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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.

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.

Ocean acidification and warming are key stressors for many marine organisms. Some organisms display physiological acclimatization or plasticity, but this may vary across species ranges, especially if populations are adapted to local climatic conditions. Understanding how acclimatization potential varies among populations is therefore important in predicting species responses to climate change. We carried out a common garden experiment to investigate how different populations of the economically important great scallop (Pecten maximus) from France and Norway responded to variation in temperature and PCO2 concentration. After acclimation, post-larval scallops (spat) were reared for 31 days at one of two temperatures (13°C or 19°C) under either ambient or elevated PCO2 (pH 8.0 and pH 7.7). We combined measures of proteomic, metabolic and phenotypic traits to produce an integrative picture of how physiological plasticity varies between the populations. The proteome of French spat showed significant sensitivity to environmental variation, with 12 metabolic, structural and stress-response proteins responding to temperature and/or PCO2. Principal component analysis revealed seven energy metabolism proteins in French spat that were consistent with countering ROS stress under elevated temperature. Oxygen uptake in French spat did not change under elevated temperature but increased under elevated PCO2. In contrast, Norwegian spat reduced oxygen uptake under both elevated temperature and PCO2. Metabolic plasticity allows French scallops to maintain greater energy availability for growth compared with Norwegian spat. However, increased physiological plasticity and growth in French spat may come at a cost, as they showed reduced survival compared with Norwegian scallops under elevated temperature.

In the face of an increasing world population and a subsequent need for an increase in sustainable and healthy food production, low trophic species, such as oysters, emerge as a promising alternative. However, regional variations in oyster production techniques, market dynamics, and consumption patterns create challenges for both the global and local industry’s growth. In this study, a descriptive qualitative analysis of oyster markets across seven Atlantic regions was carried out. The Pacific oyster (Crassostrea gigas) was found to be farmed in most Atlantic regions except the US but is classified as invasive in Sweden and potentially invasive in South Africa. Other farmed and/or harvested species include native species (C. gasar and C. rhizophorae) in Brazil, the American cupped oyster (C. virginica) in the US, and the European flat oyster (Ostrea edulis) in France, Sweden, and the US. In Irish farms, Pacific oysters are primarily for export to European markets. The marine aquaculture sectors of Sweden, South Africa, and Namibia, as well as Brazil’s farming for C. gasar, were found to be underdeveloped. This study also observed a variation in licensing, property rights, and regulatory frameworks. Financial challenges for small businesses, ecological implications of seed production techniques, biosecurity risks, and public health considerations are emphasized as critical areas for attention. This study offers valuable insights into the selected markets and can serve as a useful resource for policymakers, aquaculture practitioners, and stakeholders in optimizing global shellfish industry strategies.

Selective breeding programs have been initiated worldwide for the Pacific oyster Crassostrea gigas to improve economically important traits such as growth and disease resistance. The emergence of genomic tools has allowed novel perspectives for using genomic selection (GS) in mixed-family breeding designs, which are cheaper and easier to develop than classical breeding schemes. In this study, we evaluated the potential of GS for different growth-related and shell colour traits in two independent commercially selected populations (P1 and P2), based on mixed-family designs. From ≈14.5K informative SNPs genotyped with the bi-species Axiom Affymetrix 57K oyster array, ≈12.5K were mapped on the reference genome. A strong heterogeneity of marker density between and within chromosomes was reported, with a low linkage disequilibrium (below 0.1 at 0.1 Mb) between pairs of SNPs. The within-population structure was homogenous for each population, with effective sizes of 107 for P1 and 76 for P2. Heritability was estimated for each trait and population and ranged from 0.08 ± 0.04 (for mean darkness intensity in P1) to 0.56 ± 0.08 (for the mean upper valve b* value in P2) for a pedigree-based model and from 0.04 ± 0.02 (for mean darkness intensity in P1) to 0.69 ± 0.04 (for the mean darkness intensity in P2) for a genomic-based model. Growth-related traits were generally highly genetically and positively correlated with each other, but weakly correlated with colour traits. Accuracy of prediction was generally higher with the genomic model (GBLUP) than with the classical BLUP model, with a maximum gain of accuracy (from 0.38 to 0.66) for flesh weight adjusted by total weight in P2. Accuracy of breeding values was slightly higher for colour traits for P2, with higher heritability estimates. Overall, our results indicate that GS has a good potential to be implemented in mixed-family breeding programs in a shellfish such as C. gigas.

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.

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.

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.

The Pacific oyster, Crassostrea gigas, is a species in which true male and true female well as hermaphrodite individuals have been reported. Among the latter, most are sequential, with one or more sex changes throughout their live, while a few (<2%) are simultaneous hermaphrodites (SH) which may self-fertilize. Sex determinism and its functional bases remain unclear is this species. In this study, one SH oyster was found among a mature broodstock and used to produce a progeny by self-fertilization. Several thousand offspring were obtained for this family (SF1) but only 73 SF1 oysters survived following an episode of mass mortality at the spat stage. Six of them were conditioned for reproduction and three were found to be SH, and one produced a limited but viable progeny by self-fertilization (SF2). Oysters were sampled and genotyped with 226 SNP markers, confirming that the SF1 and the SF2 oysters were produced by self-fertilization over two successive generations. To our knowledge, it is the second study reporting the feasibility of production on an inbred line of Pacific oysters by self-fertilization using a simultaneous hermaphrodite as primary genitor, and the first study to generate two successive generations of selfing. Observed mean inbreeding coefficient of SF2 oysters produced by selfing for two generations was 0.61, ranging from 0.46 to 0.80. This coefficient was lower than the expected theoretical value (0.8125), suggesting that the most homozygous offspring died at early stages due to inbreeding depression. Our study demonstrates that inbred lines of Pacific oysters can be produced by self-fertilization but may exhibit higher heterozygosity than theoretically expected due to better survival of the most heterozygous offspring.

The conservation and active restoration of European flat oyster (Ostrea edulis) populations are a major focus of ecological restoration efforts to take advantage of the wide‐ranging ecosystem functions and services this species provides. Accordingly, additional and new demands for seed oysters have arisen. In commercial aquaculture (mariculture), the production of O. edulis is still largely based on natural seed collection. Considering the specific requirements, related to ecological restoration, such as the absence of pathogens and the preservation of high genetic diversity, the current supply is insufficient. Despite the development of breeding and controlled reproduction techniques for this species since the late 1930s, seed production today is mainly based on empirical concepts. Several of the issues that producers still face are already subjects of research; many others are still unanswered or even unaddressed. This review provides a summary of all available knowledge and technologies of O. edulis seed production. Furthermore, it provides a detailed reflection on implications for restoration, future challenges, open questions and it identifies relevant research topics for sustainable seed supply. The study covers the following aspects on (i) biology of the species, (ii) stressors – including pathogens and pollutants, (iii) genetics, (iv) history of production technologies, (v) seed production in polls, (vi) seed production in ponds and (vii) seed production in hatcheries. Future research needs on sex determinism, gametogenesis, cryopreservation, nutrition, selective breeding, pathogens and disease, and the development of reliable protocols for production are highlighted.

Activités scientifiques 2018-2019

Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic species. Recent developments of high throughput genotyping technology now enable the implementation of genomic selection, a method aiming to predict the breeding value of candidates based on their genotype at genome-wide markers. In this review article, we review the state of the arts, challenges and prospects for the application of genomic selection in aquaculture species. The particular focus is on the status of genomic selection in several major aquaculture species of International Council for the Exploration of the Sea (ICES) member countries: Atlantic salmon, rainbow trout, Atlantic cod, American catfish, Pacific oyster, European sea bass and gilthead sea bream. While the potential of genomic selection is clear, tailored species-specific applications will be needed to maximise its benefit for the aquaculture sector.

The Native Oyster Restoration Alliance (NORA) supports the protection and ecological restoration of the native European oyster, Ostrea edulis, and its habitat across its current and historical biogeographical range. NORA works to overcome barriers to the conservation, restoration, and recovery of the European oyster by providing a platform for the NORA community to collaborate and participate in knowledge exchange. NORA seeks to support responsible restoration practice, in compliance with biosecurity and sustainability. Against this background, the NORA community formulated a series of specific recommendations, the Berlin Oyster Recommendation, to support native oyster restoration by developing and applying best practice with the aim to recover healthy and resilient marine ecosystems. In combination with the Standards for Ecological Restoration (SER) and the Restoration Guidelines for Shellfish Reefs, the Berlin Oyster Recommendation is a relevant tool for successful and sustainable oyster restoration in Europe. The establishment of NORA working groups will support the implementation and further development of the six corresponding recommendations. Current NORA working groups cover site selection, biosecurity, production, and monitoring. The site selection working group will address the identification of suitable sites for oyster restoration to support policy relevant decision making and the conservation, reinforcement, or reintroduction of native oysters. The biosecurity working group will develop biosecurity guidelines for native oyster restoration in Europe. The production working group will assess the potential of standards for seed oyster production and supply in order to enhance production appropriate for restoration purposes. In close collaboration with the Native Oyster Network – UK & Ireland (NON), the monitoring working group will produce a monitoring guidelines handbook to provide metrics and methods that will be suitable across the range of O. edulis pro

Oyster reefs are among the most threatened marine habitats globally. In Europe, oyster reefs have been extirpated from most locations within their historical range. Active restoration of the native oyster (Ostrea edulis) in Europe has grown substantially in recent years. In sharing experiences between oyster restoration projects in Europe at the Native Oyster Restoration Alliance conference, NORA2, in Edinburgh in May 2019, it became apparent that a number of similar barriers are experienced. This study identified the top 40 questions, which, if answered, would have the greatest influence on the policy and practice of oyster restoration in Europe. Initially 71 people were consulted across 28 institutions and 11 European countries to generate 194 questions. An established process of one round of pre‐workshop voting followed by a one‐day online workshop and two post‐workshop rounds of voting resulted in the final 40 questions. Questions were broadly grouped into the following 10 themes: baselines, site selection, restoration methods, quantifying benefits, disease management, biosecurity, genetic diversity and population differentiation, policy and management, novel technologies, and current and future threats. We anticipate that this list will provide a starting point for developing collaborative projects across the NORA network, as well as assisting policy makers and funders with identifying key areas that need to be addressed in order to overcome existing barriers to scaling up oyster restoration in Europe.

Sex determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, non‐invasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: i) identification of heterozygote excess in one sex, ii) F ST outlier analysis between the two sexes and iii) neuronal net modelling. These methods were applied to a large SNP dataset (4604 SNPs) for 1680 thornback rays (Raja clavata ). Using method i), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata ) indicated that all 19 SNPs are likely located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method ii) identified eight SNPs probably located on different chromosomes. Method i) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

The great scallop (Pecten maximus) is a commercially important bivalve in Europe, particularly in the English Channel, where fisheries are managed at regional and local scales through the regulation of fishing effort. In the long term, knowledge about larval dispersal and gene flow between populations is essential to ensure proper stock management. Yet, previous population genetic studies have reported contradictory results. In this study, scallop samples collected across the main fishing grounds along the French and English coasts of the English Channel (20 samples with temporal replicates for three sites, n = 1059 individuals), and the population genetic structure was analysed using 13 microsatellite loci. Coupling empirical genetic data with demogenetic modelling based on a biophysical model simulating larval exchanges among scallop beds revealed a subtle genetic differentiation between south‐west English populations and the rest of the English Channel, which was consistent with larval dispersal simulations. The present study provides a step forward in the understanding of great scallop population biology in the English Channel, underlining the fact that even in a context of potentially high gene flow and recent divergence times since the end of the last glacial maximum, weak but significant spatial genetic structure can be identified at a regional scale.

Oyster reefs are among the most threatened marine habitats globally. In Europe, oyster reefs have been extirpated from most locations within their historical range. Active restoration of the native oyster (Ostrea edulis) in Europe has grown substantially in recent years. In sharing experiences between oyster restoration projects in Europe at the Native Oyster Restoration Alliance conference, NORA2, in Edinburgh in May 2019, it became apparent that a number of similar barriers are experienced. This study identified the top 40 questions, which, if answered, would have the greatest influence on the policy and practice of oyster restoration in Europe. Initially 71 people were consulted across 28 institutions and 11 European countries to generate 194 questions. An established process of one round of pre-workshop voting followed by a one-day online workshop and two post-workshop rounds of voting resulted in the final 40 questions. Questions were broadly grouped into the following 10 themes: baselines, site selection, restoration methods, quantifying benefits, disease management, biosecurity, genetic diversity and population differentiation, policy and management, novel technologies, and current and future threats. We anticipate that this list will provide a starting point for developing collaborative projects across the NORA network, as well as assisting policy makers and funders with identifying key areas that need to be addressed in order to overcome existing barriers to scaling up oyster restoration in Europe.