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2. Épigénétique

Author

Jammes, Hélène, Boudry, Pierre, and Maury, Stéphane

Subjects
genetic improvement, aquaculture, bacteria, biology, molecular biology, biotechnology, breeding, epigenetics, genetics, history, nutrition, GMO, plant pathology, philosophy, fish, research, reproduction, health, technology, virus, thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
Abstract

In this book, epigenetics is understood as the science of molecules and mechanisms involved in controlling gene activity without altering their sequence, and which thus contribute to cellular functions. It enables us to decipher the development and differentiation processes of cells in a complex organism, which perform different functions despite sharing the same nuclear genetic information. This science also supports cellular memory and responses to the environment. The book introduces the history and evolution of the concept of "epigenetics" and explains the molecular mechanisms that govern the development of mammals, fish or plants. Knowledge of the diversity of these mechanisms, and our understanding of their importance in biology, is probably just getting started. Some processes, such as X chromosome inactivation, are specific to mammals, while others, such as parental imprinting, are surprisingly common to both mammals and plants with sexual reproduction. Their importance in responses to the biotic or abiotic environment is highlighted to show possible applications in medicine or agronomy. This book is intended for students, teachers in higher education and researchers in the field of biology.

Published
2024
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3. Overcoming Ostrea edulis seed production limitations to meet ecosystem restoration demands in the UN decade on restoration

Author

Ermgassen Philine S.E. zu, Strand Åsa, Bakker Nienke, Blanco Ainhoa, Bonačić Kruno, Boudry Pierre, Brundu Gianni, Cameron Tom C., Connellan Iarfhlaith, da Costa Fiz, Debney Alison, Fabra Monica, Frankic Anamarija, Gamble Celine, Gray Mathew W., Helmer Luke, Holbrook Zoë, Hugh-Jones Tristan, Kamermans Pauline, Magnesen Thorolf, Nielsen Pernille, Preston Joanne, Ranger Christopher J., Saurel Camille, Smyth David, Stechele Brecht, Theodorou John A., and Colsoul Bérenger

Subjects
ostrea edulis, coastal restoration, aquaculture, hatchery, spatting pond, Aquaculture. Fisheries. Angling, SH1-691
Abstract

The European flat oyster, Ostrea edulis, is a habitat-forming bivalve which was historically widespread throughout Europe. Following its decline due to overfishing, pollution, sedimentation, invasive species, and disease, O. edulis and its beds are now listed as a threatened and/or declining species and habitat by OSPAR. Increasing recognition of the plight of the oyster, alongside rapidly developing restoration techniques and growing interest in marine restoration, has resulted in a recent and rapid growth in habitat restoration efforts. O. edulis seed supply is currently a major bottleneck in scaling up habitat restoration efforts in Europe. O. edulis has been cultured for centuries, however, research into its culture declined following the introduction of the Pacific oyster, Crassostrea gigas to Europe in the early 1970 s. Recent efforts to renew both hatchery and pond production of O. edulis seed for habitat restoration purposes are hampered by restoration project timelines and funding typically being short, or projects not planning appropriately for the timescales required for investment, research-and-development and delivery of oyster seed by commercial producers. Furthermore, funding for restoration is intermittent, making long-term commitments between producers and restoration practitioners difficult. Long-term, strategic investment in research and production are needed to overcome these bottlenecks and meet current ambitious restoration targets across Europe.

Published
2023
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4. Fifty years of research to counter the decline of the European flat oyster (Ostrea edulis): a review of French achievements and prospects for the restoration of remaining beds and revival of aquaculture production

Author

Pouvreau Stéphane, Lapègue Sylvie, Arzul Isabelle, and Boudry Pierre

Subjects
european flat oyster, genetics, pathology, ecology, restoration, Aquaculture. Fisheries. Angling, SH1-691
Abstract

In the fifty years since the introduction of the Pacific oyster Crassostrea gigas and the first reports of the parasites Marteilia refringens and Bonamia ostreae in European waters, numerous research projects dedicated to the native European flat oyster Ostrea edulis have been conducted, notably in France. Most of these projects have been dedicated to developing controlled reproduction and hatchery technology for seed production, examining pathological aspects to understand and control diseases, and using genetics to develop resistant lines. While the long-term objective of most studies has been to revive the aquaculture production of O. edulis, a smaller number have addressed the ecology of local remnant beds and reefs in France. This article provides an overview of the major outcomes of all these projects, focusing on results obtained in France and prospects for future work there, taking into account the rising interest in increasing aquaculture production and ecological motivation to restore declining populations as part of the framework of the Native Oyster Restoration Alliance (NORA) and in line with UN Decade for Ecosystem Restoration.

Published
2023
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5. Comparative Description and Analysis of Oyster Aquaculture in Selected Atlantic Regions: Production, Market Dynamics, and Consumption Patterns

Author

Iitembu, Johannes A., primary, Fitzgerald, Daniel, additional, Altintzoglou, Themistoklis, additional, Boudry, Pierre, additional, Britz, Peter, additional, Byron, Carrie J., additional, Delago, Daniel, additional, Girard, Sophie, additional, Hannon, Colin, additional, Kafensztok, Marcia, additional, Lagreze, Francisco, additional, Legat, Jefferson Francisco Alves, additional, Legat, Angela Puchnick, additional, Michaelis, Adriane K., additional, Pleym, Ingelinn Eskildsen, additional, Sühnel, Simone, additional, Walton, William, additional, and Strand, Åsa, additional

Published
2023
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18. Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters

Author

de Lorgeril, Julien, Lucasson, Aude, Petton, Bruno, Toulza, Eve, Montagnani, Caroline, Clerissi, Camille, Vidal-Dupiol, Jeremie, Chaparro, Cristian, Galinier, Richard, Escoubas, Jean-Michel, Haffner, Philippe, Dégremont, Lionel, Charrière, Guillaume M., Lafont, Maxime, Delort, Abigaïl, Vergnes, Agnès, Chiarello, Marlène, Faury, Nicole, Rubio, Tristan, Leroy, Marc A., Pérignon, Adeline, Régler, Denis, Morga, Benjamin, Alunno-Bruscia, Marianne, Boudry, Pierre, Le Roux, Frédérique, Destoumieux-Garzόn, Delphine, Gueguen, Yannick, and Mitta, Guillaume

Published
2018
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21. Two parallel chromosome-level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis:Ostrea edulis genomes commentary

Author

Bean, Tim, Tanguy, Arnaud, Peñaloza, Carolina, Gundappa, Manu Kumar, Boutet, Isabelle, Houston, Ross, Macqueen, Dan, and Boudry, Pierre

Subjects
shellfish, mollusc, restoration, aquaculture, genomics, bivalve
Abstract

This volume of Evolutionary Applications sees the publication of two genomes for the European native flat oyster Ostrea edulis, a species of significant evolutionary, ecological and commercial value. Each is a highly contiguous chromosome-level assembly from individuals of different genetic backgrounds, which have been benchmarked against one another. This situation has resulted from the serendipitous discovery that two independent research groups were both deep into the process of building, annotating and investigating separately produced assemblies. Due to constraints with funder requirements and the need to recognize early career researchers for their work, alongside the technical challenge of integrating assemblies from two very different genomes, there was limited capacity to merge the sequences into one publication at the stage of discovery. This issue is likely to become very common over the next few years until the technologies for working with multiple genomes at once, for example, graph genomes, become commonplace in nonmodel species. Consequently, both of our teams have decided to collaborate rather than compete, recognizing the benefit to copublishing two separate genome resources for the research community, each with distinct scientific investigations, and working collaboratively to benchmark the assemblies.

Published
2022

24. Genomic Approaches in Aquaculture and Fisheries

Author

Cancela, M. Leonor, Bargelloni, Luca, Boudry, Pierre, Boulo, Viviane, Dias, Jorge, Huvet, Arnaud, Laizé, Vincent, Lapègue, Sylvie, Leite, Ricardo, Mira, Sara, Nielsen, Einar E., Planas, Josep V., Roher, Nerea, Sarropoulou, Elena, Volckaert, Filip A.M., Cock, J. Mark, editor, Tessmar-Raible, Kristin, editor, Boyen, Catherine, editor, and Viard, Frédérique, editor

Published
2010
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36. Participatory Qualitative Modeling to Assess the Sustainability of a Coastal Socio-Ecological System

Author

Gourguet, Sophie, Marzloff, Martin Pierre, Bacher, Cédric, Boudry, Pierre, Cugier, Philippe, Dambacher, Jeffrey Mark, Desroy, Nicolas, Gangnery, Aline, Le Mao, Patrick, Monnier, Léa, Pérez Agúndez, José, Thébaud, Olivier, Aménagement des Usages des Ressources et des Espaces marins et littoraux - Centre de droit et d'économie de la mer (AMURE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), The REMAIC project was supported by the d’Excellence' LabexMER (ANR-10-LABX-19)., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Dynamiques des Écosystèmes Côtiers (DYNECO), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
participatory approach, loop analysis, socio-ecological system (SES), shellfish aquaculture, sustainability, Normand-Breton Gulf, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract

International audience; Assessing the sustainability of socio-ecological systems requires understanding the interactions between numerous ecological, economic and social components. Models are often used to investigate how interactions shape system feedbacks and drive the complex dynamics at play in such systems. However, building these models is a non-trivial exercise, which often neglects stakeholder knowledge and perceptions. We adopted a participatory approach that relies on conducting workshops to engage stakeholders into the development of qualitative models of system feedback. This type of participatory qualitative modeling is well suited to address the complexity of socio-ecological systems in a holistic manner, identify key stakes and feedbacks, and predict responses to perturbations. We use this approach to investigate the factors that condition sustainability of the socio-ecological system associated with shellfish aquaculture in the Normand-Breton Gulf in France. Six region-specific workshops were organized with shellfish producers, managers and other stakeholders to identify and describe key components, interactions and pressures that contribute to overall socio-ecological dynamics. Differences and commonalities in system perceptions were identified across the different regions and focus groups. We reconciled stakeholder-specific discrepancies in model structure into a synthetic representation that conciliates alternative views of the system. Next, we predicted how the system might respond to alternative scenarios of change. Overall, our participatory qualitative modeling exercise identified key drivers of the system under study that constitute effective management levers to maintain system sustainability. For instance, low social acceptability of the aquaculture industry generally appears to be a major constraint on the sustainability of shellfish aquaculture in the Normand-Breton Gulf, while reducing rearing density appears to be a key driver of sustainability.

Published
2021

37. Electrophysiological Evaluation of Pacific Oyster (Crassostrea gigas) Sensitivity to Saxitoxin and Tetrodotoxin

Author

Boullot, Floriane, Fabioux, Caroline, Hégaret, Hélène, Boudry, Pierre, Soudant, Philippe, Benoit, Evelyne, Service d'Ingénierie Moléculaire pour la Santé (ex SIMOPRO) (SIMoS), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), SIMOPRO, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This research was funded by the French National Research Agency (ANR) [13-CESA-0019-ACCUTOX], the French Research Network PHYCOTOX, the French National Center for Scientific Research (CNRS), and the French Alternative Energies and Atomic Energy Commission (CEA). F.B. was supported by a pre-doctoral fellowship from the Région Bretagne and the Université de Bretagne Occidentale (UBO)., ANR-13-CESA-0019,ACCUTOX,De la caractérisation des déterminants de l'accumulation des toxines paralysantes (PST) chez l'huître (Crassostrea gigas) au risque sanitaire pour l'homme dans son contexte sociétal(2013), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), ERL CNRS 9004, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
animal structures, QH301-705.5, Alexandrium minutum, [SDV]Life Sciences [q-bio], fungi, food and beverages, Crassostrea gigas, equipment and supplies, paralytic shellfish toxins, [SDV.TOX]Life Sciences [q-bio]/Toxicology, compound nerve action potential, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Biology (General), geographic locations
Abstract

Pacific oysters (Crassostrea gigas) may bio-accumulate high levels of paralytic shellfish toxins (PST) during harmful algal blooms of the genus Alexandrium. These blooms regularly occur in coastal waters, affecting oyster health and marketability. The aim of our study was to analyse the PST-sensitivity of nerves of Pacific oysters in relation with toxin bio-accumulation. The results show that C. gigas nerves have micromolar range of saxitoxin (STX) sensitivity, thus providing intermediate STX sensitivity compared to other bivalve species. However, theses nerves were much less sensitive to tetrodotoxin. The STX-sensitivity of compound nerve action potential (CNAP) recorded from oysters experimentally fed with Alexandrium minutum (toxic-alga-exposed oysters), or Tisochrysis lutea, a non-toxic microalga (control oysters), revealed that oysters could be separated into STX-resistant and STX-sensitive categories, regardless of the diet. Moreover, the percentage of toxin-sensitive nerves was lower, and the STX concentration necessary to inhibit 50% of CNAP higher, in recently toxic-alga-exposed oysters than in control bivalves. However, no obvious correlation was observed between nerve sensitivity to STX and the STX content in oyster digestive glands. None of the nerves isolated from wild and farmed oysters was detected to be sensitive to tetrodotoxin. In conclusion, this study highlights the good potential of cerebrovisceral nerves of Pacific oysters for electrophysiological and pharmacological studies. In addition, this study shows, for the first time, that C. gigas nerves have micromolar range of STX sensitivity. The STX sensitivity decreases, at least temporary, upon recent oyster exposure to dinoflagellates producing PST under natural, but not experimental environment.

Published
2021

43. Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Author

Boudry, Pierre, primary, Allal, François, additional, Aslam, Muhammad L., additional, Bargelloni, Luca, additional, Bean, Tim P., additional, Brard-Fudulea, Sophie, additional, Brieuc, Marine S.O., additional, Calboli, Federico C.F., additional, Gilbey, John, additional, Haffray, Pierrick, additional, Lamy, Jean-Baptiste, additional, Morvezen, Romain, additional, Purcell, Catherine, additional, Prodöhl, Paulo A., additional, Vandeputte, Marc, additional, Waldbieser, Geoffrey C., additional, Sonesson, Anna K., additional, and Houston, Ross D., additional

Published
2021
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44. Production durable à grande échelle de semences d'huître plate européenne (Ostrea edulis) pour la restauration écologique et l'aquaculture : une revue

Author

Colsoul, Bérenger, Boudry, Pierre, Pérez‐Parallé, María Luz, Bratoš Cetinić, Ana, Hugh‐Jones, Tristan, Arzul, Isabelle, Mérou, Nicolas, Wegner, Karl Mathias, Peter, Corina, Merk, Verena, Pogoda, Bernadette, and Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

45. An image analysis pipeline for molluscs shells phenotyping: Development and validation on the pacific oyster Crassostrea gigas

Author

Jourdan, Antoine, Bugeon, Jérôme, Lamy, Jean-Baptiste, Enez, Florian, Dégremont, Lionel, Boudry, Pierre, Haffray, Pierrick, Chesnier, Frédéric, Vetois, Emilie, Morvezen, Romain, and Bugeon, Jerome

Subjects
[SDV.BA.ZI] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing
Published
2021

46. Genetic structure of wild European populations of the invasive Pacific oyster Crassostrea gigas due to aquaculture practices

Author

Meistertzheim, Anne-Leila, Arnaud-Haond, Sophie, Boudry, Pierre, and Thebault, Marie-Therese

Subjects
Crassostrea -- Genetic aspects -- Distribution, Animal introduction -- Genetic aspects -- Distribution, Oysters -- Genetic aspects -- Distribution, Company distribution practices, Biological sciences
Abstract

As a result of aquaculture activities, Pacific oysters Crassostrea gigas (Thunberg, 1793) have invaded European coasts. Using seven microsatellites, we found virtually no genetic differentiation between natural populations throughout the European range (from the south of the Wadden Sea (the Netherlands) to the south of France) and French cultivated oysters. The genetic homogeneity of Pacific oyster samples appears to be the result of repeated transfers from same seed stocks made for aquaculture and, to a lesser extent, widespread dispersal due to specific biological traits of this species. The only genetic differentiation of Sylt population in the north of the Wadden Sea (Germany) suggests a stronger, persistent impact of ongoing supply of new genetic material from hatchery production, corresponding to seeds selection made by breeders. All of our genetic data highlighted the importance of aquaculture practices on the genetic structure of the keystone invader C. gigas in Europe., Introduction Marine ecosystems have always been subject to changes in species composition due to natural migration and can be favored by climatic variations. For several decades, the impact of human [...]

Published
2013
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