9 results on '"Griot, Ronan"'
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2. APIS: an updated parentage assignment software managing triploids induced from diploid parents.
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Roche, Julien, Griot, Ronan, Allal, François, Besson, Mathieu, Haffray, Pierrick, Patrice, Pierre, Phocas, Florence, and Vandeputte, Marc
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FALSE discovery rate , *RAINBOW trout , *GENE frequency , *PARENTS , *CENTROMERE - Abstract
In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96–192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96–0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Development and characterization of a 57K Single Nucleotide Polymorphism array for European sea bass
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Allal, François, Duranton, Maud, Morvezen, Romain, Brard-Fudulea, Sophie, Poncet, Charles, Belmonte, Elodie, Griot, Ronan, Bruant, Jean-Sébastien, Cariou, Sophie, Bajek, Aline, Peyrou, Bruno, Vandeputte, Marc, Céline, Jaimet, Haffray, Pierrick, Gagnaire, Pierre-Alexandre, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Ferme Marine du Douhet, Ecloserie Marine de Gravelines, Aquanord, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Vandeputte, Marc
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[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.SA.STP] Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.ZOO] Life Sciences [q-bio]/Agricultural sciences/Zootechny ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
4. APIS: A new auto-adaptive parentage inference software tolerant to missing parents
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Griot, Ronan, Allal, François, Brard-Fudulea, Sophie, Cariou, Sophie, Haffray, Pierrick, Vandeputte, Marc, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Ferme Marine du Douhet
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[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
5. Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata).
- Author
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Griot, Ronan, Allal, François, Phocas, Florence, Brard-Fudulea, Sophie, Morvezen, Romain, Haffray, Pierrick, François, Yoannah, Morin, Thierry, Bestin, Anastasia, Bruant, Jean-Sébastien, Cariou, Sophie, Peyrou, Bruno, Brunier, Joseph, and Vandeputte, Marc
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MARINE fishes ,SPARUS aurata ,EUROPEAN seabass ,NATURAL immunity ,SEA basses ,DISEASE outbreaks - Abstract
Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K–60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51–0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
6. Des puces pour prédire l’avenir…
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Allal, François, Griot, Ronan, Gagnaire, Pierre-Alexandre, Morvezen, Romain, Brard, Sophie, Vandeputte, Marc, Haffray, Pierrick, Vandeputte, Marc, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
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[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny ,[SDV.SA.STP] Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA] Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.ZOO] Life Sciences [q-bio]/Agricultural sciences/Zootechny ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
7. GENESEA : développement de la sélection génomique chez le bar et la daurade
- Author
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Allal, François, Griot, Ronan, Gagnaire, Pierre-Alexandre, Klopp, Christophe, Bajek, Aline, Cariou, Sophie, Bouchez, Olivier, Morvezen, Romain, Vandeputte, Marc, Haffray, Pierrick, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecloserie Marine de Gravelines, Ferme Marine de Douhet, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
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[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,[SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies ,[SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery ,[SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2017
8. APIS: An auto‐adaptive parentage inference software that tolerates missing parents.
- Author
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Griot, Ronan, Allal, François, Brard‐Fudulea, Sophie, Morvezen, Romain, Haffray, Pierrick, Phocas, Florence, and Vandeputte, Marc
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FALSE positive error , *SINGLE nucleotide polymorphisms , *ERROR rates , *EUROPEAN seabass , *PARENTS , *FISH breeding - Abstract
In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood‐based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user‐defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN), on a real European seabass (Dicentrarchus labrax) single nucleotide polymorphism data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user‐set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy‐to‐use and reliable software for parentage assignment, even when up to 50% of sires are missing. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
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9. Corrigendum: Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, The European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata).
- Author
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Griot, Ronan, Allal, François, Phocas, Florence, Brard-Fudulea, Sophie, Morvezen, Romain, Haffray, Pierrick, François, Yoannah, Morin, Thierry, Bestin, Anastasia, Bruant, Jean-Sébastien, Cariou, Sophie, Peyrou, Bruno, Brunier, Joseph, and Vandeputte, Marc
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SPARUS aurata ,MARINE fishes ,NATURAL immunity ,EUROPEAN seabass - Published
- 2021
- Full Text
- View/download PDF
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