Embryogenèse Et Succès De Reproduction Chez La Perche

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Embryogenèse Et Succès De Reproduction Chez La Perche AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Université de Lorraine Ecole doctorale Sciences et Ingénierie Ressources Procédés Produits Environnement (RP2E) Unité de Recherche Animal et Fonctionnalités des produits animaux (URAFPA) THESE Présentée à l’Université de Lorraine pour obtenir le grade de Docteur de l’Université de Lorraine Discipline : Sciences Agronomiques Présentée et soutenue publiquement le 15 décembre 2016 par Maud ALIX Etude de la variabilité de l’embryogenèse chez la perche commune : développement d’approches alternatives. Composition du jury Rapporteurs Mélanie Debiais-Thibaud Maître de Conférences, ISEM, Université de Montpellier Catherine Labbé Chargée de Recherche, LPGP, INRA, Rennes Examinateurs Sylvie Rétaux Directrice de Recherche, CNRS Gif-sur-Yvette Marc Legendre Directeur de Recherche, ISEM, IRD, Montpellier Directeur de thèse Pascal Fontaine Professeur, Université de Lorraine, Nancy Codirectrice de thèse Bérénice Schaerlinger Maître de Conférences, Université de Lorraine, Nancy Membre invité Dominique Chardard Maître de Conférences, Université de Lorraine, Nancy Unité de Recherche Animal et Fonctionnalités des Produits Animaux (UR AFPA) – Equipe Domestication en Aquaculture Continentale (DAC) – Faculté des Sciences et Technologies – Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy Cedex RESUME Résumé Etude de la variabilité de l'embryogenèse chez la perche commune : développement d'approches alternatives Aujourd’hui, la durabilité du modèle de développement de l’aquaculture est de plus en plus questionnée et une des solutions proposées consisterait à diversifier la production piscicole via la domestication de nouvelles espèces comme la perche commune, Perca fluviatilis, une espèce d’eau douce tempérée très intéressante pour la diversification de l’aquaculture continentale européenne. De nombreux aspects de la biologie de sa reproduction sont connus cependant, peu d’informations sont disponibles sur son développement. Or, des défauts de développement précoce, dont les causes sont encore mal définies, impactent actuellement la qualité de la production piscicole. C’est dans ce contexte que cette thèse vise à caractériser les succès et défauts de développement embryonnaire chez la perche commune à travers trois axes principaux : (i) déterminer une table de référence de l’embryogenèse normale permettant (ii) définir les défauts de développement tels que les malformations dans des conditions d’élevage différentes et (iii) identifier les liens entre différents paramètres de développement embryonnaire afin de déterminer des profils de développement variables. La première partie de ce travail a permis d’identifier la séquence précise de l’ontogenèse normale de cette espèce à travers la définition d’une table de développement embryonnaire alternative et flexible pour des espèces non-modèles, facilitant les comparaisons intra- et inter-espèces. Dans un second temps, l’identification la plus exhaustive possible de phénotypes anormaux a révélé 10 grandes catégories de malformations associées à des organes ou fonctions spécifiques. De plus, certains de ces défauts semblent fortement dépendants des conditions d’élevage des géniteurs ce qui permet d’identifier l’effet de potentiels facteurs extrinsèques sur le développement et d’améliorer les techniques de gestion des animaux. Enfin, l’ensemble de ces résultats et des paramètres mesurés durant l’embryogenèse ont permis d’effectuer une classification approfondie des pontes obtenues présentant des profils de développement similaires pour mettre en évidence des liens éventuels entre les divers phénotypes et paramètres utilisés. Les analyses de données effectuées ont montré que seulement 3 paramètres étaient nécessaires à la caractérisation de 4 profils de succès de développement variables Ś les taux de survie au début de l’organogenèse, d’éclosion et de malformations. A l’avenir, ces paramètres pourraient être généralisés permettant d’homogénéiser les critères d’évaluation du succès de développement chez d’autres espèces d’intérêt de poisson. L’ensemble de ces résultats constituent une base solide pour étudier l’effet des facteurs extrinsèques et/ou intrinsèques sur la qualité et le succès de développement embryonnaire. Mots clefs : Embryogenèse, Approches alternatives, Variabilité du développement, Malformations, Mortalités, Perche commune i ABSTRACT Abstract Study of the embryogenesis variability in the Eurasian perch: development of alternative approaches Currently, the durability of the aquaculture developmental model is clearly challenged and one solution consists to diversify the fish production by the domestication of new species such as the Eurasian perch (P. fluviatilis), a freshwater species promising and valuable for the diversification of European aquaculture. Several aspects of its reproductive biology are well known, nevertheless, only little information is available on its development. However, early developmental impairments, whose causes are unclear, actually impact the fish production quality. In this context, the present work aimed to characterize the developmental success and impairments in Eurasian perch on three main issues: (i) determine a model of normal embryogenesis table helping to (ii) define developmental impairments, in diverse rearing conditions and (iii) identify the relationships between various parameters of embryonic ontogenesis to characterize different patterns of developmental success. The first part of this study allowed identifying the accurate timing of normal ontogenesis of this species through the definition of an alternative and flexible developmental table to describe non- model fish species, allowing the intra- and inter-specific comparisons. In the second part, the exhaustive characterization of abnormal phenotypes revealed 10 categories of deformities linked to specific organs or functions. Moreover, some of these categories seemed to be related to rearing- conditions of the breeders allowing identifying the potential effects of extrinsic factors on the development and improving the management of fish. Finally, the previous results and the parameters measured during embryogenesis help to classify the several spawns obtained with the same developmental pattern and to highlight the potential relationships between diverse phenotypes and parameters. In addition, the data analyses showed that only 3 parameters are reliable to assess the developmental success: survival rate at the onset of the organogenesis, hatching and deformities rates. Henceforth, these parameters and this classification could be generalized as a new strategy to assess the developmental success in other fish species. All of these results provide a good basic knowledge to study the potential effects of various extrinsic and/or intrinsic factors on the developmental success and the embryonic quality. Keywords: Embryogenesis, Alternative approaches, Developmental variability, Deformities, Lethalities, Eurasian perch ii REMERCIEMENTS Remerciements Je tiens tout d’abord à remercier mes trois directeurs, Bérénice Schaerlinger, Pascal Fontaine et Dominique Chardard pour leur implication, leur soutien et leur confiance tout au long de cette thèse. Bérénice, je te remercie pour le temps que tu m’as accordé durant ces quatre années, pour tes conseils et la rigueur que tu as su me transmettre. Dominique, merci pour ta bonne humeur, ton aide et nos discussions toujours constructives. Enfin, Pascal, merci également pour ta confiance, pour m’avoir accueillie au sein de ton équipe, pour cette approche « paternelle » inimitable que tu as d’encadrer et bien sûr, merci pour les démonstrations de ton savoir-faire au Bowling. Je tiens tout particulièrement à remercier les membres de mon jury pour avoir accepté de consacrer leur temps à l’évaluation de ce travail de recherche. Je voudrais donc remercier Mme Mélanie Debiais- Thibaud, Maitre de conférences à l’Université de Montpellier et Mme Catherine Labbé, Chargée de recherche à l’INRA à Rennes qui m’ont fait l’honneur d’être rapporteurs de cette thèse. Je remercie également Mme Sylvie Rétaux, Directrice de recherche CNRS à Gif-sur-Yvette ainsi que M. Marc Legendre, Directeur de recherche à l’IRD et à l’ISEM de Montpellier pour avoir accepté d’examiner mon travail. Je souhaite également remercier les membres de mon comité de thèse, Julien Bobe, Patricia Cucchi, et Anne-Hélène Monsoro-Burq, qui ont contribué à la réflexion sur ce projet de thèse et ont accepté de le suivre. Cette thèse est l’aboutissement d’un travail d’équipe qui a été effectué grâce à de nombreux collaborateurs que je tiens vraiment à remercier pour leur disponibilité, leur patience et leur aide : Aux sociétés Lucas Perches, Asialor, GFA Kuhweg et la Pisciculture du Saulnois qui nous ont fourni les animaux et avec lesquels j’ai pu découvrir une partie de la profession de pisciculteur. A Yves Le
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