flux–gradient measurements of ammonia over four spring seasons in grazed grassland: environmental drivers, methodological challenges and uncertainties

Understanding the factors controlling surface–atmosphere exchange of ammonia (NH3) in grazed grasslands is crucial for improving atmospheric models and addressing environmental concerns associated with reactive nitrogen. This study presents high-resolution NH3 flux data collected during four spring campaigns (2021–2024) at an intensively managed grassland site in Northwestern France, using the aerodynamic gradient method (AGM) alongside continuous monitoring of environmental variables and agricultural management. AGM-derived half-hourly NH3 fluxes exhibited distinctive patterns: (i) high variability during grazing from −113 (deposition) to +3205 (emission) ng NH3 m−2 s−1, influenced by meteorology, grazing livestock density, and vegetation and soil dynamics; (ii) strong diurnal patterns and day-to-day variability; and (iii) transient volatilisation peaks following slurry applications (up to 10 235 ng NH3 m−2 s−1). Grazing-induced emission fluxes often persisted for up to 1–2 weeks following cattle departure. Relative random uncertainties associated with AGM flux measurements typically ranged from 15 % to 70 %, based on errors in vertical concentration gradient slopes and variables related to turbulence and stability. Additional methodological limitations and systematic uncertainties are discussed, in particular errors associated with fundamental AGM assumptions and flux footprint attribution in a rotational grazing setup. The mean overall cattle head-based emission factor (EF) was 6.5 g NH3-N cow−1 grazing d−1 but varied considerably between grazing events, from 1 to 23 g NH3-N cow−1 grazing d−1, reflecting the interplay between livestock management and environmental factors. This study highlights the importance of long-term, continuous, high-resolution measurements to document the large variability in grazing-induced NH3 fluxes. The findings also underscore the need for refining bi-directional exchange models that integrate physics (meteorology, turbulence), environmental biogeochemistry (the fate of excreted nitrogen in the soil), biology (dynamic vegetation processes) and pasture management (grazing intensity) in grazed grassland systems.

ano.nymous@ccsd.cnrs.fr.invalid (Mubaraq Olarewaju Abdulwahab) 27 Nov 2025

https://hal.inrae.fr/hal-05385764v1

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