Procédure de qualification des donnnées Quadrige² - Données chimie RNOPHY (Imposex)

La qualification a pour objectif d’attribuer un niveau de qualité aux données : Bon, Douteux ou Faux. Le processus de qualification consiste à rechercher des anomalies plus ou moins complexes dans les données stockées dans la base de données Quadrige², les anomalies étant définies par les responsables de programme Quadrige ou responsables thématiques. Ces recherches d’anomalies sont faites en lien avec la cellule quadrige². La qualification des données peut se faire : • de façon ponctuelle : identification d’un problème de processus analytique pour quelques données • en routine : un processus de qualification dite « automatique » permet de qualifier les enregistrements individuellement (cohérence des informations de chaque résultat individuellement). Puis une qualification dite « experte » permet de vérifier la cohérence d’un résultat par rapport aux autres résultats (séries temporelles, analyse graphique ou statistique). Le présent document décrit les processus de qualification en routine des données du réseau ROCCH – volet IMPOSEX (programme RNOPHY de Quadrige)

Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss

Marker-based parentage assignment provides the opportunity to investigate factors of efficiency for mixed-family designs and factorial mating. In such designs, family size is both uncontrolled and small, which may be thought to limit the accuracy of estimated breeding values (EBVs). The objective of this work was to estimate the accuracy of EBVs of growth and quality traits in a large factorial mating design and in commercial breeding conditions. An expected six hundred full-sib families of rainbow trout Oncorhynchus mykiss (2042 fish in total) were produced by ten factorial matings of six dams with ten sires. Fish were phenotyped for body weight, carcass yield, fillet yield, fillet fat content and fillet colour, and family information was recovered using microsatellite markers. The accuracy of EBVs was estimated using or removing individual performance to mimic combined family selection (with individual phenotype) or sib selection (without individual phenotype). The traits investigated had medium to high heritability (0.17–0.58). High to very high accuracy (0.630–0.817) was estimated for combined family selection. The accuracy of sib selection (not using individual phenotype) was 18–22% lower (0.542–0.638), but remained in the upper range reported for such traits. This level of accuracy was higher than those reported in conventional breeding programs using separate family rearing. This was true even for families with a very low number of full-sibs. Individual EBV accuracy was more closely linked to the total number of full- and half-sibs of each fish than to its number of full-sibs. We hypothesize that this was due to the factorial mating, which led to a high number of the genetic ties between sibs. These results highlight the possibility of introducing precise estimated breeding values for quality traits into combined or sib selection in breeding programs when using mixed families from factorial designs and marker-based parentage assignment in aquaculture species

Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss

Marker-based parentage assignment provides the opportunity to investigate factors of efficiency for mixed-family designs and factorial mating. In such designs, family size is both uncontrolled and small, which may be thought to limit the accuracy of estimated breeding values (EBVs). The objective of this work was to estimate the accuracy of EBVs of growth and quality traits in a large factorial mating design and in commercial breeding conditions. An expected six hundred full-sib families of rainbow trout Oncorhynchus mykiss (2042 fish in total) were produced by ten factorial matings of six dams with ten sires. Fish were phenotyped for body weight, carcass yield, fillet yield, fillet fat content and fillet colour, and family information was recovered using microsatellite markers. The accuracy of EBVs was estimated using or removing individual performance to mimic combined family selection (with individual phenotype) or sib selection (without individual phenotype). The traits investigated had medium to high heritability (0.17–0.58). High to very high accuracy (0.630–0.817) was estimated for combined family selection. The accuracy of sib selection (not using individual phenotype) was 18–22% lower (0.542–0.638), but remained in the upper range reported for such traits. This level of accuracy was higher than those reported in conventional breeding programs using separate family rearing. This was true even for families with a very low number of full-sibs. Individual EBV accuracy was more closely linked to the total number of full- and half-sibs of each fish than to its number of full-sibs. We hypothesize that this was due to the factorial mating, which led to a high number of the genetic ties between sibs. These results highlight the possibility of introducing precise estimated breeding values for quality traits into combined or sib selection in breeding programs when using mixed families from factorial designs and marker-based parentage assignment in aquaculture species

Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata

Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by crossing 40 abalones, and 5 full-sib training families (70 offspring). Based on amplification success among parents, minimum allele frequency and checks carried out against the training families, a subset of 123 markers was used to carry out parentage assignment in our mixed family cohorts. Maximum likelihood and exclusion-based methods of parentage assignment yielded consistent results, allowing parentage to be assigned in 98.9% of the studied progeny. Optimization of markers suggests that the 60 most informative SNPs may be sufficient for 95% assignment success in these progeny. The panel was also used to estimate effective population size, and revealed a low Ne due to high variance of reproductive success between parents. Our panel could be used to estimate genetic parameters of traits in mixed family cohorts, an essential stage to initiate selective breeding in H. tuberculata. It could also be useful tool in the context of monitoring stock enhancement and population genetics studies

Genetic parameters for growth and colour traits in Pacific blue shrimp Litopenaeus stylirostris in a mixed family design with SNP parentage assignement in New-Caledonia

International audienc

Manual for bivalve disease management and biosecurity

Between 2016 and 2020, the VIVALDI project (https://www.vivaldi-project.eu/) aimed to improve the sustainability and competitiveness of the European shellfish industry, which was hit by a growing number of mortality cases over the recent years. To this end, tools and strategies to better prevent and mitigate the impact of bivalve diseases have been developed. For example, environmental approaches such as passive sensors or magnetic beads and electrochemical biosensors could be useful for pathogen surveillance and the development of early warning systems. Stimulating bivalve immunity has been shown to be possible and could be of interest for hatcheries-nurseries. Work has been achieved to optimize breeding programs for oysters as well as clams. The impact of environmental parameters on the development of bivalve diseases has been studied, allowing researchers to identify conditions favoring or mitigating disease development. Best husbandry practices to reduce mortality have been identified from the literature and field studies. UV treatments were successfully used to remove pathogens, oyster gametes and larvae from the wastewater. A risk ranking shellfish farm model was designed and is now ready to be used by the competent authorities to implement risk-based surveillance of shellfish diseases. Most of these results have led the consortium to identify recommendations to better prevent, mitigate and control bivalve diseases. A co-construction process involving scientists, decision-makers, hatcheries and producers from the main European producing countries was considered as the best approach in order to make this manual relevant and easy-to-use for the greatest possible number of stakeholders. The biosecurity manual is aimed to have a long-term impact on the endusers‟ practices and biosecurity in shellfish farming. It does not have regulatory goals but it aims to provide technical advices to assist implementing the legislation. When covering farming activities, recommendations identify best practices that need to be adjusted taking into account geographic and species specificities. For each recommendation, a brief description is provided as well as the benefits and main limitations. Recommendations are organized by section and, then, by category of actions. Three main sections have been identified: communication issues, governance issues and technical issues. In addition, a glossary has been compiled to provide the precise definitions of the terms used.Entre 2016 et 2020, le projet VIVALDI (https://www. vivaldi-project.eu/) visait à améliorer la durabilité et la compétitivité du secteur conchylicole européen, frappé par un nombre croissant de cas de mortalité ces dernières années. À cette fin, des outils et des stratégies visant à mieux prévenir et à atténuer l'impact des maladies des mollusques bivalves ont été mis au point. Par exemple, les approches environnementales reposant sur l’utilisation de capteurs passifs ou les billes magnétiques et les biocapteurs électrochimiques, pourraient être utiles pour la surveillance des organismes pathogènes et le développement de systèmes d'alerte précoce. La stimulation de l'immunité des mollusques bivalves s'est avérée possible et pourrait être intéressante pour les écloseries-nurseries. Des travaux ont été réalisés pour optimiser les programmes d'élevage des huîtres ainsi que des palourdes. L'impact des paramètres environnementaux sur le développement des maladies des mollusques bivalves a été étudié, permettant aux chercheurs d'identifier les conditions favorisant ou atténuant le développement des maladies. Les meilleures pratiques d'élevage pour réduire la mortalité ont été identifiées d’après la littérature et les études de terrain. Les traitements UV ont été utilisés avec succès pour éliminer les organismes pathogènes, les gamètes et les larves d’huîtres des effluents d’élevage. Un modèle classant les exploitations conchylicoles en fonction du risque est maintenant prêt à être utilisé par les autorités compétentes pour mettre en oeuvre une surveillance des maladies des coquillages basée sur les risques. La plupart de ces résultats ont conduit le consortium à identifier des recommandations pour mieux prévenir, diminuer l’impact et contrôler les maladies des mollusques bivalves. L'approche retenue pour élaborer ce manuel a été d'impliquer conjointement des scientifiques, des décideurs, des écloseries et des producteurs des principaux pays producteurs européens afin de construire un outil à la fois pertinent et facile à utiliser pour le plus grand nombre possible de parties prenantes. Ce manuel est destiné à faire évoluer à long terme les pratiques des utilisateurs finaux et la biosécurité en conchyliculture. Il n'a pas vocation à poser des objectifs réglementaires et vise à fournir des conseils techniques pour faciliter la mise en oeuvre de la législation. En matière d'élevage conchylicole, les recommandations identifient les meilleures pratiques devant être adaptées en tenant compte des spécificités géographiques et propres aux espèces. Pour chaque recommandation, une brève description est fournie, ainsi que les avantages et les principales limitations. Les recommandations sont organisées par section et, ensuite, par catégorie d'actions. Trois sections principales ont été identifiées : la communication, la gouvernance et les points techniques. En outre, un glossaire a été établi pour fournir les définitions précises des termes utilisés.El proyecto VIVALDI (https://www.vivaldi-project. eu/), implementado entre 2016 y 2020, tenía como objetivo mejorar la sostenibilidad y la competitividad del sector marisquero europeo, afectado por un número creciente de casos de mortalidad en los últimos años. En el marco de este proyecto se han desarrollado herramientas y estrategias para prevenir y mitigar adecuadamente el impacto de las enfermedades en los cultivos de bivalvos. Por ejemplo, ciertos enfoques ambientales como el uso de sensores pasivos o partículas magnéticas y biosensores electroquímicos podrían ser útiles para la vigilancia de patógenos y el desarrollo de sistemas de alerta temprana. Se ha demostrado que es posible estimular la inmunidad de los bivalvos y podría constituir una estrategia interesante para los criaderos-viveros. Se ha trabajado para optimizar los programas de cría tanto de ostras como de almejas. Asimismo, se ha estudiado el impacto de los parámetros ambientales en el desarrollo de enfermedades en bivalvos, lo que ha permitido a los investigadores identificar las condiciones que favorecen o mitigan el desarrollo de una enfermedad. En la literatura y en los estudios de campo se han identificado las mejores prácticas de cría para reducir la mortalidad. Se han utilizado con éxito tratamientos de UV para eliminar los agentes patógenos, los gametos de las ostras y las larvas de las aguas residuales. Se ha diseñado un modelo de clasificación de riesgos de las explotaciones marisqueras, que ya pueden utilizar las autoridades competentes para la vigilancia de las enfermedades de los mariscos basada en el riesgo. Estos resultados han llevado al consorcio a redactar una serie de recomendaciones para prevenir, mitigar y controlar mejor las enfermedades en los bivalvos. Consideramos que el mejor enfoque para que este manual sea relevante y fácil de usar para el mayor número posible de interesados es que esté basado en un proceso de cocreación en el que participen científicos, responsables de la toma de decisiones, criaderos y productores de los principales países productores europeos. El manual de bioseguridad pretende tener un impacto a largo plazo en las prácticas de los usuarios finales y en la bioseguridad en el cultivo de moluscos. No tiene objetivos normativos, aunque pretende proporcionar asesoramiento técnico para ayudar a aplicar la legislación. En lo que se refiere a las actividades agrícolas, las recomendaciones identifican las mejores prácticas que deben ajustarse a las particularidades geográficas y de cada especie. Para cada recomendación se ofrece una breve descripción, así como los beneficios y las principales limitaciones. Las recomendaciones están organizadas por secciones y, posteriormente, por categorías de medidas a implementar. Pueden identificarse tres apartados principales: temas relacionados con la comunicación, temas relacionados con la gestión y temas técnicos. Además, se ha elaborado un glosario con las definiciones precisas de los términos utilizados

Genetic parameters of resistance to gastroenteritis (rtge) and rainbow trout fry syndrome (rtfs) in rainbow trout oncorhynchus mykiss and their genetic correlations with production traits

National audienc

Enquête sur la masculinisation spontanée dans les élevages français de truite arc-en-ciel monosexe femelle

Session : ReproductionEnquête sur la masculinisation spontanée dans les élevages français de truite arc-en-ciel monosexe femelle. 6. Journées de la Recherche Filière Piscicol

Mixed-family estimation of genetic parameters of growth, morphologic, immune and behavioral traits in the european abalone Haliotis tuberculata

un poster présentéInternational audienc

Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits