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International audience; L’objectif général du projet EpiCOOL est d’étudier les conséquences du stockage au froid (3°C) des œufs embryonnés de truite arc-en-ciel, l’espèce piscicole majeure de la filière française. En effet, des études récentes ont montré que l’exposition précoce à des stimuli environnementaux (tels que l’hypoxie ou la température) pouvait avoir un impact sur la physiologie, la croissance, le métabolisme et la nutrition des poissons à plus ou moins long terme. Plusieurs mécanismes peuvent être sous-jacents à cette programmation, parmi eux les modifications des patrons d’expression de gènes et les régulations épigénétiques comme par exemple la méthylation de l’ADN. Dans ce projet, nous testerons donc l’effet d’un passage des œufs au stade oeillé à basse température (3°C au lieu de 11°C) pendant 15 jours sur plusieurs caractères d’intérêt aquacole, à savoir les performances zootechniques (survie, croissance et malformations), le métabolisme intermédiaire, le développement du muscle et les qualités, ainsi que la résistance à des stress ultérieurs. Nous essaierons également de comprendre par quels mécanismes moléculaires l’exposition précoce au froid peut impacter la physiologie des poissons ultérieurement, en analysant les patrons d’expression génique et la méthylation de l’ADN (approches LUMA et RRBS). La finalité est d’utiliser la programmation précoce comme levier pour mieux maîtriser les performances des animaux à long terme. Ce projet se basera sur l’utilisation d’un modèle biologique tout à fait pertinent, deux lignées expérimentales divergentes pour la teneur en lipides du muscle : lignée grasse (LG) et lignée maigre (LM). En effet, elles ont montré une utilisation différente des aliments et possèdent un métabolisme intermédiaire et énergétique bien différencié. Il est donc possible qu’elles réagissent différemment à l’effet du froid pendant l’incubation. L’utilisation de ces deux lignées divergentes permettra de tester l’impact du fond génétique sur les réponses observées, et ainsi d’aboutir à une compréhension plus fine des mécanismes sous-jacents.Financement : FEAMP (Fonds Européen pour les Affaires Maritimes et la Pêche) – projet EpiCOOL numéro PFEA470018FA1000015

For the sustainable development of aquaculture, vegetable ingredients have been used to replace the traditional ingredients fishmeal and fish oil in aquafeeds. On the other hand, selective breeding has also been implemented at research level to obtain strains that are adapted to feeding on the plant-based diet. To better understand the underlying mechanisms prompting the adaptation to plant-based diets in fish, we investigated the hepatic expression of several microRNAs (miRNAs) that are involved in the post-transcriptional regulation of cholesterol and lipid metabolism at 8 h and 16 h after the last meal in two lines of rainbow trout: one selected for better adaptation to plant-based diets and the corresponding control line. Both groups were fed either a fishmeal and fish oil based diet or a 100% plant-based diet. Results showed that the expression of miR-33a in liver was greatly elevated in trout fed the plant-based diet, while the expression of miR-122 and miR-128 was much higher in the selected line at 8 h after the last meal regardless of the diet. Furthermore, our results indicated that some genes involved in immune processes (caspase 6 apoptosis-related cysteine peptidase like 2, casp6l2) and cAMP signal transduction (phosphodiesterase 4B cAMP-specific a, pde4ba) were also potentially regulated by miRNAs. They were newly identified as putative direct targets of miRNAs and affected in trout fed the plant-based diet. Though further investigations are still needed to establish a valid relationship between miRNAs and their target genes, our study found miR-33a, miR-122 and miR-128 as potential candidates for further study and provided new perspectives to understand the role of miRNAs in the selective breeding for adaptation to the plant-based diets.

Cet article fait partie du dossier : Caractérisation des différents types de fibres musculaires dans plusieurs espèces : production et utilisation d’anticorps monoclonaux dirigés contre les chaînes lourdes de myosine rapide IIa et IIb

International audience; Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW−) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23−) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW− and E8/E23− (Both−), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both− (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates’ own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.

International audience; In fish, the presence of predator cues in the parental or juvenile environment engenders plasticity in the expression of fear-related behaviours. Whether these cues may engender developmental plasticity when they are present in the environment of embryos remains unexplored. Here, we tested in rainbow trout, Oncorhynchus mykiss: (1) whether exposure to alarm cues during embryonic stages engendered developmental plasticity; and (2) whether an abiotic stressor could also orient the behavioural development of fry. We divided fertilized eggs into three groups: a control nonstressed group (Control), a group of embryos exposed to a conspecific alarm pheromone (e.g. predator-related cue stressor, PS), and a group of embryos that were chronically air exposed for 1 min (e.g. abiotic stressor, AS). Stressors were applied once a day, 3 times per week from 19 days postfertilization (dpf) until 52 dpf. Between 57 and 143 dpf, and for each individual, we assessed the propensity to express fear responses in different contexts and learning performances. When exposed to a novel environment or a novel object, PS fish showed significantly less fear-related behaviour, less freezing and higher activity levels than Control fish. PS fish also showed slower acquisition of a learning task than controls. AS fish did not differ from controls in any test situation. Our results show that in ovo exposure to a natural but not an abiotic signal is a prominent inducer of rainbow trout behavioural plasticity across a number of contexts. Our study provides evidence that the expression of neophobia by fish fry may be modulated by the level of risk perceived by embryos in the environment.

Flesh quality recovery in female rainbow trout (Oncorhynchus mykiss) after egg production. Aquaculture Europe 2019

GWAS reveals several genomic regions governing spontaneous XX-maleness in rainbow trout. Aquaculture Europe 2019

International audience

Session : Reproduction; Impact positif d’une restriction alimentaire modérée sur les performances de reproduction de la truitearc en ciel Oncorhynchus mykiss. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et qualité; Restauration de la qualité de la chair chez la truite arc-en-ciel femelle (Oncorhynchus mykiss) après laproduction d’œufs. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et Qualité; Apport de la métabolomique par 1H-RMN pour le développement de nouveaux aliments chez la truite arc en ciel. 6. Journées de la Recherche Filière Piscicole

Session : Systèmes d'élevages, environnement et durabilité; Approche de l'aquaponie par bilan de masse : étude des flux de matière et caractérisation de la capacité épuratoire d'un système aquaponique truite arc-en-ciel (oncorhynchus mykiss) salade (Lactuca sativa). 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et qualité; Optimisation de la qualité de la chair de grande truite arc-en-ciel (Oncorhynchus mykiss) après ovulation- projet QualiPostOv. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et Qualité; Incorporation d'une fraction de levure riche en protéines dans une formule tout végétal chez la truite arc-en-ciel : impact sur les performances zootechniques et sur la santé intestinale. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et qualité; Conséquences de l’alimentation maternelle sur le développement comportemental des alevins de truitearc-en-ciel. 6. Journées de la Recherche Filière Piscicole

Session : Génétique et Sélection; Nouveaux ingrédients et amélioration génétique : des solutions prometteuses pour améliorer les performances de croissance de la truite arc-en-ciel sur aliment végétal. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et Qualité; Influence du selenium de l'aliment des géniteurs de truite arc-en-ciel sur le statut anti-oxydant de la descendance. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et Qualité; Effet de la composition en macronutriments du régime alimentaire sur les mécanismes de croissance musculaire de la truite arc-en-ciel. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et Qualité; Alimentation végétale supplémentée en DHA d'origine micro-algale au cours du cycle de reproduction de la truite arc-en-ciel : conséquences métaboliques chez les descendants. 6. Journées de la Recherche Filière Piscicole

Session : Nutrition et qualité; Evolution de la qualité de truites arc-en-ciel (Oncorhynchus mykiss) apres la ponte : effet de l’élevagebiologique versus conventionnel et comparaison avec des truites triploïdes. 6. Journées de la Recherche Filière Piscicole

Session : Génétique et Sélection; Masculinisation spontanée chez la truite arc-en-ciel : de nouvelles régions du génome identifiées. 6. Journées de la Recherche Filière Piscicole

Session : Reproduction; Enquête sur la masculinisation spontanée dans les élevages français de truite arc-en-ciel monosexe femelle. 6. Journées de la Recherche Filière Piscicole

National audience

Résumé; Exploring the adaptation of rainbow trout metabolome to novel aquafeeds by H-NMR metabolomics. Metabolomics 2019. 15. Annual Conference of the Metabolomics Society

The aquatic metabolic unit used in this study was cofounded by The Netherlands Organization for Scientific Research (code 805-34.025). Currently it is part of a large-scale EU research facility program. The study was funded by the EU-FP7 project AQUAEXCEL (262336). LM is currently supported by a Fundação para a Ciência e a Tecnologia (FCT) research position (IF/01314/2014/CP1231/CT0001) from Portugal. This study had also the support of FCT through strategic projects UID/Multi/04423/2019 and UID/MAR/04292/2013 granted to CIIMAR and MARE, respectively. SN has support from FCT grant (SFRH/BPD/94500/2013). This work was also supported by the Integrated Programme of SR&TD “Smart Valorization of Endogenous Marine Biological Resources Under a Changing Climate” (reference Centro01-0145-FEDER-000018), co-funded by Centro 2020 program, Portugal 2020, European Union, through the European Regional Development Fund. In aquaculture, fish may be exposed to sub-optimal rearing conditions, which generate a stress response if full adaptation is not displayed. However, our current knowledge of several coexisting factors that may give rise to a stress response is limited, in particular when both chronic and acute stressors are involved. This study investigated changes in metabolic parameters, oxidative stress and innate immune markers in a rainbow trout (Oncorhynchus mykiss) isogenic line exposed to a combination of dietary (electrolyteimbalanced diet, DEB 700 mEq Kg−1 ) and environmental (hypoxia, 4.5 mg O2 L −1 ) challenges and their respective controls (electrolyte-balanced diet, DEB 200 mEq Kg−1 and normoxia, 7.9 or mg O2 L −1 ) for 49 days. At the end of this period, fish were sampled or subjected to an acute stressor (2 min of handling/confinement) and then sampled. Feeding trout an electrolyte-imbalanced diet produced a reduction in blood pH, as well as increases in cortisol levels, hepato-somatic index (HSI) and total energy content in the liver. The ratio between the lactate dehydrogenase (LDH) and isocitrate dehydrogenase (IDH) activities decreased in the liver of trout fed the DEB 700 diet, but increased in the heart, suggesting a different modulation of metabolic capacity by the dietary challenge. Several markers of oxidative stress in the liver of trout, mainly related to the glutathione antioxidant system, were altered when fed the electrolyteimbalanced diet. The dietary challenge was also associated with a decrease in the alternative complement pathway activity (ACH50) in plasma, suggesting an impaired innate immune status in that group. Trout subjected to the acute stressor displayed reduced blood pH values, higher plasma cortisol levels as well as increased levels of metabolic markers associated with oxidative stress in the liver. An interaction between diet and acute stressor was detected for oxidative stress markers in the liver of trout, showing that the chronic electrolyte-imbalance impairs the response of rainbow trout to handling/confinement. However, trout reared under chronic hypoxia only displayed changes in parameters related to energy use in both liver and heart. Taken together, these results suggest that trout displays an adaptative response to chronic hypoxia. Conversely, the dietary challenge profoundly affected fish homeostasis, resulting in an impaired physiological response leading to stress, which then placed constraints on a subsequent acute challenge. info:eu-repo/semantics/publishedVersion

The formation of new myofibers in vertebrates occurs by myoblast fusion and requires fusogenic activity of the muscle-specific membrane protein myomaker. Here, using in silico (BLAST) genome analyses, we show that the myomaker gene from trout includes 14 minisatellites, indicating that it has an unusual structure compared with those of other animal species. We found that the trout myomaker gene encodes a 434 –amino acid (aa) protein, in accordance with its apparent molecular mass (40 kDa) observed by immunoblotting. The first half of the trout myomaker protein (1–220 aa) is similar to the 221-aa mouse myomaker protein, whereas the second half (222–234 aa) does not correspond to any known motifs and arises from two protein extensions. The first extension (70 aa) apparently appeared with the radiation of the bony fish clade Euteleostei, whereas the second extension (up to 236 aa) is restricted to the superorder Protacanthopterygii (containing salmonids and pike) and corresponds to the insertion of minisatellites having a length of 30 nucleotides. According to gene expression analyses, trout myomaker expression is consistently associated with the formation of new myofibers during embryonic development, postlarval growth, and muscle regeneration. Using cell-mixing experiments, we observed that trout myomaker has retained the ability to drive the fusion of mouse fibroblasts with C2C12 myoblasts. Our work reveals that trout myomaker has fusogenic function despite containing two protein extensions., SCOPUS: ar.j, DecretOANoAutActif, info:eu-repo/semantics/published

Rainbow trout (Oncorhynchus mykiss) egg production is a key sector for aquaculture. This industry relies on well-controlled reproductive cycles and the extensive use of photoperiod control to obtain year-round egg production. However, feed management practices are very diverse among producers and not always designed to optimize egg production. Among these different practices, feed restriction is of major interest due to its direct impact on the reduction of egg production costs. It is however not always used under optimal conditions. The aim of the present study was to evaluate the impact of moderate feed restriction on reproductive performances and egg quality in rainbow trout. For that purpose, two feeding strategies were implemented during the last five months before the second reproduction. Females were either fed (1) ad libitum, or (2) 80% of ad libitum (i.e. restricted) with a commercial diet. An artificial photoperiod was applied to trigger reproduction during the summer. As expected, feed restriction resulted in smaller females in comparison to those fed ad libitum whereas gonado-somatic index was significantly higher in restricted females. In addition, hatching rate was significantly higher for eggs from originating from restricted females. Feed restriction led to the production of bigger eggs with less size variability and lower number of non-viable eggs. These restricted females also exhibited lower viscero-somatic index suggesting an impact of feed restriction on the allocation of reserves. However, lipid content in eggs and muscle were not different between groups, while fatty acid profile of eggs presented some differences. PUFA analysis revealed that proportions of ALA, AA and EPA were higher in eggs from restricted females, a feature possibly linked to higher egg quality. Together, these results demonstrate that feed intake of female rainbow trout broodstock can be reduced by at least 20% without any negative impact on egg production and egg quality.

Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolutionary history. In addition to a teleost-specific whole genome duplication approximately 320–350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome duplication event approximately 80 million years ago. Through the recent sequencing of salmonid genome sequences, including the rainbow trout, the identification and study of duplicated genes has become available. A particular focus of interest has been the evolution and regulation of rainbow trout gluconeogenic genes, as recent molecular and gene expression evidence points to a possible contribution of previously uncharacterized gluconeogenic gene paralogues to the rainbow trout long-studied glucose intolerant phenotype. Since the publication of the initial rainbow trout genome draft, resequencing and annotation have further improved genome coverage. Taking advantage of these recent improvements, we here identify a salmonid-specific genome duplication of ancestral mitochondrial phosphoenolpyruvate carboxykinase 2 isoenzyme, we termed pck2a and pck2b. Cytosolic phosphoenolpyruvate carboxykinase (Pck1) and, more recently mitochondrial Pck2, are considered to be the rate-limiting enzymes in de novo gluconeogenesis. Following in silico confirmation of salmonid pck2a and pck2b evolutionary history, we simultaneously profiled cytosolic pck1 and mitochondrial pck2a and pck2b expression in rainbow trout liver under several experimental conditions known to regulate hepatic gluconeogenesis. Cytosolic pck1 abundance was increased by nutritional (diets with a high protein to carbohydrate ratio compared to diets with a low carbohydrate to protein ratio) and glucoregulatory endocrine factors (glucagon and cortisol), revealing that the well-described transcriptional regulation of pck1 in mammals is present in rainbow trout. Conversely, and in contrast to mammals, we here describe endocrine regulation of pck2a (decrease in abundance in response to glucagon infusion), and nutritional, social-status-dependent and hypoxia-dependent regulation of pck2b. Specifically, pck2b transcript abundance increased in trout fed a diet with a low protein to carbohydrate ratio compared to a diet with a high protein to carbohydrate ratio, in dominant fish compared to subordinate fish as well as hypoxia. This specific and differential expression of rainbow trout pck2 ohnologues is indicative of functional diversification, and possible functional consequences are discussed in light of the recently highlighted gluconeogenic roles of mitochondrial pck2 in mammalian models.

Background: Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a signifcant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fxation index (FST), linkage disequilibrium (LD), efective population size (Ne) and inbreeding coefcient derived from runs of homozygosity (ROH). Results: Our results showed a moderate level of genetic diferentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the frst 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to diferences in local rates of recombination or due to key genes that tended to have fxed favorable alleles for domestication or production. Conclusions: This is the frst report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder efects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efcient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fsh genome.

Carnivorous rainbow trout exhibit prolonged postprandial hyperglycemia when fed a diet exceeding 20% carbohydrate content. This poor capacity to utilize carbohydrates has led to rainbow trout being classified as “glucose-intolerant” (GI). The metabolic phenotype has spurred research to identify the underlying cellular and molecular mechanisms of glucose intolerance, largely because carbohydrate-rich diets provide economic and ecological advantages over traditionally used fish meal, considered unsustainable for rainbow trout aquaculture operations. Evidence points to a contribution of hepatic intermediary carbohydrate and lipid metabolism, as well as upstream insulin signaling. Recently, microRNAs (miRNAs), small noncoding RNAs acting as negative posttranscriptional regulators affecting target mRNA stability and translation, have emerged as critical regulators of hepatic control of glucose-homeostasis in mammals, revealing that dysregulated hepatic miRNAs might play a role in organismal hyperglycemia in metabolic disease. To determine whether hepatic regulatory miRNA networks may contribute to GI in rainbow trout, we induced prolonged postprandial hyperglycemia in rainbow trout by using a carbohydrate-rich diet and profiled genome-wide hepatic miRNAs in hyperglycemic rainbow trout compared with fasted trout and trout fed a diet devoid of carbohydrates. Using small RNA next-generation sequencing and real-time RT-PCR validation, we identified differentially regulated hepatic miRNAs between these groups and used an in silico approach to predict bona fide mRNA targets and enriched pathways. Diet-induced hyperglycemia resulted in differential regulation of hepatic miRNAs compared with fasted fish. Some of the identified miRNAs, such as miRNA-27b-3p and miRNA-200a-3p, are known to be responsive to hyperglycemia in the liver of hyperglycemic glucose-tolerant fish and mammals, suggesting an evolutionary conserved regulation. Using Gene Ontology term-based enrichment analysis, we identify intermediate carbohydrate and lipid metabolism and insulin signaling as potential targets of posttranscriptional regulation by hyperglycemia-regulated miRNAs and provide correlative expression analysis of specific predicted miRNA-target pairs. This study identifies hepatic miRNAs in rainbow trout that exhibit differential postprandial expression in response to diets with different carbohydrate content and predicts posttranscriptionally regulated target mRNAs enriched for pathways involved in glucoregulation. Together, these results provide a framework for testable hypotheses of functional involvement of specific hepatic miRNAs in GI in rainbow trout.

Evolutionary novelties require rewiring of transcriptional networks and/or the evolution of new gene functions. Sex determination (SD), one of the most plastic evolutionary processes, requires such novelties. Studies on the evolution of vertebrate SD revealed that new master SD genes are generally recruited from genes involved in the downstream SD regulatory genetic network. Only a single exception to this rule is currently known in vertebrates: the intriguing case of the salmonid master SD gene (sdY), which arose from duplication of an immune-related gene. This exception immediately posed the question of how a gene outside from the classical sex differentiation cascade could acquire its function as a male SD gene. Here we show that SdY became integrated in the classical vertebrate sex differentiation cascade by interacting with the Forkhead box domain of the female-determining transcription factor, Foxl2. In the presence of Foxl2, SdY is translocated to the nucleus where the SdY:Foxl2 complex prevents activation of the aromatase (cyp19a1a) promoter in cooperation with Nr5a1 (Sf1). Hence, by blocking a positive loop of regulation needed for the synthesis of estrogens in the early differentiating gonad, SdY disrupts a preset female differentiation pathway, consequently allowing testicular differentiation to proceed. These results also suggest that the evolution of unusual vertebrate master sex determination genes recruited from outside the classical pathway like sdY is strongly constrained by their ability to interact with the canonical gonadal differentiation pathway.

International audience; Rainbow trout (Oncorhynchus mykiss) is recognized as a typical “glucose-intolerant” fish, and the limits of dietary carbohydrate utilization have been investigated for many years. In this study, the objective was to test the molecular effects of dietary carbohydrates on intermediary metabolism in two major metabolic tissues, liver and muscle. Another objective was also to study if the response to carbohydrate intake depended on the genetic background. We fed two isogenic lines of rainbow trout (named A22h and N38h) with high carbohydrate diet (carbohydrate, 22.9%) or low carbohydrate diet (carbohydrate, 3.6%) for 12 weeks. Carbohydrates were associated with higher feed utilization owned by the well-known protein-sparing effect, with better fish growth performance. However, atypical regulation of glycolysis and gluconeogenesis in liver and absence of hk and glut4 induction in muscle, were also observed. Regarding the effects of carbohydrates on other metabolism, we observed an increased, at a molecular level, of hepatic cholesterol biosynthesis, fatty acid oxidation and mitochondrial energy metabolism. Genetic variability (revealed by the differences between the two isogenic lines) was observed for some metabolic genes especially for those involved in the EPA and DHA biosynthetic capacity. Finally, our study demonstrates that dietary carbohydrate not only affect glucose metabolism but also strongly impact the lipid and energy metabolism in liver and muscle of trout.

Impacts des traitements technologiques sur la valeur nutritionnelle de la graine de féverole pour la truite arc-en-ciel. 2. Rencontres Francophones sur les Légumineuses (RFL2)

National audience

Rainbow trout (Oncorhynchus mykiss) freshwater recirculating aquaculture system: nutrient flow management with aquaponics. World Aquaculture 2018

UMR BFP - Equipe Métabolisme; Metabolomic application in fish nutrition: profiling novel aquaculture feeds and assessing their impact on rainbow trout plasma. EUROMAR - European Magnetic Resonance Meeting

UMR BFP - Equipe Métabolisme; NMR-based metabolomics workflow for characterization and effect assessment of alternative plant-based diets onplasma and microbiote in rainbow trout. EUROMAR - European Magnetic Resonance Meeting

Résumé; Effects of dietary protein level and non-protein energy source on muscle growth mechanisms in rainbow trout (Oncorhynchus mykiss) juveniles. 18. ISFNF International Symposium on Fish Nutrition and Feeding "40 years of research in fish nutrition"

Résumé; Regulation of miR-33a and cholesterol metabolism related gene expression in rainbow trout (Oncorhynchus mykiss): in vivo and in vitro approaches. 18. ISFNF International Symposium on Fish Nutrition and Feeding "40 years of research in fish nutrition"

Résumé; Integrative 1H-NMR metabolomic investigation of the effect of alternative diets on rainbow trout plasma. 18. ISFNF International Symposium on Fish Nutrition and Feeding "40 years of research in fish nutrition"

Résumé; Effect of food restriction on reproductive performances and egg quality in rainbow trout (Oncorhynchus mykiss). 18. ISFNF International Symposium on Fish Nutrition and Feeding "40 years of research in fish nutrition"

This study aims to shed light on corticosteroid regulation of stress in teleost fish with focus on the corticosteroid signalling system. The role of the mineralocorticoid-like hormone 11-deoxycorticosterone (DOC) in fish is still enigmatic, as is the function of the mineralocorticoid receptor, MR. Low plasma DOC levels and ubiquitous tissue distribution of MR question the physiological relevance of the mineralocorticoid-axis. Furthermore, the particular purpose of each of the three corticosteroid receptors in fish, the glucocorticoid receptors, GR1 and GR2, and the MR, is still largely unknown. Therefore we investigate the regulation of cortisol and DOC in plasma and mRNA levels of MR, GR1 and GR2 in the HPI-axis tissue (hypothalamus, pituitary and interrenal gland) during a detailed confinement stress time-course. Here we show a sustained up-regulation of plasma DOC levels during a confinement stress time-course. However, the low DOC levels compared to cortisol measured in the plasma do not favour an activity of DOC through MR receptors. Furthermore, we show differential contribution of the CRs in regulation and control of HPI axis activity following confinement stress. Judged by the variation of mRNA levels negative feedback regulation of cortisol release occurs on the level of the pituitary via MR and on the level of the interrenal gland via GR2. Finally, as a significant effect of confinement stress on CR expressions was observed in the pituitary gland, we completed this experiment by demonstrating that corticosteroid receptors (GR1, GR2 and MR) are co-expressed in the ACTH cells located in the adenohypophysis. Overall, these data suggest the involvement of these receptors in the regulation of the HPI axis activity by cortisol.

In the context of the exponential development of aquaculture, fish meal and oils, previously the main components of aquaculture feed, have been increasingly replaced by a blend of plant products. However, total replacement is not yet possible without impairing fish performance (survival and growth). To continue its sustainable development, aquaculture must further decrease its reliance on both fish oil and fish meal. In addition to the changes in diet composition, a possible way forward is the use of the genetic variability for the ability to survive and grow with plant-based diets (V diets) existing in trout populations. However, very few studies have investigated the mechanisms implemented by some genotypes to use these diets more efficiently. The objective of this thesis was to study the characteristics that led to a better utilisation of V diet in different rainbow trout genotypes. The originality of this PhD work relies on the genetic rainbow trout lines whose responses to a 100% V diet were studied by combining nutritional physiology and molecular biology with or without a priori approaches. Thus, the transcriptomes of three isogenic lines, which have contrasting performances when fed V diets, were compared at short and long term. Then nutrition-related traits, as well as the expression of some genes identified through the transcriptomics analysis, were studied in a line selected for its ability to survive and grow with a V diet. The results obtained led to the conclusion that the acceptance of V diets plays a key role, particularly in the early stages. The results also highlight the essential role of the immune system, which is impacted differently according to genotypes. Finally, after 6 months of feeding, while lipid metabolism seems to play a role in the differences between genotypes for their ability to efficiently utilize the V diet, this pathway does not appear to play a determinant role in the selected line. Overall, our results suggest that there are a wide variety of mechanisms allowing trout to survive and grow with a total plant-based diet, devoid of both fish meal and oils.; Dans le contexte du développement spectaculaire de l’aquaculture, les farines et huiles de poissons, qui étaient les composantes principales des aliments aquacoles, ont progressivement été remplacées par des mélanges de produits végétaux. Cependant, le remplacement total n’est pas encore possible sans dégrader les performances des poissons (croissance et survie). Pour continuer son développement durable, l’aquaculture doit davantage s'affranchir de ces matières premières. Une voie de progrès possible est l'utilisation de la variabilité génétique existante dans les populations de truites pour la capacité à survivre et grandir avec des aliments à base de végétaux (Aliments V). Cependant très peu d'études se sont intéressées aux mécanismes mis en place par certains génotypes pour utiliser plus efficacement ces aliments. L'objectif de la thèse était d'étudier les caractéristiques à l'origine d'une meilleure utilisation des aliments V chez différents génotypes de truite arc-en-ciel (trois lignées isogéniques et lignée sélectionnée). L'originalité de ce travail repose sur l'étude de la réponse de différentes lignées à un aliment 100 % V, en combinant des approches de physiologie nutritionnelle et de biologie moléculaire sans a priori ou ciblées. Ainsi les transcriptomes de trois lignées isogéniques, ayant des performances contrastées lorsqu'elles sont nourries avec des aliments V, ont été comparés à court et long terme. Puis des caractères liés à la nutrition, ainsi que l'expression de certains gènes, identifiés grâce à l'étude transcriptomique, ont été étudiés chez une lignée sélectionnée pour sa capacité à survivre et grandir avec un aliment V. Les résultats obtenus ont permis de conclure que l'acceptation de l'aliment V joue un rôle clef, notamment lors des stades précoces. Les résultats obtenus mettent également en avant le rôle prépondérant de la composante immunitaire qui est impactée différemment en fonction des génotypes. Finalement, après 6 mois d'alimentation, alors que le métabolisme des lipides participe à expliquer les différences d’utilisation de l’aliment V chez les lignées isogéniques, il ne parait pas déterminant chez la lignée sélectionnée. Globalement, nos résultats suggèrent l'existence d'une grande diversité de mécanismes dans les populations de truites leur permettant de survivre et grandir avec un aliment à base de végétaux dépourvu de farine et huiles de poisson.

In the context of the exponential development of aquaculture, fish meal and oils, previously the main components of aquaculture feed, have been increasingly replaced by a blend of plant products. However, total replacement is not yet possible without impairing fish performance (survival and growth). To continue its sustainable development, aquaculture must further decrease its reliance on both fish oil and fish meal. In addition to the changes in diet composition, a possible way forward is the use of the genetic variability for the ability to survive and grow with plant-based diets (V diets) existing in trout populations. However, very few studies have investigated the mechanisms implemented by some genotypes to use these diets more efficiently. The objective of this thesis was to study the characteristics that led to a better utilisation of V diet in different rainbow trout genotypes. The originality of this PhD work relies on the genetic rainbow trout lines whose responses to a 100% V diet were studied by combining nutritional physiology and molecular biology with or without a priori approaches. Thus, the transcriptomes of three isogenic lines, which have contrasting performances when fed V diets, were compared at short and long term. Then nutrition-related traits, as well as the expression of some genes identified through the transcriptomics analysis, were studied in a line selected for its ability to survive and grow with a V diet. The results obtained led to the conclusion that the acceptance of V diets plays a key role, particularly in the early stages. The results also highlight the essential role of the immune system, which is impacted differently according to genotypes. Finally, after 6 months of feeding, while lipid metabolism seems to play a role in the differences between genotypes for their ability to efficiently utilize the V diet, this pathway does not appear to play a determinant role in the selected line. Overall, our results suggest that there are a wide variety of mechanisms allowing trout to survive and grow with a total plant-based diet, devoid of both fish meal and oils.; Dans le contexte du développement spectaculaire de l’aquaculture, les farines et huiles de poissons, qui étaient les composantes principales des aliments aquacoles, ont progressivement été remplacées par des mélanges de produits végétaux. Cependant, le remplacement total n’est pas encore possible sans dégrader les performances des poissons (croissance et survie). Pour continuer son développement durable, l’aquaculture doit davantage s'affranchir de ces matières premières. Une voie de progrès possible est l'utilisation de la variabilité génétique existante dans les populations de truites pour la capacité à survivre et grandir avec des aliments à base de végétaux (Aliments V). Cependant très peu d'études se sont intéressées aux mécanismes mis en place par certains génotypes pour utiliser plus efficacement ces aliments. L'objectif de la thèse était d'étudier les caractéristiques à l'origine d'une meilleure utilisation des aliments V chez différents génotypes de truite arc-en-ciel (trois lignées isogéniques et lignée sélectionnée). L'originalité de ce travail repose sur l'étude de la réponse de différentes lignées à un aliment 100 % V, en combinant des approches de physiologie nutritionnelle et de biologie moléculaire sans a priori ou ciblées. Ainsi les transcriptomes de trois lignées isogéniques, ayant des performances contrastées lorsqu'elles sont nourries avec des aliments V, ont été comparés à court et long terme. Puis des caractères liés à la nutrition, ainsi que l'expression de certains gènes, identifiés grâce à l'étude transcriptomique, ont été étudiés chez une lignée sélectionnée pour sa capacité à survivre et grandir avec un aliment V. Les résultats obtenus ont permis de conclure que l'acceptation de l'aliment V joue un rôle clef, notamment lors des stades précoces. Les résultats obtenus mettent également en avant le rôle prépondérant de la composante immunitaire qui est impactée différemment en fonction des génotypes. Finalement, après 6 mois d'alimentation, alors que le métabolisme des lipides participe à expliquer les différences d’utilisation de l’aliment V chez les lignées isogéniques, il ne parait pas déterminant chez la lignée sélectionnée. Globalement, nos résultats suggèrent l'existence d'une grande diversité de mécanismes dans les populations de truites leur permettant de survivre et grandir avec un aliment à base de végétaux dépourvu de farine et huiles de poisson.

Mise en évidence d'étapes de transition successives des cellules souches germinales qui conduisent à l'apparition de progéniteurs au cours de l’ontogénèse de la truite arc-en-ciel (Oncorhynchus mykiss). Journées d'Animation Scientifique du département Phase (JAS Phase 2018)

Gene expression profiling during rainbow trout ontogenesis reveals successive changes gated in teleosts in germ stem cell molecular signature and regulatory pathways

International audience; MicroRNAs (miRNAs) are a class of small non-coding RNAs which are known to posttranscriptionally regulate the expression of most genes in both animals and plants. Meanwhile, studies have shown that numbers of miRNAs are present in body fluids including the plasma. Despite the mode of action of these circulating miRNAs still remains unknown, they have been found to be promising biomarkers for disease diagnosis, prognosis and response to treatment. In order to evaluate the potential of miRNAs as non-invasive biomarkers in aquaculture, a time-course experiment was implemented to investigate the postprandial regulation of miRNAs levels in liver and plasma as well as the hepatic expression of genes involved in cholesterol metabolism. We showed that miR-1, miR-33a, miR-122, miR-128 and miR-223 were expressed in the liver of rainbow trout and present at detectable level in the plasma. We also demonstrated that hepatic expression of miR-1, miR-122 and miR-128 were regulated by feed intake and reached their highest levels 12 hours after the meal. Interestingly, we observed that circulating levels of miR-128 and miR-223 are subjected to postprandial regulations similar to that observed in their hepatic counterparts. Statistical correlations were observed between liver and plasma for miR-128 and miR-223 and between hepatic and circulating miR-122, miR-128 and miR-223 and expression of genes related to cholesterol synthesis and efflux or glucose phosphorylation. These results demonstrated that circulating miR-122, miR-128 and miR-223 are potential biomarkers of cholesterol metabolism in rainbow trout.

The formation of the intramuscular connective tissue was investigated in rainbow trout Oncorhynchus mykiss by combining histological and in situ gene‐expression analysis. Laminin, a primary component of basement membranes, surrounded superficial slow and deep fast muscle fibres in O. mykiss as soon as the hatching stage (c. 30 days post fertilization (dpf)). In contrast, type I collagen, the primary fibrillar collagen in muscle of vertebrates, appeared at the surface of individual slow and fast muscle fibres only at c. 90 dpf and 110 dpf, respectively. The deposition of type I collagen in laminin‐rich endomysium ensheathing individual muscle fibres correlated with the late appearance of collagen type 1 α 1 chain (col1α1) expressing fibroblasts inside slow and then fast‐muscle masses. Double in situ hybridization indicated that coll1α1 expressing muscle resident fibroblasts also expressed collagen type 5 α 2 chain (col5α2) transcripts, showing that these cells are a major cellular source of fibrillar collagens within O. mykiss muscle. At c. 140 dpf, the formation of perimysium‐like structure was manifested by the increase of type I collagen deposition around bundles of myofibres concomitantly with the alignment and elongation of some collagen‐expressing fibroblasts. Overall, this study shows that the formation of O. mykiss intramuscular connective tissue network is completed only in aged fry when fibroblast‐like cells expressing type I and V collagens arise inside of the growing myotome.

L'analyse histologique, transcriptomique et in vitro révèlent un état activé des précurseurs myogéniques du muscle hyperplasique de la truite . Journées d'Animation Scientifique du département Phase (JAS Phase 2018)

Rainbow trout (Oncorhynchus mykiss) was recognized as a typical ‘glucose-intolerant’ fish and poor dietary carbohydrate user. Our first objective was to test the effect of dietary carbohydrates themselves (without modification of dietary protein intake) on hepatic glucose gene expression (taking into account the paralogs). The second aim was to research if two isogenic trout lines had different responses to carbohydrate intake, showing one with a better use dietary carbohydrates. Thus, we used two isogenic lines of rainbow trout (named A32h and AB1h) fed with either a high carbohydrate diet or a low carbohydrate diet for 12 weeks. We analysed the zootechnical parameters, the plasma metabolites, the hepatic glucose metabolism at the molecular level and the hormonal-nutrient sensing pathway. Globally, dietary carbohydrate intake was associated with hyperglycaemia and down regulation of the energy sensor Ampk, but also with atypical regulation of glycolysis and gluconeogenesis in the liver. Indeed, the first steps of glycolysis and gluconeogenesis catalysed by the glucokinase and the phospenolpyruvate carboxykinase are regulated at the molecular level by dietary carbohydrates as expected (i.e. induction of the glycolytic gck and repression of the gluconeogenic pck); by contrast, and surprisingly, for two other key glycolytic enzymes (phosphofructokinase enzyme – pfkl and pyruvate kinase – pk) some of the paralogs (pfklb and pklr) are inhibited by carbohydrates whereas some of the genes coding gluconeogenic enzymes (the glucose-6-phosphatase enzyme g6pcb1b and g6pcb2a gene and the fructose1-6 biphosphatase paralog fbp1a) are induced. On the other hand, some differences for the zootechnical parameters and metabolic genes were also found between the two isogenic lines, confirming the existence of genetic polymorphisms for nutritional regulation of intermediary metabolism in rainbow trout. In conclusion, our study determines some new and unexpected molecular regulations of the glucose metabolism in rainbow trout which may partly lead to the poor utilization of dietary carbohydrates and it underlines the existence of differences in molecular regulation of glucose metabolism between two isogenic lines which provides arguments for future selection of rainbow trout., Summary: Using isogenic lines, this study determines some new, unexpected molecular regulation of the glucose metabolism in rainbow trout, which may partly lead to the poor utilization of dietary carbohydrates.