Scientific publication

Unit publications on the Hal-INRAE institutional portal.

Last scientifics articles

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

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

ano.nymous@ccsd.cnrs.fr.invalid (Sara Álvarez) 12 Dec 2024
https://hal.inrae.fr/hal-04832467v1
[hal-04821220] Postmortem proteolysis and its indicators vary within bovine muscles: Novel insights in muscles that differ in their contractile, metabolic, and connective tissue properties

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

ano.nymous@ccsd.cnrs.fr.invalid (Chandler Stafford) 05 Dec 2024
https://hal.inrae.fr/hal-04821220v1
[hal-04843455] Révéler et valoriser vos données avec le thésaurus INRAE

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

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Aubin) 17 Dec 2024
https://hal.inrae.fr/hal-04843455v1
[hal-04820215] Améliorer conjointement la santé et le bien-être des animaux dans la transition des systèmes d’élevage vers la durabilité

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

ano.nymous@ccsd.cnrs.fr.invalid (Christian Ducrot) 05 Dec 2024
https://hal.inrae.fr/hal-04820215v1
[hal-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 Review in Advance. Changes may still occur before final publication.

ano.nymous@ccsd.cnrs.fr.invalid (Huaijun Zhou) 03 Dec 2024
https://hal.science/hal-04802793v1
[hal-04764494] Effect of using germinated and fermented lupin and oats as a dietary protein source on laying hen performance and egg quality

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

ano.nymous@ccsd.cnrs.fr.invalid (Koffigan Kponouglo) 04 Nov 2024
https://hal.science/hal-04764494v1
[hal-04675948] Partitioning of energy intake in broiler breeders from 27 to 63 weeks old

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

ano.nymous@ccsd.cnrs.fr.invalid (Guilherme Ferreira da Silva Teofilo) 23 Aug 2024
https://hal.inrae.fr/hal-04675948v1
[hal-04685713] GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations

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

ano.nymous@ccsd.cnrs.fr.invalid (Fabien Degalez) 03 Sep 2024
https://hal.inrae.fr/hal-04685713v1
[hal-04718511] Stocking density at feeders and drinkers and temporal feed restriction affects dairy cows’ drinking behavior

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

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 02 Oct 2024
https://hal.inrae.fr/hal-04718511v1
[hal-04618232] Association between body condition profiles, milk production and reproduction performance in Holstein and Normande cows

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

ano.nymous@ccsd.cnrs.fr.invalid (C. Dezetter) 20 Jun 2024
https://hal.inrae.fr/hal-04618232v1
[hal-04706111] Work: a barrier to reducing pesticide use in Breton dairy farms?

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

ano.nymous@ccsd.cnrs.fr.invalid (Anne-Lise Jacquot) 23 Sep 2024
https://hal.science/hal-04706111v1
[hal-04581102] Post-milking application of a Lacticaseibacillus paracasei strain impacts bovine teat microbiota while preserving the mammary gland physiology and immunity

Bovine mastitis (BM) is a major disease in dairy industry. The current approaches – mainly antibiotic treatments are not entirely effective and may contribute to antimicrobial resistance dissemination, rising the need for alternative treatment. The present study aims to evaluate the impact of post-milking application of Lacticaseibacillus paracasei CIRM BIA 1542 (Lp1542) on the teat skin (TS) of 20 Holstein cows in mid lactation, in order to reinforce the barrier effect of the microbiota naturally present on the teat. Treatment (Lp1542, iodine or no treatment) was applied post-milking twice a day on the 4 teats of healthy animals for 15 days. Blood and milk samples, and TS swabs were collected at day (D)1, D8, D15 and D26 before morning milking and at D15 before evening milking (D15E) to evaluate Lp1542 impact at the microbial, immune and physiological levels. Lp1542 treatment resulted in a higher lactic acid bacteria and total microbial populations on TS and in foremilk (FM) at D15(E) compared with iodine treatment. Metabarcoding analysis revealed changes in the composition of TS and FM microbiota, beyond a higher Lacticaseibacillus abundance. This included a higher abundance of Actinobacteriota, including Bifidobacterium, and a lower abundance of Pseudomonadota on TS of Lp1542 compared with iodine- treated quarters. In addition, Lp1542 treatment did not trigger any major inflammatory response in the mammary gland, except interleukin 8 production and expression which tended to be slightly higher in Lp1542-treated cows compared with the others. Finally, Lp1542 treatment had no impact on the mammary epithelium functionality (milk yield and composition) and integrity (epithelial cell exfoliation into milk and milk Na + /K + ratio). Altogether, these results indicate that a topical treatment with Lp1542 is safe with regard to mammary gland physiology and immune system, while impacting its microbiota, inviting us to further explore its effectiveness for mastitis prevention.

ano.nymous@ccsd.cnrs.fr.invalid (Coralie Goetz) 21 May 2024
https://hal.inrae.fr/hal-04581102v1
[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-04538081] Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions

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

ano.nymous@ccsd.cnrs.fr.invalid (Maria Bernard) 09 Apr 2024
https://hal.inrae.fr/hal-04538081v1
[hal-04495275] Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability

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

ano.nymous@ccsd.cnrs.fr.invalid (Christian Ducrot) 08 Mar 2024
https://hal.inrae.fr/hal-04495275v1
[hal-04696591] On farm precision feeding of gestating sows based on energy and amino acids on farrowing performances and feeding behavior over 3 consecutive gestations

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

ano.nymous@ccsd.cnrs.fr.invalid (Clément Ribas) 13 Sep 2024
https://hal.inrae.fr/hal-04696591v1
[hal-04283061] Genetic covariance components for measures of nitrogen utilization in grazing dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (E. Tavernier) 13 Nov 2023
https://hal.inrae.fr/hal-04283061v1
[hal-04634569] Sows and piglets adjust their use of an outdoor paddock with season and piglet age during the first weeks of life in an organic farm

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

ano.nymous@ccsd.cnrs.fr.invalid (Anissa Jahoui) 04 Jul 2024
https://hal.inrae.fr/hal-04634569v1
[hal-04609533] Effects of replacing corn silage and soybean meal with an increasing percentage of fresh herbage on dairy cow nitrogen use efficiency and flows

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

ano.nymous@ccsd.cnrs.fr.invalid (Manon Ferreira) 12 Jun 2024
https://hal.inrae.fr/hal-04609533v1
[hal-04527102] The genetics of resilience and its relationships with egg production traits and antibody traits in chickens

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

ano.nymous@ccsd.cnrs.fr.invalid (Tom Berghof) 04 Apr 2024
https://hal.inrae.fr/hal-04527102v1
[hal-04709369] Assessing the contribution of French dairy ruminant farms to the production of food for human consumption

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

ano.nymous@ccsd.cnrs.fr.invalid (Benoit Rouille) 25 Sep 2024
https://hal.inrae.fr/hal-04709369v1
[hal-04437975] Potential applications of biosurfactants in animal production and meat research

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

ano.nymous@ccsd.cnrs.fr.invalid (Cerine Yasmine Boulahlib) 05 Feb 2024
https://hal.inrae.fr/hal-04437975v1
[hal-04666242] Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers

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

ano.nymous@ccsd.cnrs.fr.invalid (Mathilde Doublet) 01 Aug 2024
https://hal.inrae.fr/hal-04666242v1
[hal-04746222] Sorted stem/progenitor epithelial cells of pubertal bovine mammary gland present limited potential to reconstitute an organised mammary epithelium after transplantation

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

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Finot) 21 Oct 2024
https://hal.inrae.fr/hal-04746222v1
[hal-04575196] Face au changement climatique, quelles stratégies d’atténuation et d’adaptation pour les productions avicoles ?

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

ano.nymous@ccsd.cnrs.fr.invalid (Anne Collin) 15 May 2024
https://hal.inrae.fr/hal-04575196v1
[hal-04677211] Organic rearing of non-castrated male pigs: welfare indicators, carcass traits, pork quality and boar taint in Duroc and Pietrain crossbreds

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

ano.nymous@ccsd.cnrs.fr.invalid (Bénédicte Lebret) 25 Aug 2024
https://hal.inrae.fr/hal-04677211v1
[hal-04283002] Nitrogen offset potential in a multi-year farmlet-scale study; milk and herbage production from grazed perennial ryegrass/white clover swards

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

ano.nymous@ccsd.cnrs.fr.invalid (Á. Murray) 13 Nov 2023
https://hal.inrae.fr/hal-04283002v1
[hal-04703322] Interaction between drinker density and cow social dominance affects drinking behavior

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

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 20 Sep 2024
https://hal.inrae.fr/hal-04703322v1
[hal-04619014] From the biochemical pieces to the nutritional puzzle: using meta-reactions in teaching and research

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

ano.nymous@ccsd.cnrs.fr.invalid (Jaap J. van Milgen) 20 Jun 2024
https://hal.inrae.fr/hal-04619014v1
[hal-04628706] Effects of parity and week after calving on the metabolic, redox and immune status of dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (Angélique Corset) 02 Oct 2024
https://hal.inrae.fr/hal-04628706v1
[hal-04664474] Effects of natural oral alternatives to parental iron supplementation on haematological and health-related blood parameters of organic piglets

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

ano.nymous@ccsd.cnrs.fr.invalid (Elodie Merlot) 30 Jul 2024
https://hal.inrae.fr/hal-04664474v1
[hal-04586224] Strategies of maize silage supplementation of grazing dairy cows: Effects on milk production, pasture intake, grazing behaviour and methane emissions

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

ano.nymous@ccsd.cnrs.fr.invalid (Rémy Delagarde) 24 May 2024
https://hal.inrae.fr/hal-04586224v1
[hal-04773240] Impact of genome build on RNA-seq interpretation and diagnostics

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

ano.nymous@ccsd.cnrs.fr.invalid (Rachel Ungar) 08 Nov 2024
https://hal.inrae.fr/hal-04773240v1
[hal-04448073] Bioaccessibility and associated concepts: Need for a consensus

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

ano.nymous@ccsd.cnrs.fr.invalid (Myriam M.L. Grundy) 09 Feb 2024
https://hal.inrae.fr/hal-04448073v1
[hal-04549544] Porcine ear necrosis is associated with social behaviours in weaned piglets

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

ano.nymous@ccsd.cnrs.fr.invalid (Gwenaël Boulbria) 17 Apr 2024
https://hal.inrae.fr/hal-04549544v1
[hal-04568409] Data-independent acquisition-based SWATH-MS proteomics profiling to decipher the impact of farming system and chicken strain and discovery of biomarkers of authenticity in organic versus antibiotic-free chicken meat

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

ano.nymous@ccsd.cnrs.fr.invalid (Laura Alessandroni) 04 May 2024
https://hal.inrae.fr/hal-04568409v1
[hal-04415987] Meat Omics: Trends and applications of Omics strategies in meat research

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

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 26 Jan 2024
https://hal.inrae.fr/hal-04415987v1
[hal-04309414] Assessment of beef sensory attributes and physicochemical characteristics: A comparative study of intermediate versus normal ultimate pH striploin cuts

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

ano.nymous@ccsd.cnrs.fr.invalid (Iliani Patinho) 04 Dec 2023
https://hal.inrae.fr/hal-04309414v1
[hal-04653317] Quels défis au développement de la production porcine en agriculture biologique en France ?

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

ano.nymous@ccsd.cnrs.fr.invalid (Lucile Montagne) 18 Jul 2024
https://hal.inrae.fr/hal-04653317v1
[hal-04617235] CowPILOT -Piloter la note d'état corporel pour optimiser la reproduction des vaches laitières

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

ano.nymous@ccsd.cnrs.fr.invalid (Fabrice Bidan) 19 Jun 2024
https://hal.inrae.fr/hal-04617235v1
[hal-04636071] Yaks are dependent on gut microbiota for survival in the environment of the Qinghai Tibet plateau

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

ano.nymous@ccsd.cnrs.fr.invalid (Runze Wang) 05 Jul 2024
https://hal.inrae.fr/hal-04636071v1
[hal-04536609] Decreased lactose percentage in milk associated with quarter health disorder and hyperketolactia, a proxy for negative energy balance, in dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (Auxane Hamon) 08 Apr 2024
https://hal.inrae.fr/hal-04536609v1
[hal-04510660] Sensitivity analysis of the INRA 2018 feeding system for ruminants by a one-at-a-time approach: Effects of dietary input variables on predictions of multiple responses of dairy cattle

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

ano.nymous@ccsd.cnrs.fr.invalid (Seoyoung Jeon) 19 Mar 2024
https://hal.science/hal-04510660v1
[hal-04603561] Intake profile, milk production and energy balance of early lactation spring calving Holstein Friesian and Jersey x Holstein Friesian dairy cows in high utilisation pasture-based systems

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

ano.nymous@ccsd.cnrs.fr.invalid (S. Walsh) 06 Jun 2024
https://hal.inrae.fr/hal-04603561v1
[hal-04582488] Evidence of stable preferential affiliative relationships in the domestic pig

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

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Clouard) 22 May 2024
https://hal.inrae.fr/hal-04582488v1
[hal-04687408] Eco-friendly diet: nutrient digestibility, nitrogen and energy balances and growth performance of growing pigs

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

ano.nymous@ccsd.cnrs.fr.invalid (Francine de Quelen) 04 Sep 2024
https://hal.inrae.fr/hal-04687408v1
[hal-04802821] BIOMARQ'LAIT -Identification of biomarkers in milk to monitor the nutritional status of dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (Marine Gele) 25 Nov 2024
https://hal.inrae.fr/hal-04802821v1
[hal-04586201] Monitoring individual drinking behaviour and the social hierarchy in dairy cows using electronic drinkers

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

ano.nymous@ccsd.cnrs.fr.invalid (Ellynn Nizzi) 24 May 2024
https://hal.inrae.fr/hal-04586201v1
[hal-04693509] Dataset describing the effects of housing environment, dominance status and parity on the PBMC transcriptome of sows during gestation and lactation

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

ano.nymous@ccsd.cnrs.fr.invalid (Mariana Mescouto Lopes) 10 Sep 2024
https://hal.science/hal-04693509v1
[hal-04703177] Quelles génétiques pour les systèmes d’élevages certifiés en agriculture biologique ?

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

ano.nymous@ccsd.cnrs.fr.invalid (Laurianne Canario) 19 Sep 2024
https://hal.inrae.fr/hal-04703177v1
[hal-04364631] Pea cell wall polysaccharides and their structural integrity influence protein bioaccessibility and hydrolysis

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

ano.nymous@ccsd.cnrs.fr.invalid (Maxence Noel) 27 Dec 2023
https://hal.science/hal-04364631v1
[hal-04603863] Three-dimensional imaging to estimate in vivo body and carcass chemical composition of growing beef-on-dairy crossbred bulls

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

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Xavier) 06 Jun 2024
https://hal.inrae.fr/hal-04603863v1
[hal-04575157] Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

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

ano.nymous@ccsd.cnrs.fr.invalid (Fabien Degalez) 15 May 2024
https://hal.inrae.fr/hal-04575157v1
[hal-04808292] Impact of milking interval and time on milk spontaneous lipolysis and composition in dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (Catherine Hurtaud) 28 Nov 2024
https://hal.inrae.fr/hal-04808292v1
[hal-04536587] The fate of Cu and Zn along the feed-animal-excreta-effluent continuum in swine systems according to feed and effluent treatment strategies

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

ano.nymous@ccsd.cnrs.fr.invalid (Emma Gourlez) 08 Apr 2024
https://hal.inrae.fr/hal-04536587v1
[hal-04741493] Qualité et authentification des produits animaux issus de l’agriculture biologique vs conventionnelle

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

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Prache) 17 Oct 2024
https://hal.inrae.fr/hal-04741493v1
[hal-04557071] Synthesis of milk components involves different mammary metabolism adaptations in response to net energy and protein supplies in dairy cows

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

ano.nymous@ccsd.cnrs.fr.invalid (Jean-Charles Anger) 24 Apr 2024
https://hal.inrae.fr/hal-04557071v1
[hal-04661694] The use of computed tomography for in vivo estimation of reticulo-rumen and omasum contents in Alpine goats

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

ano.nymous@ccsd.cnrs.fr.invalid (J.A.A. Pires) 25 Jul 2024
https://hal.inrae.fr/hal-04661694v1
[hal-04533050] Genetic background of body reserves in laying hens through backfat thickness phenotyping

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

ano.nymous@ccsd.cnrs.fr.invalid (Nicolas Bédère) 30 Apr 2024
https://hal.inrae.fr/hal-04533050v1
[hal-04502991] Meat by-products as a source of bioactive peptides and functional ingredients: Regulatory and safety barriers to valorization

Proposals for sustainable use of meat industry waste and by-products have seen a remarkable growth in recent decade. This paper aims to shed light on the often-overlooked realm of meat by-products, positioning them as an invaluable source of bioactive peptides and functional ingredients. It emphasized on the first part the main strategies for valorization of meat industry by-products into diverse bioactive peptides, and then it introduces in the second part the diverse and current methods of identification and characterization of bioactive peptides and protein hydrolysates. While the promise of these macromolecules is immense, the paper focuses and takes an in-depth look in the third part at the regulatory and safety barriers hindering their efficient valorization. By addressing regulatory and safety concerns, this review aims to pave the way for a more sustainable and responsible utilization of meat by-products, ensuring not only the economic viability of the meat sector, but also fostering a holistic and safe approach towards enhanced food and animal production sustainability.

ano.nymous@ccsd.cnrs.fr.invalid (Mohammed Gagaoua) 13 Mar 2024
https://hal.inrae.fr/hal-04502991v1
[hal-04675026] Exposure to natural stray currents of low voltage affects the behaviour and some stress biomarkers of weaned piglets

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

ano.nymous@ccsd.cnrs.fr.invalid (Théo Nicolazo) 22 Aug 2024
https://hal.inrae.fr/hal-04675026v1
[hal-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-04666195] Sequential window acquisition of all theoretical mass spectra (SWATH-MS) as an emerging proteomics approach for the discovery of dark-cutting beef biomarkers

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

ano.nymous@ccsd.cnrs.fr.invalid (Laura González-Blanco) 01 Aug 2024
https://hal.inrae.fr/hal-04666195v1
[hal-04456512] Biopreservation of pre-processed fresh fish by bio-based coatings

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

ano.nymous@ccsd.cnrs.fr.invalid (Don Hettiarachchige Udana Eranda) 19 Feb 2024
https://hal.inrae.fr/hal-04456512v1
[hal-04299155] Challenges and future perspectives for the European grading of pig carcasses – A quality view

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

ano.nymous@ccsd.cnrs.fr.invalid (Marjeta Čandek-Potokar) 22 Nov 2023
https://hal.inrae.fr/hal-04299155v1
[hal-04604803] In-depth exploration of the high and normal pH beef proteome: First insights emphasizing the dynamic protein changes in longissimus thoracis muscle from pasture-finished Nellore bulls over different postmortem times

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

ano.nymous@ccsd.cnrs.fr.invalid (Iliani Patinho) 07 Jun 2024
https://hal.inrae.fr/hal-04604803v1
[hal-04565725] Barriers and drivers of farmers to provide outdoor access in pig farming systems: a qualitative study

Part of the farmers have chosen to raise pigs with outdoor access. However, providing outdoor access to pigs is not a simple matter, and many farmers are hesitating or feel powerless to engage in this transition. A better understanding of their needs and challenges could facilitate the development of innovations that generate commitment. This survey aimed to identify the French pig farmers’ barriers to and drivers for providing outdoor access to pigs. A total of 36 farmers, aged 25–60, who worked in all types of pig farming systems (from full indoor to free-range) participated in a semi-structured interview that lasted 1.25–2.25 h. The topics covered included a historical overview, a description of the farm and practices, as well as opinions about the impact of outdoor access on farmers, animals, production and economic performance, environment, and society. Qualitative data were analysed using thematic analysis. Most of the participants agreed that rearing pigs indoors is a different job from that of rearing pigs with outdoor access and that it is above all a matter of choice, farmer work conception, and work comfort. Farmers generally agreed that working outdoors is particularly arduous, but this could be compensated by the satisfaction of being in contact with nature and seeing animals in a more complex environment. A large majority of farmers managing a system with outdoor access raised the issue of lack of support, highlighting the need for refinement and diffusion of guides of practices as well as day-to-day support. The impact of outdoor access on the health and welfare of pigs was discussed, especially regarding climatic hazards and the risk of zoonoses, and several outdoor farmers explained how their relationship with the animals changes when pigs are raised outside. Given that zootechnical performance may significantly decrease in farms with outdoor access, various strategies can be employed to maintain profitability, such as feed production, circularity, direct sales, or work diversification. They could be either motivating or demotivating factors depending on the individuals. Concerns about social criticism were prominent among many indoor farmers while farmers providing outdoor access generally felt more serene and proud. Overall, this study can serve as a basis to identify levers that could remove barriers, foster the adherence of more farmers, and facilitate the transition towards more pig farming systems with outdoor access, provided that those systems are viable and beneficial for the welfare and health of the animals and farmers.

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Brajon) 02 May 2024
https://hal.science/hal-04565725v1
[hal-04724456] Effect of sward species diversity combined with a reduction in nitrogen fertilizer on the performances of spring calving grazing dairy cows

The objective of this study was to evaluate the impact of sward diversification combined with a reduction of chemical nitrogen (N) fertilizer on the performance of spring calving grazing dairy cows within a farm systems experiment. Three farmlets were created; a monoculture of perennial ryegrass (Lolium perenne L.; PRG) fertilized with 250 kg N/ha (PRG-250N), a PRG - white clover (Trifolium repens; WC) sward fertilized with 125 kg N/ha (PRGWC-125N) and a multispecies sward (MSS) comprising of grasses, legumes and herbs also fertilized with 125 kg N/ha (MSS-125N). Each farmlet had its own herd of dairy cows on a total area of 18.7 ha divided into 20 paddocks. Each herd was comprised of pure Holstein-Friesian (HF) and HF Jersey crossbred (JFX) animals and randomly assigned through the 3 treatments. For 3 years (2021 to 2023), the performances of both swards (grass yield, botanical composition, nutritive value) and grazing animals (milk production and composition, body weight (BW) and body condition score (BCS)) were recorded. There were no significant differences in pasture production or sward nutritive value between sward systems and grazing season length was also similar (264 d). On average over the 3 years, PRGWC-125N contained 150 g/kg DM of legumes and the MSS-125N contained 160 g/kg DM legumes, 130 g/kg DM plantain and 40 g/kg DM chicory. Both individual cow milk and fat plus protein (Milk solids; MS) yield were lower for PRG-250N (5,018 and 452 kg, respectively), intermediate for PRGWC-125N (5,139 and 463 kg, respectively) and highest for MSS-125N (5,297 and 476 kg, respectively) while milk and MS production per hectare from grazing were similar during the study period (11,523 and 1,016 kg/ha, respectively). Breed also had a significant effect with the JFX having lower milk yield but higher fat and protein concentration compared with HF. This resulted in higher MS production per kg of BW for the JFX compared with HF (0.96 and 0.87 kg MS/kg BW, respectively). The results of this study highlight the possibility for more diverse pastures to reduce chemical N fertilizer input requirements and maintain pasture productivity while increasing animal performance within pasture-based spring calving systems.

ano.nymous@ccsd.cnrs.fr.invalid (A. Jezequel) 07 Oct 2024
https://hal.inrae.fr/hal-04724456v1
[hal-04455106] One-shot technology for 3D imaging of large animals: perspectives for ruminant management

In numerous systems of animal production, there is increasing interest in the use of 3D imaging technology on farms for its ability to easily and safely measure traits of interest on living animals. With this information, it is possible to evaluate multiple morphological indicators of interest, either directly or indirectly, and follow them through time. Several tools for this purpose were developed, but one of their main weaknesses was their sensitivity to light and animal movement, which limited their potential for large-scale application on farms. To address this, a new device, called Deffilait3D and based on depth camera technology, was developed. In tests on 31 Holstein dairy cows and 13 Holstein heifers, the values generated for most measured indicators were highly repeatable and reproducible, with coefficients of variation lower than 4%. A comparison of measurements obtained from both Deffilait3D and previous validated system, called Morpho3D, revealed a high degree of similarity for most selected traits, e.g., less than 0.2% variation for animal volume and 1.2% for chest depth, with the highest degree of difference (8%) noted for animal surface area. Previously published equations used to estimate body weight with the Morpho3D device were equally valid using Deffilait3D. This new device was able to record 3D images regardless of the movement of animals and it is affected only by direct daylight. The on-going step is now to develop methods for automated analysis and extraction from images, which should enable the rapid development of new tools and potentially lead to the large-scale adoption of this type of device on commercial farms.

ano.nymous@ccsd.cnrs.fr.invalid (Yannick Le Cozler) 13 Feb 2024
https://hal.science/hal-04455106v1
[hal-04389098] Calculating herbage utilization and intake by dairy cows under subtropical conditions using conventional field measurement techniques or the HerbValo method

This study aimed to evaluate the HerbValo method in comparison to conventional field measurement techniques as a tool for estimating the herbage utilization and dry matter (DM) intake by grazing dairy cows under subtropical conditions. It was carried out during 18 months in a commercial farm of Southern Brazil. The herbage utilization was estimated monthly in two to four randomly selected paddocks (total n = 40) using the rising-plate meter or the double-sampling technique. In parallel, the herbage utilization was estimated by the HerbValo method, which is based on simple descriptions of the herd, supplements, pasture and grazing management. Values of herbage utilization estimated by field techniques were linearly (P < 0.01) related to those estimated by HerbValo, with no effect of pasture type (tropical vs. temperate) on the origin or on the slope of the regression (slope = 0.97; origin = -0.1; R-2 = 0.81; rsd = 0.17 t DM/ha). At cow x day level, values of herbage intake estimated by field techniques were also linearly related to those estimated by HerbValo (P < 0.01; R-2 = 0.82; rsd = 1.30 kg DM/cow/day). A negative linear relationship (P < 0.01) between herbage and supplement intake was obtained for both field (slope = -1.06; R-2 = 0.72; rsd = 1.64) and HerbValo (slope = -0.92; R-2 = 0.82; rsd = 1.08) approaches. Herbage utilization and intake by a dairy herd in a subtropical grazing-based system can be reliably estimated by the HerbValo method with the advantage of not requiring direct field pasture measurements.

ano.nymous@ccsd.cnrs.fr.invalid (Letícia Wlodarski) 11 Jan 2024
https://hal.inrae.fr/hal-04389098v1
[hal-04717884] Effects of reducing copper and zinc supplementation on the performance and mineral status of fattening pigs

Pig manure with high copper (Cu) and zinc (Zn) concentration is applied to the soil, and these trace minerals can accumulate in the topsoil and decrease its fertility. Thus, adjusting concentrations of Cu and Zn in pig diets below current maximum allowance can prevent this risk. Reduction of dietary concentrations of Cu and Zn reduces their faecal excretion since only a small portion is retained in the pig's body. The aim of this study was to evaluate the effects of reducing concentration of dietary Cu and Zn or withdrawing their supplementation on the performance and mineral status of fattening pigs. Four dietary treatments were compared: a basal diet (WS; withdraw supplementation), with no Cu or Zn supplementation (5 and 29 mg/kg of native Cu and Zn, respectively); intermediate concentration (O-INT), supplemented with Cu and Zn oxides to obtain mean dietary concentration of 7.4 and 47.5 mg/kg of Cu and Zn, respectively; and two diets supplemented with oxides (O-REG) or sulphates (S-REG) at concentration similar to European Union limits (i.e. 25 and 120 mg/kg of total Cu and Zn, respectively), as commonly used on commercial farms. Ninety-six pigs (24.3 +/- 3.3 kg BW) were each assigned to one of the four treatments and reared in individual pens for 14 weeks (up to 110.3 +/- 8.9 kg BW). Animal performances were measured, and samples of plasma (on day 1 and day 41 of experimentation and at slaughter), bones and the liver (at slaughter) were collected from all pigs. Faecal samples were collected from all pigs every 3 weeks to determine the Cu and Zn excretion. Over the entire experiment, neither the concentration nor the source of Cu and Zn influenced feed intake, BW or the feed conversion ratio. Plasma Cu and Zn concentrations were not influenced by the treatment but increased as the age of the pigs increased. Liver Cu concentration increased (P &lt; 0.05) as dietary concentrations increased (O-REG&gt; WS). Neither the concentration nor the source of Cu and Zn influenced bone Cu and Zn concentration or physical bone parameters. However, S-REG had a higher maximum load until bone breaking (P &lt; 0.05) than O-REG. As expected, faecal excretion of Cu and Zn decreased (P &lt; 0.01) as dietary concentration decreased. Dietary Cu and Zn can be reduced without decreasing the performance or mineral status of pigs, and these results should be validated on commercial farms that have more challenging health conditions.

ano.nymous@ccsd.cnrs.fr.invalid (Emma Gourlez) 02 Oct 2024
https://hal.science/hal-04717884v1
[hal-04579500] Feed restriction affects milk performances and decreases milk lipolysis in dairy ewes

Spontaneous lipolysis results in the breakdown of milk fat by the lipoprotein lipase (LPL; EC: 3.1.1.34), an enzyme present in milk. Free fatty acids (FFA) and by-products released in milk during lipolysis can alter both the organoleptic value of milk (off-flavours release) and technological properties of dairy products (decrease in creaming capabilities). Current climate change is having significant impacts on the feeding of grazing animals, with negative consequences on the availability and quality of grass. We and others have demonstrated that dietary restriction increases milk lipolysis in the cow species. However, no data about the impact of feed restriction on milk lipolysis is available in the ewe species. Thus, this paper aims to investigate the effect of feed restriction on milk characteristics with regard to lipolysis values in dairy ewes. Two groups of 24 multiparous Lacaune ewes in mid-lactation received a “non-restricted” (NON RESTR) control diet (100 % of ad libitum DM intake) or a “restricted” (RESTR) diet (65 % of ad libitum DM intake) according to a 2 X 2 crossover design. Milk gross composition together with lipolysis analyses were performed. Blood samples were also screened for metabolites or hormones concentrations. The RESTR treatment induced a decrease in milk production (- 21 % compared with control treatment) and a modification of the metabolism of dairy ewes characterized by an increase in plasma non-esterified fatty acids (NEFA), which represents the balance between adipose tissue mobilization and the use of NEFA by other tissues (+ 153 %), cholesterol (+ 17 %) and beta-hydroxybutyrate (+ 4 %) levels. As a result, a decrease in body weight of dairy ewes was observed (- 7 %). Feed restriction also resulted in a decrease in milk lipolysis estimated by the milk FFA measured by the copper-soap method (- 63 % and - 62 %, respectively for morning and evening milking) or by the reference Bureau of Dairy Industry (BDI) method (- 51 % and – 57 %, respectively for morning and evening milking). The decrease in milk spontaneous lipolysis under feed restriction was not associated with a decrease in lipoprotein lipase activity in ewes. These results will be completed with proteomic and lipidomic studies in milk samples to better understand mechanisms initiated in the ewe species specifically with regard to lipolysis in milk.

ano.nymous@ccsd.cnrs.fr.invalid (Laurence Bernard) 28 Jun 2024
https://hal.inrae.fr/hal-04579500v1
[hal-04495509] Quel modèle pour couvrir ses besoins dans le cadre d’une alimentation durable ? Focus sur les protéines et le calcium

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

ano.nymous@ccsd.cnrs.fr.invalid (Bernard Guy-Grand) 08 Mar 2024
https://hal.inrae.fr/hal-04495509v1
[hal-04409031] Getting to grips with Resilience: Toward large-scale phenotyping of this complex trait

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ano.nymous@ccsd.cnrs.fr.invalid (Nicolas N.C. Friggens) 06 Dec 2024
https://hal.science/hal-04409031v1
[hal-04438202] Data quantifying the behaviour of macro and trace elements along the feed – manure – treated waste continuum in pig production

Manure from animal production is commonly spread on agricultural soil as an organic fertiliser to provide macro and trace elements to crops. However, some trace elements can accumulate in the soil and become toxic to plants and microorganisms. These elements include copper (Cu) and zinc (Zn), which can be applied in large quantities when pig manure is spread. The feeding strategy and manure management (e.g. through treatment chains) are two mechanisms identified to better control the use of these elements, but their fate from the feed to the soil in pig production remains poorly documented. Better understanding the fate of Cu and Zn, as well as that of other trace and macro elements, along the feed – excreta – waste chain is required to develop alternative ways to reduce their environmental impacts. This dataset provides insight into the composition (Cu, Zn and other trace and macro elements) of organic products along two contrasting manure management chains: (1) only storage or (2) in-building separation, anaerobic digestion (AD) of solids, and digestate drying. Feed, raw slurry, liquid and solid phases after separation of the manure and AD products were sampled and then analysed to measure their total compound contents.

ano.nymous@ccsd.cnrs.fr.invalid (Emma Gourlez) 08 Feb 2024
https://hal.inrae.fr/hal-04438202v1
[hal-04801625] Environmental benefits of crude protein reduction in growing pig diets: is it worth going further?

Nitrogen (N) excretion and emissions can be reduced in fattening pigs by reducing dietary crude protein (CP) levels. Effects of this strategy are well documented for moderate CP reduction, but little literature exists on further CP reduction made possible by free isoleucine, histidine, and leucine. This trial evaluated the effects of 2 levels of reduction in CP on growth performance, N balance, and gaseous emissions. Forty-eight pigs were allocated to 12 gaseous emission-measuring chambers at 28 kg live weight. Three dietary treatments (CTRL; −1.2pt; −2.4pt), with a CP content, respectively, of 18.1%, 16.9%, and 15.0% in phase 1 (28 to 48 kg) and 16.1%, 15.0%, and 13.8% in phase 2 (48 to 80 kg), were fed ad libitum. Growth performance was recorded for each phase. Body lipid and protein composition were analyzed by dual-energy X-ray absorptiometry in 2 animals per chamber at the beginning and end of the trial. These results were used to calculate the N balance. Slurry volume and composition were measured at the end of the trial. Ammonia, methane, and nitrous oxide emissions were recorded continuously. Data were analyzed with a general linear model including the linear and quadratic effect of CP reduction and phase as fixed effects. A trend for a quadratic effect of CP reduction on feed intake was observed (P = 0.085) with a decrease from CTRL to −1.2pt and then an increase with the −2.4pt treatment. Daily gain and gain to feed were improved by the low CP diets in phase 1 but were degraded in phase 2 (phase × CP interaction, P &lt; 0.001) while body composition was not affected. Nitrogen excretion decreased with CP reduction (linear effect, P = 0.023) but tended to plateau with the low CP diets (quadratic effect, P = 0.081). Methane emissions per kg of gain were reduced with CP reduction (linear effect, P = 0.031). Ammonia emissions decreased with CP reduction, mostly in phase 1 (phase × CP interaction, P = 0.015); however, the emission factor (g N-NH3 / g urinary N) was not affected. Nitrous oxide emissions were not affected by CP reduction and its emission factor (g N-N2O / g N) tended to increase (linear effect, P = 0.07). Slurry ammonia-N decreased (linear effect, P &lt; 0.023; quadratic effect, P = 0.049), but other slurry components were not significantly impacted. In this trial, a plateau in N excretion and emission reduction was reached with the −2.4pt treatment. Nevertheless, it is important to study such a reduction in conditions closer to commercial ones.

ano.nymous@ccsd.cnrs.fr.invalid (Léa Cappelaere) 25 Nov 2024
https://hal.inrae.fr/hal-04801625v1
[hal-04683286] Integrated Chemometrics and Data-Independent Acquisition Proteomics for the Discovery of Meat Authenticity Biomarkers: A Study on Early Post-Mortem Pectoralis major Muscle Proteomes of Ross 308 and Ranger Classic Chicken Produced by Organic versus Antibiotic-Free Farming Systems

Many factors, such as the farming systems and preslaughter rearing practices, can influence the physiological and metabolic functions of poultry with consequent effects on poultry meat quality. In this trial, label-free shotgun proteomics was used to analyze the early post-mortem Pectoralis major muscle proteomes of Ross 308 and Ranger Classic chicken strains raised under two divergent farming systems these being organic and antibiotic-free. The combination of chemometrics using partial-least-square discriminant analysis (PLS-DA) and shotgun proteomics allowed clear discrimination between the different groups. Chicken strains were discriminated by differences in the abundance of 73 and 62 proteins within the antibiotic-free and organic farming systems, respectively. The abundances of 71 and 52 proteins were impacted by the farming system within the Ross 308 and Ranger Classic chicken strains, respectively. The analyses allowed for the proposal of several putative biomarkers of meat authenticity, which were found to be related to muscle structure and energy metabolism pathways. This study is a significant step forward in elucidating the potential of proteomics profiling and chemometrics in chicken meat, which may provide opportunities for the efficient assessment of chicken authenticity.

ano.nymous@ccsd.cnrs.fr.invalid (Laura Alessandroni) 01 Sep 2024
https://hal.inrae.fr/hal-04683286v1
[hal-04399175] Proteomics and bioinformatics analyses based on two-dimensional electrophoresis and LC-MS/MS for the primary characterization of protein changes in chicken breast meat from divergent farming systems: Organic versus antibiotic-free

Proteomics is a key analytical method in meat research thanks to its potential in investigating the proteins at interplay in post-mortem muscles. This study aimed to characterize the differences in early post-mortem muscle proteomes of chickens raised under two farming systems: organic versus antibiotic-free. Forty post-mortem Pectoralis major muscle samples from two chicken strains (Ross 308 versus Ranger Classic) reared under organic versus antibiotic-free farming systems were characterized and compared using two-dimensional electrophoresis and LC-MS/MS mass spectrometry. Within antibiotic-free and organic farming systems, 14 and 16 proteins were differentially abundant between Ross 308 and Ranger Classic, respectively. Within Ross 308 and Ranger Classic chicken strains, 12 and 18 proteins were differentially abundant between organic and antibiotic-free, respectively. Bioinformatics was applied to investigate the molecular pathways at interplay, which highlighted the key role of muscle structure and energy metabolism. Antibiotic-free and organic farming systems can significantly impact the muscle proteome of chicken breast meat. This paper further proposes a primary list of putative protein biomarkers that can be used for chicken meat or farming system authenticity.

ano.nymous@ccsd.cnrs.fr.invalid (Laura Alessandroni) 18 Jan 2024
https://hal.inrae.fr/hal-04399175v1
[hal-04449380] Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine

Background Heat stress (HS) is an increasing threat for pig production with a wide range of impacts. When submitted to high temperatures, pigs will use a variety of strategies to alleviate the effect of HS. While systemic adaptations are well known, tissue-specific changes remain poorly understood. In this study, thirty-two pigs were submitted to a 5-day HS at 32 °C. Results Transcriptomic and metabolomic analyses were performed on several tissues. The results revealed differentially expressed genes and metabolites in different tissues. Specifically, 481, 1774, 71, 1572, 17, 164, and 169 genes were differentially expressed in muscle, adipose tissue, liver, blood, thyroid, pituitary, and adrenal glands, respectively. Regulatory glands (pituitary, thyroid, and adrenal) had a lower number of regulated genes, perhaps indicating an earlier sensitivity to HS. In addition, 7, 8, 2, and 8 metabolites were differentially produced in muscle, liver, plasma, and urine, respectively. The study also focused on the oxidative stress pathway in muscle and liver by performing a correlation analysis between genes and metabolites. Conclusions This study has identified various adaptation mechanisms in swine that enable them to cope with heat stress (HS). These mechanisms include a global decrease in energetic metabolism, as well as changes in metabolic precursors that are linked with protein and lipid catabolism and anabolism. Notably, the adaptation mechanisms differ significantly between regulatory (pituitary, thyroid and adrenal glands) and effector tissues (muscle, adipose tissue, liver and blood). Our findings provide new insights into the comprehension of HS adaptation mechanisms in swine.

ano.nymous@ccsd.cnrs.fr.invalid (Guilhem Huau) 12 Feb 2024
https://hal.inrae.fr/hal-04449380v1
[hal-04836336] Responses of dairy cows to weekly individualized feeding strategies regarding their metabolic status

In dairy farms, cows are commonly fed a mixture of forages and concentrates ad libitum. To improve the energy status and productivity of dairy cows, individualized feeding strategies have been proposed. One of these strategies is to provide supplemental concentrates to adjust the forage-to-concentrate ratio based on factors like individual milk yield or calculated energy balance. This strategy can affect milk production and cow health, although consistent rules for adjustment are lacking. The objectives of this study were to evaluate the effects of an individualized feeding strategy, adjusted weekly based on the BW gain of dairy cows, on production performance; and to determine whether the metabolic status of the cows could be predicted early in lactation to later be included in the decisions rules of the strategy. A total of 40 multiparous Holstein cows were involved in a 4-mo trial. The cows entered the experiment individually after calving and were initially fed a standard ration with a fixed 3 kg of extra concentrate per day for the first 8 d (on average). The cows were then paired based on calving date, parity (2 or 3), and BW gain over the initial week. One cow from each pair was assigned to the standard feeding strategy, which continued on the fixed ration, and the other was assigned to the precision feeding strategy, which received a variable amount of extra concentrate adjusted weekly based on BW gain. Measurements included weekly BW, daily milk yield, and daily intakes of concentrates and forages. Blood samples were collected to measure metabolites (glucose, BHB, nonesterified fatty acids) for metabolic profiling. The results showed no significant differences in overall BW gain, milk yield, or intakes (concentrates, forages, total intake). Two metabolic clusters were identified based on blood metabolites (glucose, BHB, nonesterified fatty acids), predicting cows' metabolic status with 90% accuracy. The balanced cluster had higher milk production, feed intake, and lost more BW than the imbalanced cluster. Alternative variables such as BW gain and total feed intake can be used to predict metabolic clusters, achieving up to 70% accuracy. To conclude, cows fed this precision feeding strategy had similar performances than those fed the standard feeding strategy. The long-term effect of this strategy should be studied. Metabolic profiling predicted cows' metabolic status, suggesting its potential for enhancing individualized feeding decisions.

ano.nymous@ccsd.cnrs.fr.invalid (Charlotte Gaillard) 13 Dec 2024
https://hal.inrae.fr/hal-04836336v1
[hal-04601713] Sound feeding signal for gestating sows: Evaluation of an individual learning strategy and its beneficial effects in groups

Competition for feed in a group of gestating sows leads to aggression around feeding stations, which has a negative impact on their welfare. This study investigates the potential of teaching gestating sows an individual sound signal to reduce aggression resulting from competition for feed access, and thus improve their welfare in a group. A total of 32 sows were used. In a test room, “learning” sows (n = 16) went through 4 individual learning phases (27 days in total) to associate the individual sound signal with an invitation to feed from a one-way feeding station and to discriminate this individual sound signal from other unknown sound signals. After the learning phases, sows were subjected to a 3-day evaluation phase in groups of 4 sows. The "naive" sows (n = 16) were also introduced to the test room individually for 18 days, and in groups of 4 for 3 days without following the learning procedure. Learning sows correctly responded to 100% of their individual sound signal after only 8 days of individual learning, suggesting that they successfully associated the sound signal with feed access. Distinguishing between different sounds was harder as shown by only 18.8% of success after an unknown sound emission at the end of the individual learning phases. Naïve sows reduced the time spent in the feeder compared to learning sows (P &lt; 0.001). On the second day of the group phase, learning sows were less aggressive than naïve sows (P &lt; 0.05). Compared to high-ranking sows, low-ranking sows displayed a reduced number of spontaneous approaches to the feeder during the last individual learning phase (P &lt; 0.001), and higher success rates in the group phase (P &lt; 0.05). The study suggests that, for group-housed sows fed by an individual feeder, teaching sows an individual sound signal can modify their feeding and social behaviors, enhancing their overall well-being during feeding time. Furthermore, the results suggest that this individual learning may be particularly beneficial for low-ranking sows.

ano.nymous@ccsd.cnrs.fr.invalid (Anna Blanc) 11 Jun 2024
https://hal.inrae.fr/hal-04601713v1
[hal-04582528] Feeding strategy in organic pig farming as a lever to improve various quality dimensions of pork

Since 2022, European specifications for organic pig farming have evolved to distribute 100 % organic feed, to reinforce the link to the soil with feed resources that should primarily be obtained from the farm or the same region. Feeding strategy acts as a lever to improve various quality dimensions of organic (as well as conventional) pork, including intrinsic dimensions (carcass composition, nutritional, organoleptic, technological, sanitary qualities) and extrinsic dimensions related to animal farming (image). Diet may also influence the risk of undesirable odours or flavours that may be found in pork from non-castrated male pigs. This study aimed at evaluating the effects of a specific feeding strategy on several quality dimensions of organic meat from non-castrated male pigs. The experiment was conducted with 77 organic non-castrated male pigs (Piétrain NN × Large White) reared according to organic specifications and distributed in two batches. Within litters, male littermates were allocated at around 33 kg of live weight to either a Control group which received a Control feed (C) corresponding to the organic specifications, or in a Bio+ group which received an organic test feed based mainly on French raw materials and which contained more fibres (faba bean and access to roughages) and omega-3 fatty acids (linseed, camelina). All pigs were reared in the same building on deep straw bedding (1.3 m²/pig) with free outdoor access (1.0 m²/pig) using one pen per experimental group. Pigs were fed ad libitum until slaughter at about 125 kg live weight. Average daily gain, carcass weight and lean meat content did not differ significantly between C and Bio+ pigs. Compared to C, Bio+ pigs had higher (P &lt; 0.05) ultimate pH in the loin (Longissimus muscle) and ham (Gluteus medius, and Semimembranosus) muscles, associated to a lower Longissimus muscle glycolytic potential (P &lt; 0.001). Loin and ham meat from Bio+ vs C pigs was less light (P &lt; 0.05) and had a more intense red color (P &lt; 0.10). The Bio+ strategy led to lower Longissimus muscle n-6:n-3 fatty acid ratio (P &lt; 0.001), indicating an improvement in pork nutritional value. Backfat skatole concentration was lower in Bio+ than C pigs whereas backfat androstenone was higher in Bio+ than C pigs (P &lt; 0.05). Altogether, we demonstrated that the Bio+ strategy had positive impacts on several qualities of organic pork from entire male pigs.

ano.nymous@ccsd.cnrs.fr.invalid (Chloé Van Baelen) 13 Jun 2024
https://hal.inrae.fr/hal-04582528v2
[hal-04764976] Fatty acids composition of pasture grass, yak milk and yak ghee from the four altitudes of Qinghai–Tibet Plateau: a predictive modelling approach to evaluate the correlation among altitude, pasture grass, yak milk and yak ghee

This study investigates the effect of altitude on the fatty acid composition of pasture grass, yak milk, and yak ghee on the Qinghai–Tibet Plateau, aiming to understand how environmental factors influence the nutritional quality of these products. Samples were collected from four different altitudes and analyzed for fatty acid profiles using gas chromatography. The analysis reveals that higher altitudes are associated with an increased prevalence of beneficial unsaturated fatty acids, such as oleic acid (C18:1) and linoleic acid (C18:2n6c). These findings highlight the significant influence of altitude on yak lipid metabolism, ultimately enhancing the nutritional value of dairy products. This adaptation not only supports the health and resilience of yaks, but also provides vital nutritional benefits to residents in high-altitude regions. The research underscores the importance of further investigations to optimize dairy production practices, ensuring improved food security and health outcomes for residents of the plateau.

ano.nymous@ccsd.cnrs.fr.invalid (Runze Wang) 04 Nov 2024
https://hal.inrae.fr/hal-04764976v1
[hal-04764456] Performance, egg quality, and composition in isa brown laying hens fed with different levels of desmodium tortuosum leaf flour

The objective of this study was to investigate the effects on laying performance, egg quality traits, color, and composition of supplementing a white corn-based diet with Desmodium tortuosum leaf flour. Three hundred 32-week-old hens were distributed to 30 pens of 10 hens each and allocated to six dietary treatments (five replicates per treatment) for 13 weeks. Two control groups of 50 hens received one of either diet Y, based on yellow corn, or diet W, based on white corn. The other groups received a diet based on white corn supplemented with Desmodium tortuosum leaf flour at 2.5%, 5%, 7.5%, or 10% (diet D). Diet D improved laying performance and yolk color at a reduced feed cost per egg but had no effect on cholesterol content. In conclusion, the inclusion of Desmodium tortuosum leaf flour, in a white corn-based diet, is effective in lowering feed cost, increasing egg production, and improving yolk color.

ano.nymous@ccsd.cnrs.fr.invalid (Gningnini Alain Koné) 04 Nov 2024
https://hal.inrae.fr/hal-04764456v1
[hal-04702517] Review: Improving residual feed intake modelling in the context of nutritional- and genetic studies for dairy cattle

The residual feed intake (RFI) model has recently gained popularity for ranking dairy cows for feed efficiency. The RFI model ranks the cows based on their expected feed intake compared to the observed feed intake, where a negative phenotype (eating less than expected) is favourable. Yet interpreting the biological implications of the regression coefficients derived from RFI models has proven challenging. In addition, multitrait modelling of RFI has been proposed as an alternative to the least square RFI in nutrition and genetic studies. To solve the challenge with the biological interpretation of RFI regression coefficients and suggest ways to improve the modelling of RFI, an interdisciplinary effort was required between nutritionists and geneticists. Therefore, this paper aimed to explore the challenges with the traditional least square RFI model and propose solutions to improve the modelling of RFI. In the traditional least square RFI model, one set of fixed effects is used to solve systematic effects (e.g., seasonal effects and age at calving) for traits with different means and variances. Thereby, measurement and model fitting errors can accumulate in the phenotype, resulting in undesirable effects. A multivariate RFI model will likely reduce this problem, as trait-specific fixed effects are used. In addition, regression coefficients for DM intake on milk energy tend to have more biologically meaningful estimates in multitrait RFI models, which indicates a confounding effect between the fixed effects and regression coefficients in the least square RFI model. However, defining precise expectations for regression coefficients from RFI models or sourcing for accurate feed norm coefficients seems difficult, especially if the coefficients are applied to a wide cattle population with varying diets or management systems, for example. To improve multitrait modelling of RFI, we suggest improving the modelling of changes in energy status. Furthermore, a novel method to derive the energy density of the diet and individual digestive efficiency is proposed. Digestive efficiency is defined as the part of the efficiency associated with digestive processes, which primarily reflects the conversion from gross energy to metabolisable energy. We show the model was insensitive to prior values of energy density in feed and that there was individual variation in digestive efficiency. The proposed method needs further development and validation. In summary, using multitrait RFI can improve the accuracy of the ranking of dairy cows’ feed efficiency, consequently improving economic and environmental sustainability on dairy farms.

ano.nymous@ccsd.cnrs.fr.invalid (R.B. Stephansen) 19 Sep 2024
https://hal.inrae.fr/hal-04702517v1
[hal-04356432] Epigenetics, genes and the environment: what importance for breeding practices and selection methods in poultry?

Epigenetics is commonly defined as the set of molecular mechanisms involved in gene expression regulation that are reversible and transmissible during development, and sometimes between generations, without altering the DNA sequence. Several epigenetic marks involved in chromatin regulation are now well known, such as the methylation of DNA cytosines, histone post -translational modifications, and non -coding RNA. Thanks to the technological development of high -throughput DNA sequencing, epigenetic marks can now be investigated at the whole-genome scale. It is also well known that the epigenome (the whole set of epigenetic marks in a tissue) is sensitive to environmental fluctuations, including temperature or nutrition, and can be considered as a mediator between the genes and the environment. Phenotypic programming strategies based on epigenetic mechanisms could thus be used as a lever to adjust the phenotype of individuals with their living conditions. Moreover, over the last decades, genetic selection has contributed to a considerable improvement in animal performances. Although the genetic component can be estimated with some accuracy, a large part of the phenotypic variability, considered to be of environmental origin, is not directly accessible by genetic approaches. In a context of diversification of production environments (climate change, production methods that are more respectful of welfare and the environment...), it is necessary to understand the impact of the environment on phenotypic variation via epigenetic marks, to optimize breeding systems and to predict the phenotype of an animal. Like genomic selection a few years ago, the contribution of epigenetic research could contribute to more efficient and sustainable production systems in poultry farming.

ano.nymous@ccsd.cnrs.fr.invalid (Vincent Coustham) 20 Dec 2023
https://hal.inrae.fr/hal-04356432v1
[hal-04323941] Nouvelles références sur l'herbe valorisée au pâturage grâce à la méthode HerbValo

L'outil HerbValo a été créé pour calculer la quantité d'herbe valorisée dans les parcelles pâturées sans avoir à y réaliser de mesures. Plus de 400 parcelles ont été suivies avec cette méthode en 2018 et 2019 pour créer un premier référentiel de l'herbe valorisée à l'échelle des régions partenaires et décrire la variabilité observée. En moyenne, ce sont 6,1t MS (Matière Sèche) d'herbe qui ont été valorisées par hectare et par an sur les parcelles suivies avec une variabilité importante (coefficient de variation interparcelles de 43 %). La région, la profondeur de sol, l'âge de la prairie et la présence d'au moins une fauche par an sont les principaux facteurs qui expliquent cette variabilité. La méthode HerbValo s'est révélée plus robuste que la méthode de la biomasse disparue pour estimer l'herbe valorisée, offrant ainsi des perspectives d'utilisation moins chronophages pour disposer de cette valeur tant en fermes expérimentales que commerciales.

ano.nymous@ccsd.cnrs.fr.invalid (Stéphanie Guibert) 05 Dec 2023
https://hal.inrae.fr/hal-04323941v1
[hal-04315092] Can healthy diets be achieved worldwide in 2050 without farmland expansion?

This paper analyses to what extent it would be possible to ensure food availability to the world population by 2050 with two objectives: healthy diets and no farmland expansion. Assumptions were made to project exogenous demand and supply variables. Climate change impacts on crop yields, grazing use intensities and maximum cultivable areas were taken into account. Cropland and pastureland needs were then estimated for 21 regions using a global biomass balance model. Simulation results established for two sets of crop yield projections (‘moderate’ versus ‘high’ growth) show that several regions (India, Rest of Asia, Near- and Middle-East countries and North Africa, as well as West Africa in the case of ‘moderate’ yield growth) would be constrained by their maximum cultivable areas with no deforestation. Our scenarios would be technically infeasible because of additional pastureland needs notably in sub-Saharan Africa. As a consequence, we analyse to what extent additional levers could reduce pastureland needs in sub-Saharan Africa.

ano.nymous@ccsd.cnrs.fr.invalid (Agneta Forslund) 30 Nov 2023
https://hal.inrae.fr/hal-04315092v1
[hal-04131807] Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens

To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for routine use for genomic selection. An alternative and cost-efficient solution is to use restriction site-associated DNA sequencing (RADseq) techniques to sequence only a fraction of the genome using restriction enzymes. From this perspective, use of RADseq techniques followed by an imputation step on HD chip as alternatives to LD chips for genomic selection was studied in a pure layer line. Results Genome reduction and sequencing fragments were identified on reference genome using four restriction enzymes (EcoRI, TaqI, AvaII and PstI) and a double-digest RADseq (ddRADseq) method (TaqI-PstI). The SNPs contained in these fragments were detected from the 20X sequence data of the individuals in our population. Imputation accuracy on HD chip with these genotypes was assessed as the mean correlation between true and imputed genotypes. Several production traits were evaluated using single-step GBLUP methodology. The impact of imputation errors on the ranking of the selection candidates was assessed by comparing a genomic evaluation based on ancestry using true HD or imputed HD genotyping. The relative accuracy of genomic estimated breeding values (GEBVs) was investigated by considering the GEBVs estimated on offspring as a reference. With AvaII or PstI and ddRADseq with TaqI and PstI, more than 10 K SNPs were detected in common with the HD SNP chip, resulting in an imputation accuracy greater than 0.97. The impact of imputation errors on genomic evaluation of the breeders was reduced, with a Spearman correlation greater than 0.99. Finally, the relative accuracy of GEBVs was equivalent. Conclusions RADseq approaches can be interesting alternatives to low-density SNP chips for genomic selection. With more than 10 K SNPs in common with the SNPs of the HD SNP chip, good imputation and genomic evaluation results can be obtained. However, with real data, heterogeneity between individuals with missing data must be considered.

ano.nymous@ccsd.cnrs.fr.invalid (Florian Herry) 17 Jun 2023
https://hal.inrae.fr/hal-04131807v1
[hal-04370809] Estimation of carcass chemical composition in beef-on-dairy cattle using dual-energy X-ray absorptiometry (DXA) scans of cold half-carcass or 11th rib cut

The aim of the present study was to estimate the chemical composition (water, lipid, protein, mineral, and energy contents) of carcasses measured postmortem using dual-energy X-ray absorptiometry (DXA) scans of cold half-carcass or 11th rib cut. One hundred and twenty beefon-dairy (dam: Swiss Brown, sire: Angus, Limousin, or Simmental) bulls (n = 66), heifers (n = 42), and steers (n = 12) were included in the study. The reference carcass composition measured after grinding, homogenization, and chemical analyses was estimated from DXA variables using simple or multiple linear regressions with model training on 70% (n = 84) and validation on 30% (n = 36) of the observations. In the validation step, the estimates of water and protein masses from the half-carcass (R 2 = 0.998 and 0.997; root mean square error of prediction [RMSEP], 1.0 and 0.5 kg, respectively) and 11th rib DXA scans (R 2 = 0.997 and 0.996; RMSEP, 1.5 and 0.5 kg, respectively) were precise. Lipid mass was estimated precisely from the half-carcass DXA scan (R 2 = 0.990; RMSEP = 1.0 kg) with a slightly lower precision from the 11th rib DXA scan (R 2 = 0.968; RMSEP = 1.7 kg). Mineral mass was estimated from half-carcass (R² = 0.975 and RMSEP = 0.3 kg) and 11th rib DXA scans (R 2 = 0.947 and RMSEP = 0.4 kg). For the energy content, the R 2 values ranged from 0.989 (11th rib DXA scan) to 0.996 (half-carcass DXA scan), and the RMSEP ranged from 36 (half-carcass) to 55 MJ (11th rib). The proportions of water, lipids, and energy in the carcasses were also precisely estimated (R 2 ≥ 0.882) using either the half-carcass (RMSEP ≤ 1.0%) or 11th rib-cut DXA scans (RMSEP ≤ 1.3%). Precision was lower for the protein and mineral proportions (R 2 ≤ 0.794, RMSEP ≤ 0.5%). The cattle category (sex and breed of sire) effect was observed only in some estimative models for proportions from the 11th rib cut. In conclusion, DXA imaging of either a cold half-carcass or 11th rib cut is a precise method for estimating the chemical composition of carcasses from beef-on-dairy cattle.

ano.nymous@ccsd.cnrs.fr.invalid (Caroline Xavier) 03 Jan 2024
https://institut-agro-rennes-angers.hal.science/hal-04370809v1
[hal-04193855] Datasets on the nutritional and environmental (including biodiversity) characteristics of food products consumed in France

Analysing the nutritional and environmental impacts of our current diets and promoting sustainable dietary shifts require quantified data on the characteristics of foods. We have jointly studied environmental and nutritional performances of more than 200 generic foods consumed in France, by combining and completing different databases. Several environmental issues calculated by Life Cycle Assessment (LCA) were selected, including impacts on biodiversity. This required to (1) model diets for given subpopulations; (2) adapt the LCA database of food products, Agribalyse 3.0, to link selected food and environmental inventories (3) compile characterization factors to assess impacts on biodiversity. Additionally, modifying Agribalyse 3.0 required to also modify the characterization method on Land Competition. This data paper compiles all the data used to obtain the results presented in the companion article entitled: Environmental trade-offs of fulfilling nutritionally adequacy with reduced animal protein share for French adult populations [1]; i.e. (i) the characterization methods used, (ii) the modifications made to Agribalyse 3.0 and (iii) the nutrient content and quantities consumed of generic foods (iv) the optimized quantities of simulated diets reaching nutrient recommendations with low share of animal-based proteins. It also comprises (iv) Life Cycle Impact Assessment for all Agribalyse 3.0 processes of food having a CIQUAL code (2,497 processes).

ano.nymous@ccsd.cnrs.fr.invalid (Samuel Le Féon) 01 Sep 2023
https://hal.inrae.fr/hal-04193855v1
[hal-04217636] Fourth report on chicken genes and chromosomes 2022

[...]

ano.nymous@ccsd.cnrs.fr.invalid (Jacqueline Smith) 26 Oct 2023
https://hal.inrae.fr/hal-04217636v1
[hal-04178183] Quality of animal-source foods: lessons from a collective scientific expertise

This article critically reviews the state of knowledge on the quality of animal-source foods according to animal production and food processing conditions, including consumer expectations-behaviours and the effects of consumption of animal-source foods on human health. Quality has been defined through seven core attributes: safety, commercial, sensory, nutritional, technological, convenience, and image. Image covers ethical cultural and environmental dimensions associated with the origin of the food and the way it is produced and processed. This framework enables to highlight the priorities given to the different quality attributes. It also helps to identify potential antagonisms and synergies among quality attributes, between production and processing stages, and among stakeholders. Primacy is essentially given to commercial quality attributes, especially for standard-commodity animal-source foods. This primacy has strongly influenced genetic selection and farming practices in all livestock commodity chains and enabled substantial quantitative gains, although at the expense of other quality traits. Focal issues are the destructuring of chicken muscle that compromises sensory, nutritional and image quality attributes, and the fate of males in the egg and dairy sectors, which have heavily specialized their animals. Quality can be gained but can also be lost throughout the farm-to-fork continuum. Our review highlights critical factors and periods throughout animal production and food processing routes, such as on-farm practices, notably animal feeding, pre-slaughter and slaughter phases, food processing techniques, and food formulation. It also reveals on-farm and processing factors that create antagonisms among quality attributes, such as the castration of male pigs, the substitution of marine-source feed by plant-based feed in fish, and the use of sodium nitrite in meat processing. These antagonisms require scientific data to identify trade-offs among quality attributes and/or solutions to help overcome these tensions. There are also food products that value synergies between quality attributes and between production and processing phases, particularly Geographical Indications. Human epidemiological studies have found associations between consumption of animal-source foods and increased or decreased risk for chronic non-communicable diseases. These associations have informed public health recommendations. However, they have not yet considered animal production and food processing conditions. A concerted and collaborative effort is needed from scientists working in animal science, food process engineering, consumer science, human nutrition and epidemiology in order to address this research gap. Avenues for research and main options for policy action are discussed.

ano.nymous@ccsd.cnrs.fr.invalid (Sophie Prache) 07 Aug 2023
https://hal.inrae.fr/hal-04178183v1
[hal-04037306] Stress at slaughter: a key factor in the determination of meat quality?

With these papers, this Special Issue illustrates the effects of stress on various meat quality traits in very different settings and species, including pigs, catfish, game species, fowl, and cattle. The stressors described were of very different types, often with both a psychological and physical origin. This knowledge should help designing protocols trying to unravel the complex factors that determine meat quality traits, by including stress measurements of the animals from which the meat will be studied. The reduction in stress before slaughter is likely to improve meat quality. The reduction in stress before slaughter should certainly be the objective for ethical reasons.

ano.nymous@ccsd.cnrs.fr.invalid (Claudia Terlouw) 20 Mar 2023
https://hal.inrae.fr/hal-04037306v1
[hal-03965647] A blend of functional amino acids and grape polyphenols improves the pig capacity to cope with an inflammatory challenge caused by poor hygiene of housing conditions

Background: Dietary supplementation with a blend of functional amino acids (AA) and grape extract polyphenols contributes to preserve intestinal health and growth performance of piglets during the post-weaning period. In the present experiment, we assessed if a supplementation with a mix of AA and grape extract polyphenols during the post-weaning period would persist to improve the pig capacity to cope with a subsequent challenge caused by poor hygiene of housing conditions. Eighty pigs weaned at 28 days of age were fed a standard diet supplemented (AAP) or not (CNT) with 0.2% of a blend of AA (glutamine, arginine, cystine, valine, isoleucine, and leucine) and grape extract polyphenols during the post-weaning period (from week 0 to 6). At week 6, pigs were transferred to a growing unit where 50% of pigs previously fed AAP and CNT diets were housed in good and the other 50% in poor hygiene conditions for 3 weeks (from week 7 to 9; challenge period). All pigs were fed a standard growing diet that was not supplemented with AAP. We measured pig growth performance, plasma indicators of inflammation, digestive integrity, and oxidative status, and scored fecal consistency. Differences were considered significant at P ≤ 0.05. Results One week post-weaning, pigs fed AAP had lower plasma concentrations of haptoglobin than CNT pigs ( P = 0.03). Six weeks post-weaning, plasma concentrations of diamine oxidase (DAO) were lower ( P = 0.03) whereas those of vitamin E and A were greater ( P ≤ 0.05) in pigs fed AAP compared to CNT pigs. The prevalence of diarrhea was higher in CNT pigs compared to AAP pigs ( P < 0.01). During the challenge period, only pigs previously fed CNT diet had lower growth rate in poor than good conditions ( P ≤ 0.05). They had also greater plasma concentrations of haptoglobin and oxidative stress index (OSI) and lower plasma concentrations of vitamin E in poor than good hygiene conditions ( P ≤ 0.05). Conclusions Pigs fed AAP diet during post-weaning had less diarrhea and plasma concentrations of a digestive integrity marker, as well as greater plasma concentrations of antioxidant indicators during the post-weaning period. The beneficial effects of AAP supplementation persisted after the post-weaning period as evidenced by the absence of effects of the hygiene challenge on growth and health indicators in pigs previously fed APP. This clearly indicated a greater ability of pigs fed AAP to cope with the poor hygiene conditions.

ano.nymous@ccsd.cnrs.fr.invalid (Alícia Zem Fraga) 31 Jan 2023
https://hal.science/hal-03965647v1
[hal-03899905] A marginal abatement cost curve for climate change mitigation by additional carbon storage in French agricultural land

Following the Paris agreement in 2015, the European Union (EU) set a carbon neutrality objective by 2050, and so did France. The French agricultural sector can contribute as a carbon sink through carbon storage in biomass and soil, in addition to reducing GHG emissions. The objective of this study is to quantitatively assess the additional storage potential and cost of a set of eight carbon-storing practices. The impacts of these agricultural practices on soil organic carbon storage and crop production are assessed at a very fine spatial scale, using crop and grassland models. The associated area base, GHG budget, and implementation costs are assessed and aggregated at the region level. The economic model BANCO uses this information to derive the marginal abatement cost curve for France and identify the combination of carbon storing practices that minimizes the total cost of achieving a given national net GHG mitigation target. We find that a substantial amount of carbon, 36.2 to 52.9 MtCO2e yr-1, can be stored in soil and biomass for reasonable carbon prices of 55 and 250 € tCO2e-1, respectively (corresponding to current and 2030 French carbon value for climate action), mainly by developing agroforestry and hedges, generalising cover crops, and introducing or extending temporary grasslands in crop sequences. This finding questions the 3-5 times lower target of 10 MtCO2e.yr-1 retained for the agricultural carbon sink by the French climate neutrality strategy. Overall, this would decrease total French GHG emissions by 9.2 to 13.8%, respectively (reference year 2019).

ano.nymous@ccsd.cnrs.fr.invalid (Laure Bamière) 15 Dec 2022
https://hal.inrae.fr/hal-03899905v1
[hal-03929067] On the use of impedance detuning for gastrointestinal segment tracking of ingestible capsules

During their travel through the gastrointestinal (GI) tract, ingestible antennas encounter detuning in their impedance response due to varying electromagnetic (EM) properties of the surrounding tissues. This communication investigates the possibility of using this impedance detuning to detect in which segment of the GI tract—stomach, small intestine, or large intestine—the capsule is located. Meandered dipole antennas operating in the 433 MHz industrial, scientific, and medical (ISM) band are designed for this purpose. The antennas conform to the inner surface of 3-D printed polylactic acid (PLA) capsules with a shell thickness of 0.6 or 0.4 mm. The impedance response is first optimized numerically in a homogeneous cylindrical phantom with time-averaged EM properties. The magnitude and the phase of the reflection coefficient are then obtained in different tissues and compared with simulations and measurements. The experimental demonstration is carried out first using tissue-mimicking liquids and then in a recently deceased ex vivo porcine model. The minimum change in the phase between different GI tissues was determined to be around 10° in the porcine model, indicating that the changes in the impedance response, particularly the changes in the phase, provide sufficient information to follow the position of the capsule in the GI tract.

ano.nymous@ccsd.cnrs.fr.invalid (Erdem Cil) 14 Mar 2023
https://hal.science/hal-03929067v1
[hal-03965662] Apparent jejunal amino acid digestibility, gut morphology, and the expression of intestinal amino acid transporters in pigs fed protein or free amino acids

Dietary amino acids (AA) supplied as protein or in free form are digested and absorbed at different rates, but can also induce differences in the intestinal physiology of pigs. We compared the apparent jejunal AA digestibility, intestinal morphology, and gene expression of AA transporters of pigs fed diets providing different forms of AA. Thirty growing pigs (33.7 ± 4.1 kg) were fed one of three experimental diets that provided AA either as protein from feather meal (INT), as free AA and small peptides obtained by extensive acid hydrolysis of feathers (HYD), or as a mix of individual purified AA with the same AA profile as HYD (FAA). Pigs were fed the same quantity of feed, energy, and AA. After 14 days, pigs were slaughtered 3 h after feeding a meal with indigestible markers. Digesta and tissue were collected from different sections of the small intestine. Jejunal digesta was used to measure apparent jejunal digestibility of AA. Samples of the duodenum, jejunum, and ileum were used to measure intestinal morphology and the gene expression of intestinal AA transporters. The measured apparent jejunal digestibility of AA of INT was lower compared to HYD and FAA (P &lt; 0.05). The apparent jejunal digestibility of Cys, Gly, His, Met, and Pro was lower for FAA compared to HYD (P &lt; 0.05). This may be due to the small peptides in HYD, which are absorbed faster than individual AA. The villi area in the ileum of HYD fed pigs was the highest (P &lt; 0.05) among the treatments, which may be associated with the reabsorption of endogenous proteins, which occurs mostly in the ileum. In the duodenum, HYD and FAA had lower expression of PepT1 (P &lt; 0.01) probably due to the rapid transit time of digesta compared to INT fed pigs. Pigs fed HYD expressed more ASCT2 (P = 0.02) and CAT-1 (P = 0.04) in the jejunum compared to the pigs fed the other diets. The expression of these transporters along the intestine depended on the relative abundance of readily absorbable dietary AA. Results showed that dietary AA form can have an influence on the morphology and on the expression of different AA transporters along the different sections of the small intestine.

ano.nymous@ccsd.cnrs.fr.invalid (Francis Amann Eugenio) 06 May 2024
https://hal.science/hal-03965662v1

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Scientific publication

HAL : Dernières publications

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

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

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

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

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

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

[hal-04802793] Comparative Genomics and Epigenomics of Transcriptional Regulation

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

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

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

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

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

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

[hal-04581102] Post-milking application of a Lacticaseibacillus paracasei strain impacts bovine teat microbiota while preserving the mammary gland physiology and immunity

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[hal-04502991] Meat by-products as a source of bioactive peptides and functional ingredients: Regulatory and safety barriers to valorization

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

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

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

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

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

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

[hal-04565725] Barriers and drivers of farmers to provide outdoor access in pig farming systems: a qualitative study

[hal-04724456] Effect of sward species diversity combined with a reduction in nitrogen fertilizer on the performances of spring calving grazing dairy cows

[hal-04455106] One-shot technology for 3D imaging of large animals: perspectives for ruminant management

[hal-04389098] Calculating herbage utilization and intake by dairy cows under subtropical conditions using conventional field measurement techniques or the HerbValo method

[hal-04717884] Effects of reducing copper and zinc supplementation on the performance and mineral status of fattening pigs

[hal-04579500] Feed restriction affects milk performances and decreases milk lipolysis in dairy ewes

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

[hal-04409031] Getting to grips with Resilience: Toward large-scale phenotyping of this complex trait

[hal-04438202] Data quantifying the behaviour of macro and trace elements along the feed – manure – treated waste continuum in pig production

[hal-04801625] Environmental benefits of crude protein reduction in growing pig diets: is it worth going further?