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Genetic and Genomic Variation of Resistance to Viral Nervous Necrosis in Wild Populations of European Seabass (Dicentrachus Labrax) Quoc Khanh Doan

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Genetic and Genomic Variation of Resistance to Viral Nervous Necrosis in Wild Populations of European Seabass (Dicentrachus Labrax) Quoc Khanh Doan Genetic and genomic variation of resistance to viral nervous necrosis in wild populations of european seabass (Dicentrachus labrax) Quoc Khanh Doan To cite this version: Quoc Khanh Doan. Genetic and genomic variation of resistance to viral nervous necrosis in wild populations of european seabass (Dicentrachus labrax). Animal genetics. Université Montpellier, 2017. English. NNT : 2017MONTT094. tel-01693577 HAL Id: tel-01693577 https://tel.archives-ouvertes.fr/tel-01693577 Submitted on 26 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Écologie, Evolution, Ressources Génétique, Paléobiologie École doctorale GAIA Unité de recherche UMR MARBEC - Ifremer Titre de la thèse GENETIC AND GENOMIC VARIATION OF RESISTANCE TO VIRAL NERVOUS NECROSIS IN WILD POPULATIONS OF EUROPEAN SEABASS ( Dicentrachus labrax ) Présentée par Quoc Khanh DOAN Le 28/11/2017 Sous la direction de Béatrice CHATAIN Devant le jury composé de Mme. Béatrice CHATAIN, (C3 EPIC, Thèse d’Etat) , IFREMER Directeur de these Mme. Mathilde DUPONT-NIVET, (DR, HDR), INRA Rapporteur M. Pierre BOUDRY , (C3 EPIC, HDR), IFREMER Rapporteur M. Luca BARGELLONI, Full Professor, Université de Padoue Examinateur M. Pierre -Alexandre GAGNAIRE, CR, CNRS Examinateur M. Patrick PRUNET , (DR, HDR), INRA Président du jury M. Marc VANDEPUTTE, ( IR, HDR), INRA Invité M. François ALLAL, (C1 EPIC), IFREMER Invité ACKNOWLEDGEMENTS Firstly, I would like to express my sincere gratitude to my advisors Dr. Béatrice CHATAIN, Dr. Marc VANDEPUTTE and Dr. François ALLAL for the continuous support of my Ph.D study and related researches, for their patience, motivation, and immense knowledge. Their guidance helped me in all the time of research and writing of this thesis. I could not have imagined having a better advisors and mentors for my Ph.D study. Besides my advisors, I am also grateful to the members of my committees during PhD. course for their insightful comments and encouragement, but also for the hard question which incented me to widen my research from various perspectives. Furthermore, I would like to thank the technical team of the L-SEA (Laboratoire de Service Experimental Aquacole) of Ifremer, especially Alain for his everyday technical support and my fellow labmates in the L-3AS (Laboratoire d’Adaptation et d’Adaptabilité des Animaux et des Systèmes aquacole) for the stimulating discussions, and for all the fun we have had in the last three years. My sincere thanks also goes to Vietnamese government which funded full grants for my PhD. course. I also thank the RE-SIST project “Improvement of disease resistance of farmed fish by selective breeding” selected at the 15 th “Fonds Unique Interministériel”, which supported the experimental costs of the thesis experiments. Also, I would like to thank my mixed unit of research MARBEC (Marine Biology Exploitation and Conservation) which welcomed me and supported international conference and courses fees. Last but not the least, I am thankful to my family: my wife and my daughter for supporting me spiritually throughout performing this thesis and my life in general. List of publications and manuscripts Publications Doan, Q.-K. , Vandeputte, M., Chatain, B., Morin, T., Allal, F., 2017. Viral encephalopathy and retinopathy in aquaculture: a review. J. Fish Dis., 40 , 717-742. Khanh Doan Q. , Marc Vandeputte, Béatrice Chatain, Pierrick Haffray, Alain Vergnet, Gilles Breuil and François Allal, 2017. Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European seabass (Dicentrarchus labrax). Aquaculture , 478, 1-8. Manuscripts Doan, Q.-K. , Marc Vandeputte, Béatrice Chatain, Pierrick Haffray, Alain Vergnet, François Allal. Construction of a medium-density SNP linkage map and mapping of QTL for resistance to viral nervous necrosis of European seabass. Doan, Q.-K. , Marc Vandeputte, Béatrice Chatain, Pierrick Haffray, Alain Vergnet, François Allal. Genome-wide association study and genomic evaluations for resistance to viral nervous necrosis of European seabass. Conference papers Doan Q.K. , Vandeputte M., Chatain B., Vergnet A., Allal F., 2015. Combining VITASsIGN and COLONY: An efficient practical procedure for parentage assignment with missing parent genotypes. Poster presentation, International symposium on genetics in aquaculture XII, Spain, June 21 st -17 th , 2015 Doan Q.K. 2015. Selective Breeding: The perspective procedure adapting to climate change in Aquaculture. International Conference on "Livelihood Development and Sustainable Environment Management in the Context of Climate Change". November 13-14, 2015 at TUAF, Thai Nguyen City, Vietnam. Doan, Q-K. , Vandeputte, M., Chatain, B., Morin, T., Allal, F., 2015. Selective Breeding for Resistance to Viral Nervous Necrosis Disease: Prospective Procedure for Sustainable Development in Aquaculture. Sustainable Fishery Development Workshop, November 17 – 28, 2015 in Taiwan . Allal F., Doan Q.K. , Chatain B., Vergnet A. and Vandeputte M. 2015. Combining vitassign and colony for pedigree reconstruction in a case of factorial mating with missing parental genotypes. Conference: Aquaculture Europe 2015, At Rotterdam, The Netherlands . Table of contents Résumé substantiel en français .................................................................................................. 1 Chapter 1: General introduction ............................................................................................... 16 1.1. Sustainable aquaculture and its challenges ....................................................................... 17 1.2. Selective breeding as a key for sustainable aquaculture development .............................. 17 1.3. European seabass: biology, production, markets .............................................................. 19 1.4. Viral encephalopathy and retinopathy in European seabass aquaculture ......................... 20 1.5. Challenges and Opportunities for selective breeding for resistance to VNN ................... 21 1.6. The objectives of thesis ..................................................................................................... 24 Chapter 2: Viral encephalopathy and retinopathy in aquaculture: a review ............................ 25 Abstract .................................................................................................................................... 26 2.1. Introduction ....................................................................................................................... 27 2.2. Nervous Necrosis Virus .................................................................................................... 27 2.2.1. General morphology: .................................................................................. 28 2.2.2. Molecular structure: .................................................................................... 28 2.2.3. Classification: ............................................................................................. 29 2.3. Distribution and Transmission .......................................................................................... 30 2.3.1. Distribution: ................................................................................................ 30 2.3.2. Transmission: .............................................................................................. 33 2.4. Diagnosis/Detection .......................................................................................................... 36 2.4.1. First diagnostic approaches: ........................................................................ 36 2.4.2. Direct molecular methods: .......................................................................... 37 2.4.3. Indirect serological methods: ...................................................................... 40 2.5. Control procedures ............................................................................................................ 40 2.6. Selective breeding to VNN resistance: Prospective procedures ....................................... 43 2.6.1. Disease resistance heritability in fish .......................................................... 43 2.6.2. Genetic Selection to Viral Disease Resistance in Fish ............................... 45 2.7. Conclusion ......................................................................................................................... 49 Chapter 3: Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European seabass ( Dicentrarchus labrax ) .. 50 Abstract .................................................................................................................................... 51 3.1. Introduction ....................................................................................................................... 52 3.2. Materials and methods .....................................................................................................
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