Publications 2020

Jehl, F. ; Désert, C. ; Klopp, C. ; Brenet, M. ; Rau, A. ; Leroux, S. ; Boutin, M. ; Lagoutte, L. ; Muret, K. ; Blum, Y. ; Esquerré, D. ; Gourichon, D. ; Burlot, T. ; Collin, A. ; Pitel, F. ; Benani, A. ; Zerjal, T. ; Lagarrigue, S.BMC Genomics, 2019, 20 (1)ArticlePièces jointes : 2019_jehl_bmg_genomics.pdfBackground: Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a multi-tissue transcriptomic analysis. Study was designed to compare effects of the nutritional intervention in two layer chicken lines divergently selected for residual feed intake. Results: Chicken adapted to the diet in terms of production by significantly increasing their feed intake and decreasing their body weight and body fat composition, while their egg production was unchanged. No significant interaction was observed between diet and line for the production traits. The low energy diet had no effect on adipose tissue and liver transcriptomes. By contrast, the nutritional challenge affected the blood transcriptome and, more severely, the hypothalamus transcriptome which displayed 2700 differentially expressed genes. In this tissue, the low-energy diet lead to an over-expression of genes related to endocannabinoid signaling (CN1R, NAPE-PLD) and to the complement system, a part of the immune system, both known to regulate feed intake. Both mechanisms are associated to genes related polyunsaturated fatty acids synthesis (FADS1, ELOVL5 and FADS2), like the arachidonic acid, a precursor of anandamide, a key endocannabinoid, and of prostaglandins, that mediate the regulatory effects of the complement system. A possible regulatory role of NR1H3 (alias LXRα) has been associated to these transcriptional changes. The low-energy diet further affected brain plasticity-related genes involved in the cholesterol synthesis and in the synaptic activity, revealing a link between nutrition and brain plasticity. It upregulated genes related to protein synthesis, mitochondrial oxidative phosphorylation and fatty acid oxidation in the hypothalamus, suggesting reorganization in nutrient utilization and biological synthesis in this brain area. Conclusions: We observed a complex transcriptome modulation in the hypothalamus of chicken in response to low-energy diet suggesting numerous changes in synaptic plasticity, endocannabinoid regulation, neurotransmission, lipid metabolism, mitochondrial activity and protein synthesis. This global transcriptomic reprogramming could explain the adaptive behavioral response (i.e. increase of feed intake) of the animals to the low-energy content of the diet.

Massimino, W. ; Davail, S. ; Bernadet, M.-D. ; Pioche, T. ; Tavernier, A. ; Ricaud, K. ; Gontier, K. ; Bonnefont, C. ; Manse, H. ; Morisson, M. ; Fauconneau, B. ; Collin, A. ; Panserat, S. ; Houssier, M.Frontiers in Physiology, 2019, 10ArticlePièces jointes : 2019_Massimino_FrontiersPhysiol.pdfAnimal studies have shown that very early life events may have programing effects on adult metabolism and health. In this study, we aim, for the first, time to elucidate the effects of embryonic thermal manipulation (TM) on the performance of overfed mule ducks, in particular for the production of foie gras (fatty liver). We designed three embryonic TMs with different protocols for increasing the incubation temperature during the second part of embryogenesis, to determine whether hepatic metabolism could be “programed” to improve its fattening response to overfeeding at the age of three months. Initial results confirm that an increase in the incubation temperature leads to faster development (observed for all treated groups compared to the control group), and a decrease in the body surface temperature at birth. Thereafter, in a very innovative way, we showed that the three TM conditions specifically increased liver weights, as well as liver lipid content after overfeeding compared to the non-TM control group. These results demonstrate that embryonic TM effectively “programs” the metabolic response to the challenge of force-feeding, resulting in increased hepatic steatosis. Finally, our goal of improving foie gras production has been achieved with three different embryonic thermal stimuli, demonstrating the high reproducibility of the method. However, this repeatability was also perceptible in the adverse effects observed on two groups treated with exactly the same cumulative temperature rise leading to a reduction in hatchability (75 and 76% vs. 82% in control), in addition to an increase in the melting rate after cooking. These results suggest that embryonic thermal programing could be an innovative and inexpensive technique for improving foie gras production, although the specific protocol (duration, level or period of temperature increase), remains to be elucidated in order to avoid adverse effects

Metayer, J. P. ; Travel, A. ; Mika, A. ; Bailly, J.-D. ; Cleva, D. ; Boissieu, C. ; Guennec, J. ; Froment, P. ; Albaric, O. ; Labrut, S. ; Lepivert, G. ; Marengue, E. ; Tardieu, D. ; Guerre, P.Toxins, 2019, 11 (8) : 455. ArticlePièces jointes : 2019_Metayer_Toxins.pdfFusarium mycotoxins (FUS) occur frequently in poultry diets, and regulatory limits are laid down in several countries. However, the limits were established for exposure to a single mycotoxin, whereas multiple contamination is more realistic, and different studies have demonstrated that it is not possible to predict interactions between mycotoxins. The purpose of this study was thus to compare the toxic effect of deoxynivalenol (DON), fumonisins (FB) and zearalenone (ZON), alone and in combination on broiler chickens, at the maximum tolerated level established by the EU for poultry feed. Experimental corn-soybean diets incorporated ground cultured toxigenic Fusarium strains. One feed was formulated for chickens 0 to 10 days old and another for chickens 11 to 35 days old. The control diets were mycotoxin free, the DON diets contained 5 mg DON/kg, the FB diet contained 20 mg FB1 + FB2/kg, and the ZON diet contained 0.5 mg ZON/kg. The DONFBZON diet contained 5, 20, and 0.5 mg/kg of DON, FB1 + FB2, and ZON, respectively. Diets were distributed ad libitum to 70 broilers (male Ross PM3) separated into five groups of 14 chickens each reared in individual cages from one to 35 days of age. On day 35, after a starvation period of 8 h, a blood sample was collected, and all the animals were killed and autopsied. No difference between groups that could be attributed to FUS was observed in performances, the relative weight of organs, biochemistry, histopathology, intestinal morphometry, variables of oxidative damage, and markers of testicle toxicity. A significant increase in sphinganine and in the sphinganine to sphingosine ratio was observed in broilers fed FB. Taken together, these results suggest that the regulatory guidelines established for single contamination of broiler chickens fed with DON, FB, and ZON can also be used in the case of multiple contamination with these toxins.

Pitel, F. ; Calenge, F. ; Aigueperse, N. ; Estelle Fabrellas, J. ; Coustham, V. ; Calandreau, L. ; Morisson, M. ; Chavatte-Palmer, P. ; Ginane, C.INRA Productions Animales, 2019, 32 (2) : 247-262. ArticlePièces jointes : pitel_productions-animales_2019.pdfLes animaux d’élevage sont confrontés à de multiples contraintes environnementales auxquelles ils doivent s’adapter. De plus en plus d’études s’intéressent à l’impact de l’environnement précoce sur les phénotypes des animaux et leurs capacités à s’adapter aux différents challenges rencontrés ultérieurement. Dans cette revue, nous nous intéressons aux connaissances actuelles sur l’influence de l’environnement précoce sur la construction et la variabilité des phénotypes et de l’adaptation des animaux d’élevage à leur milieu, en prenant des exemples dans différentes espèces. Nous nous focalisons sur les rôles de trois contributeurs importants de la construction des phénotypes : les mécanismes épigénétiques, le microbiote et les processus comportementaux. Les mécanismes épigénétiques, qui modulent l’expression du génome sous l’effet de perturbations environnementales intervenues pendant le développement, peuvent induire une variété de phénotypes dont les caractéristiques peuvent perdurer jusqu’à l’âge adulte, voire se transmettre à la génération suivante. La constitution du microbiote digestif est elle aussi très dépendante de l’environnement précoce, et joue un rôle important dans l’expression des phénotypes, notamment dans le domaine de la santé. Enfin, l’expérience précoce influence considérablement le comportement de l’animal, en particulier ses capacités d’apprentissage, qui peuvent lui conférer une meilleure adaptation à des situations nouvelles ultérieures. Les études menées dans ces domaines permettent de définir de nouveaux leviers d’action pour tenter d’optimiser les capacités d’adaptation de nos animaux, notamment par les voies de l’alimentation des animaux jeunes ou de leurs parents voire de leurs grands-parents, de l’acclimatation pendant le développement, ou plus généralement par des modifications de l’environnement, en particulier de l’environnement social.

Peyraud, J.-L. ; Aubin, J. ; Barbier, M. ; Baumont, R. ; Berri, C. ; Bidanel, J. P. ; Citti, C. ; Cotinot, C. ; Ducrot, C. ; Dupraz, P. ; Faverdin, P. ; Friggens, N. ; Houot, S. ; Nozières-Petit, M.-O. ; Rogel-Gaillard, C. ; Sante-Lhoutellier, V.INRA Productions Animales, 2019, 32 (2) : 323-338. ArticlePièces jointes : Peyraud_2019_InraPA.pdfThe ambition of the foresight on livestock farming was to rethink the place, the roles of livestock and how it should be transformed to fully contribute to the development of more sustainable agri-food systems. It was also to identify cross-disciplinary research themes that explore promising fronts of science or methodologies to solve knowledge locks. The foresight was managed by a group of 15 researchers and mobilized a hundred researchers. Based on an analysis of the context and the drivers for the evolution of the systems, we propose a new conceptual framework to think about innovations. Livestock farming must be part of circular agri-food systems in which it must contribute, beyond an increased efficiency of production factors, to the preservation of the quality of the resources and to the production of a food at an affordable price. Systems need to be rethought to be climate-smart and to respond to the health and welfare challenges of animals and people, rethink the linkages between livestock, crop production and territories to maximize recycling and rethink livestock linkages, processing and consumption of livestock products. Innovations should be based on the principles of agro-ecology supplemented by those of the circular economy and mobilizing levers of (bio) technologies and organizational innovation. The text describes 4 major scientific priorities with their research issues and produces recommendations for an action plan.

Conde-Aguilera, J. A. ; Lefaucheur, L. ; Gondret, F. ; Delgado-Andrade, C. ; Mercier, Y. ; Tesseraud, S. ; van Milgen, J.European Journal of Nutrition, 2019, sous presse (sous presse) : sous presse. ArticlePurpose A total sulfur amino acid (TSAA) deficient diet can affect the amino acid composition of skeletal muscles. However, it is unknown how the different muscle proteins are affected by the TSAA deficiency. Methods The proteomic profiles of the fast-twitch glycolytic longissimus (LM) and the slow-twitch oxidative rhomboideus (RM) muscles were compared in 42-day-old piglets fed either a 28% deficient (TSAA-) or a sufficient (TSAA+) diet in TSAA for 10 days. Differentially regulated proteins were identified and submitted to Gene Ontology Pathways Analysis to identify biological processes affected by TSAA deficiency. Results A total of 36 proteins in LM and 24 proteins in RM differed in abundance between the two dietary treatments. In both muscles, an increased oxidative energy metabolism was observed in TSAA- piglets. However, a greater mitochondrial oxidation of pyruvate generated from glycolysis was observed in LM of TSAA- piglets, whereas fatty acid beta-oxidation and glycogen sparing were favored in RM. This suggests a muscle-specific reorientation of energy metabolism in response to a TSAA- deficiency. In both muscles, the protein abundance and enzyme activity of superoxide dismutase were increased in TSAA- piglets. Other enzymes involved in antioxidant defense, heat shock proteins coping with cellular stress, and annexins involved in the regulation of apoptosis were generally found to be more expressed in the LM of TSAA- piglets, with no or minor changes in RM. Conclusions Skeletal muscle proteome in young growing piglets was modulated in a muscle-dependent manner by a deficient TSAA supply, with accentuated changes in fast-twitch glycolytic muscle.

Riou, C. ; Brionne, A. ; Cordeiro, L. ; Harichaux, G. ; Gargaros, A. ; Labas, V. ; Gautron, J. ; Gérard, N.Reproduction (Cambridge), 2019ArticleAvian uterine fluid (UF) and uterovaginal sperm storage tubules (SST) are key components in accepting sperm in SST, maintaining sperm function for several weeks, releasing sperm from SST and their ascent through the uterus. To improve understanding of sperm storage processes requires investigating UF and SST. This study aimed to identify proteins modulated by sperm in the hen’s genital tract, and to highlight their role during sperm storage. Two genetic lines of hens exhibiting long (F+) or short (F-) sperm storage ability were used. GeLC MS/MS analysis was used to establish a quantitative inventory of proteins regulated after insemination in both lines. The proteomic data are available via ProteomeXchange with identifier PXD013514. Immunohistochemistry was used to identify high (ANXA4/ANXA5/OCX32) and low (HSPA8/PIGR) fertility markers in the uterovaginal junction. Our results demonstrated that sperm induced a significant and rapid change in the UF proteomic content, and also in the SST epithelium. In F+ hens, mobilization of the ANXA4 protein in the apical part of SST cells after insemination was associated with increased levels of some proteoglycans and binding proteins, and also antimicrobial eggshell matrix protein (OCX32) in the UF. We also observed increased levels of lipid transporters involved in egg formation (VTG1-2, APOA1-4-H). In F- hens, insemination induced increased levels of PIGR in both UF and SST, of ANXA5 in SST, of UF enzymes exhibiting metallopeptidase activity, and mucins. In conclusion, sperm induced significant changes in the UF proteomic content. This study also provides evidence that the SST immune system plays a major role in regulating sperm storage.

Brionne, A. ; Juanchich, A. ; Hennequet-Antier, C.BioData Mining, 2019, 12 : 13 p. ArticlePièces jointes : Brionne_et_al-2019-BioData_Mining.pdfThe main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. ViSEAGO is publicly available on .

Berri, C. ; Picard, B. ; Lebret, B. ; Andueza Urra, J. D. ; Lefèvre, F. ; Le Bihan-Duval, E. ; Beauclercq, S. ; Chartrin, P. ; Vautier, A. ; Legrand, I. ; Hocquette, J.-F.Foods, 2019, 8 (436) : 1-22. ArticlePièces jointes : 2019_Berri_Foods.pdfThis review is aimed at providing an overview of recent advances made in the field of meat quality prediction, particularly in Europe. The different methods used in research labs or by the production sectors for the development of equations and tools based on different types of biological (genomic or phenotypic) or physical (spectroscopy) markers are discussed. Through the various examples, it appears that although biological markers have been identified, quality parameters go through a complex determinism process. This makes the development of generic molecular tests even more difficult. However, in recent years, progress in the development of predictive tools has benefited from technological breakthroughs in genomics, proteomics, and metabolomics. Concerning spectroscopy, the most significant progress was achieved using near-infrared spectroscopy (NIRS) to predict the composition and nutritional value of meats. However, predicting the functional properties of meats using this method—mainly, the sensorial quality—is more difficult. Finally, the example of the MSA (Meat Standards Australia) phenotypic model, which predicts the eating quality of beef based on a combination of upstream and downstream data, is described. Its benefit for the beef industry has been extensively demonstrated in Australia, and its generic performance has already been proven in several countries.

Gautron, J.Biochimica et Biophysica Acta - Proteins and Proteomics, 2019, 19 (13) : 2 p. ArticleEggs are widely consumed all over the world. The eggshell is its protective barrier whose original function is to protect the embryo during development. Avian eggshells are made of calcium carbonate with a small amount of organic matrix (proteins and proteoglycans). During eggshell formation, the mineral precursors interact with matrix proteins to regulate the calcification of this highly resistant biomineral. In order to better characterize the functions of matrix proteins in eggshell biominerals, many proteomics studies have been performed during the last 15 years. The chicken eggshell is the main model studied in birds, but there is a need for comparative approaches in order to determine whether there is a general protein toolkits associated with calcitic biomineralization, and to determine its components. The study by Zhu et al., reported in article number 1900011, volume 19, issue 11, is a major step forward as it is the first shell proteomics survey performed on duck. Thus, it will contribute to improved knowledge of the eggshell mineralization process and will provide new insight for shell quality improvement and to guide biomimetic efforts in material sciences.