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Pierrick Haffray

41
Documents
Identifiants chercheurs

Présentation

After 3 years as biologist in the INRA-Ifremer experimental station of marine salmonids (SEMII, Camaret, France) and in the rainbow trout companies Pisciculture Bellet (Angoulême, France) and Truite de Bretagne (Morlaix, France), I joined (1990) the French association of poultry and aquaculture breeders (SYSAAF, Rennes, France) to develop first commercial breeding programs in the French aquaculture, primarily in salmonids as rainbow trout or charrs, followed by marine fishes as sea bass, sea bream or meagre (1992), sturgeons (1996), Pacific or flat oyster and clam (2001) and shrimps (2009). I'm now managing a team of 6 geneticist and 3 PhD students at the Aquaculture section of SYSAAF that advise 25 breeding companies selecting 18 aquaculture species in France and in Madagascar, Mozambique, Mexico, Thailand and in the past in Indonesia. My main research interests were the adaptation of principles of domestication and genetic selection to aquaculture species in using DNA-parentage assignment in combining mass and sib-selection, the development of high through put technologies to phenotype quality traits (micro-wave, artificial vision, ultrasound, MRI, RMN), the optimisation of gametes collection and larval conservation and cryoconservation, the monosexing and the triploidisation and recently (since 2014) the improvement of disease resistances to nine different diseases based on challenge tests (OHsV1, IPN, VHS, VNN, F. psychrophilum, P. piscicidae, E. tarda, V. harveyi, V. tapetis) and sib selection. My current primary research interests are the development and the application of genomic tools in genomic selection in different species (rainbow trout, sea bass, sea bream, Pacific oyster, white leg shrimp), the application of spectrometry (NIR, Raman) to target new traits as fatty acid composition to improve aquaculture nutritional value and since the two years the breeding of pearl oyster. Past Board member of the European Forum for Farm Animal Breeders (EFFAB), the European platform on Farm Animal Breeding and REproduction (FABRE) and the Labogena genotyping laboratory, I'm co-authored over 100 scientific publications and I was awarded (2019) by the French Academy of Agriculture for my inputs in the development of breeding programs in aquaculture.

Publications

florence-phocas

Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas

Antoine Jourdan , Romain Morvezen , Florian Enez , Pierrick Haffray , Adeline Lange
Aquaculture, 2023, 576, pp.739878. ⟨10.1016/j.aquaculture.2023.739878⟩
Article dans une revue hal-04158060v1
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Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

Emilie Delpuech , Marc Vandeputte , Romain Morvezen , Anastasia Bestin , Mathieu Besson
Genetics Selection Evolution, 2023, 55, pp.30. ⟨10.1186/s12711-023-00805-2⟩
Article dans une revue hal-04116035v1
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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)

Ronan Griot , François Allal , Florence Phocas , Sophie Brard-Fudulea , Romain Morvezen
Frontiers in Genetics, 2021, 12, pp.665920. ⟨10.3389/fgene.2021.665920⟩
Article dans une revue hal-03360561v1
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Genetic parameters and genome-wide association studies of quality traits characterised using imaging technologies in Rainbow trout, Oncorhynchus mykiss

Carole Blay , Pierrick Haffray , Jérôme Bugeon , Jonathan D’ambrosio , Nicolas Dechamp
Frontiers in Genetics, 2021, 12, pp.1-17. ⟨10.3389/fgene.2021.639223⟩
Article dans une revue hal-03154333v1
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Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Carole Blay , Pierrick Haffray , Jonathan D’ambrosio , Enora Prado , Nicolas Dechamp
BMC Genomics, 2021, 22 (1), pp.788. ⟨10.1186/s12864-021-08062-7⟩
Article dans une revue hal-03432316v1

Genetic architecture and genomic selection of female reproduction traits in rainbow trout

J. D’ambrosio , Romain Morvezen , S. Brard-Fudulea , Anastasia Bestin , A. Acin Perez
BMC Genomics, 2020, 21 (1), pp.1-14. ⟨10.1186/s12864-020-06955-7⟩
Article dans une revue hal-02938176v1

Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Clémence Fraslin , Florence Phocas , Anastasia Bestin , Mathieu Charles , Maria Bernard
Scientific Reports, 2020, 10, pp.1-13. ⟨10.1038/s41598-020-74757-8⟩
Article dans une revue hal-02988446v1

APIS: An auto-adaptive parentage inference software that tolerates missing parents

Ronan Griot , Francois Allal , Sophie Brard-Fudulea , Romain Morvezen , Pierrick Haffray
Molecular Ecology Resources, 2019, pp.1-12. ⟨10.1111/1755-0998.13103⟩
Article dans une revue hal-02434174v1

Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm

Clémence Fraslin , S. Brard‐fudulea , Jonathan d'Ambrosio , Anastasia Bestin , Mathieu Charles
Animal Genetics, 2019, 50 (3), pp.293-297. ⟨10.1111/age.12777⟩
Article dans une revue hal-02166481v1
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Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

Jonathan D’ambrosio , Florence Phocas , Pierrick Haffray , Anastasia Bestin , Sophie Brard-Fudulea
Genetics Selection Evolution, 2019, 51 (1), pp.26. ⟨10.1186/s12711-019-0468-4⟩
Article dans une revue hal-02151750v1
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CASDAR ABEILLE : Première estimation de paramètres et de valeurs génétiques chez l'abeille avec l'abeille ligérienne 6 ème Journées Techniques Inter-Filières SYSAAF -11 et 12 octobre, Rennes

Jonathan D’ambrosio , Benjamin B. Basso , Florence Phocas , Pierrick Haffray
Journées Techniques Interfilières du SYSAAF, Oct 2023, Rennes, France
Communication dans un congrès hal-04386716v1

Phenomic selection, an alternative to genomic selection in animal breeding?

Faten Jaouahdou , Florian Enez , Christophe Eklouh-Molinier , Jérôme Doerflinger , Guylaine Collewet
Workshop spectroscopie et microscopie du milieu marin, Feb 2023, Brest, France
Communication dans un congrès hal-04185933v1
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GENOME WIDE ASSOCIATION STUDIES OF PRODUCTION TRAITS IN RAINBOW TROUT USING WHOLE GENOME SEQUENCING

Valentin Thomas , Florian Enez , Pierrick Haffray , Boudjema Imarazene , Mathilde Dupont-Nivet
Aquaculture Europe 2023, Sep 2023, Vienne, Austria
Communication dans un congrès hal-04386683v1
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AN R-BASED PIPELINE FOR GENOTYPE CALLING AND PARENTAGE ASSIGNMENT OF TRIPLOID OFFSPRING TO THEIR DIPLOID PARENTS

Mathieu Besson , Julien Roche , Pierre Patrice , Pierrick Haffray , François Allal
Aquaculture Europe 2023, Sep 2023, Vienne, Austria
Communication dans un congrès hal-04385840v1
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Phénomix : Estimation de l'héritabilité de spectres Raman et premiers résultats d'évaluation phénomique chez la truite

Florence Phocas , Pierrick Haffray , Florian Enez , Francois Allal , Pierre Boudry
Journées Techniques Interfilières du SYSAAF, Oct 2022, Rennes, France
Communication dans un congrès hal-04386542v1

Fine mapping for Viral Nervous Necrosis resistance in European sea bass (Dicentrarchus labrax) identified by whole genome sequencing

Emilie Delpuech , Marc Vandeputte , Florence Phocas , Anastasia Bestin , Mathieu Besson
Aquaculture Europe 2022, Sep 2022, Rimini, Italy
Communication dans un congrès hal-04185721v1
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WHOLE GENOME SEQUENCING TO REFINE THE DETECTION OF QTL FOR VIRAL NERVOUS NECROSIS IN EUROPEAN SEA BASS (DICENTRARCHUS LABRAX)

Emilie Delpuech , Marc Vandeputte , Florence Phocas , Anastasia Bestin , Mathieu Besson
6th symposium on Genomics in Aquaculture Symposium, May 2022, Grenade, Spain
Communication dans un congrès hal-04116026v1

Cartographie fine de la résistance à la nécrose nerveuse virale chez le bar identifiée par séquençage du génome entier

Emilie Delpuech , Marc Vandeputte , Florence Phocas , Yoannah François , Anastasia Bestin
7èmes Journées Recherche Filière Piscicole, Jul 2022, Paris, France
Communication dans un congrès hal-04185459v1

IFI6, an interferon alpha induced protein, identified by whole genome sequencing as involved in Viral Nervous Necrosis resistance in European sea bass (Dicentrarchus labrax)

Emilie Delpuech , Marc Vandeputte , Romain Morvezen , Anastasia Bestin , Mathieu Besson
International Symposium on Genetics in Aquaculture XIV, Nov 2022, Puerto Varas, Chile
Communication dans un congrès hal-04185918v1
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Implementation of genomic selection on production and quality traits and linkage disequilibrium in Crassostrea gigas

Antoine Jourdan , Pierre Boudry , Florian Enez , Pierrick Haffray , F Chenier
12. World congress on genetics applied to livestock production (WCGALP), Jul 2022, Rotterdam, Netherlands. ⟨10.3920/978-90-8686-940-4_567⟩
Communication dans un congrès hal-04013016v1
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GENETIC PARAMETERS AND GENOME-WIDE ASSOCIATION STUDY OF RESISTANCE TO ACUTE HYPERTHERMIA IN RAINBOW TROUT

Henri Lagarde , Delphine Lallias , Pierre Patrice , Martin Prchal , Yoannah François
World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands
Communication dans un congrès hal-03779084v1
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UNE SÉLÉCTION SUR LA PERFORMANCE TRIPLOÏDES EST-ELLE NÉCESSAIRE EN TRUTTICULTURE ?

Pierre Patrice , Yoannah François , Pierrick Haffray , Thierry Morin , Mathilde Dupont-Nivet
7emes Journées de la Recherche Filière Piscicole, Jul 2022, Paris, France
Communication dans un congrès hal-04386701v1

Phenomic selection, an alternative to genomic selection in animal breeding?

Faten Jaouahdou , Florian Enez , Christophe Eklouh-Molinier , Jérôme Doerflinger , Guylaine Collewet
International Symposium on Genetics in Aquaculture XIV, Nov 2022, Puerto Varas, Chile
Communication dans un congrès hal-04185835v1
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GENOME-WIDE ASSOCIATION STUDY OF HYPOXIA STRESS TOLERANCE IN RAINBOW TROUT

Martin Prchal , Delphine Lallias , Henri Lagarde , Jonathan D’ambrosio , Pierre Patrice
Aquaculture Europe 2021, Oct 2021, Funchal (Madeira), Portugal
Communication dans un congrès hal-03778912v1

Genome wide association studies revealed one strong effect QTLfor viral nervous necrosis resistance in European sea bass (Dicentrarchus labrax)

Ronan Griot , François Allal , Florence Phocas , Sophie Brard-Fudulea , Romain Morvezen
Aquaculture Europe 2020, Apr 2021, Cork, Ireland
Communication dans un congrès hal-03198222v1

GWAS reveals several genomic regions governing spontaneous XX-maleness in rainbow trout

Clémence Fraslin , Anastasia Bestin , Nicolas Dechamp , Jonathan d'Ambrosio , Francine Krieg
Aquaculture Europe 2019, European Aquaculture Society (EAS). BEL., Oct 2019, Berlin, Germany
Communication dans un congrès hal-02317177v1
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Factors of variation of genomic selection accuracy for female reproduction traits with a constant reference population size of rainbow trouts

Jonathan d'Ambrosio , Romain Morvezen , S. Brard-Fudulea , Anastasia Bestin , Pierrick Haffray
Gordon Research Conference - Quantitative genetics and genomics, Feb 2019, Lucca, Italy
Communication dans un congrès hal-02788345v1
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Development of genomic predictions for female reproduction traits in rainbow trout (Oncorhynchus mykiss)

Jonathan d'Ambrosio , Romain Morvezen , S. Brard-Fudulea , Anastasia Bestin , Pierrick Haffray
Gordon Research conference - Quantitative genetics and genomics, Feb 2019, Lucca, Italy
Communication dans un congrès hal-02787972v1

Masculinisation spontanée chez la truite arc-en-ciel : de nouvelles régions du génome identifiées

Clémence Fraslin , Anastasia Bestin , Nicolas Dechamp , Francine Krieg , Elodie Belmonte
6. Journées de la Recherche Filière Piscicole, Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). FRA., Jul 2019, Paris, France
Communication dans un congrès hal-02182569v1
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Heterogeneity of genetic diversity throughout the genome in rainbow trout populations

Jonathan d'Ambrosio , Florence Phocas , Pierrick Haffray , Edwige Quillet , Anastasia Bestin
International symposium of Genetics in Aquaculture, International Association for Genetics in Aquaculture (IAGA). INT., Jul 2018, Cairns, Australia
Communication dans un congrès hal-02735029v1

Genomic estimates of diversity between and within french rainbow trout populations

J. d'Ambrosio , Florence Phocas , Pierrick Haffray , Edwige Quillet , Anastasia Bestin
Aqua 2018 - World Aquaculture Society Meeting, Aug 2018, Montpellier, France
Communication dans un congrès hal-02193895v1
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CONFIRMATION DE DEUX QTLs D'IMPORTANCE POUR LA RÉSISTANCE À LA NPI DANS UNE LIGNÉE COMMERCIALE DE TRUITE FRANÇAISE

Jonathan D’ambrosio , Pierre Patrice , Yoannah François , Thierry Morin , Pierrick Haffray
7emes Journées de la Recherche Filière Piscicole, Jul 2022, Paris, France
Poster de conférence hal-04386355v1
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IMPROVING RESISTANCE TO ACUTE HYPERTHERMIA BY GENOMIC SELECTION TO ADAPT RAINBOW TROUT LINES TO CLIMATE CHANGE

Henri Lagarde , Delphine Lallias , Pierre Patrice , Martin Prchal , Yoannah François
International Symposium on Genetics in Aquaculture, Nov 2022, Puerto Varas, Chile.
Poster de conférence hal-03778988v1
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IS SELECTION ON TRIPLOID INDIVIDUALS PERFORMANCES USEFUL IN RAINBOW TROUT (ONCORHYNCHUS MYKISS) BREEDING PROGRAMS?

Pierre Patrice , Yoannah François , Alexandre Desgranges , G. Labbé , Pierrick Haffray
International Symposium on Genetics In Aquaculture 2022, Nov 2022, Puerta Varas, Chile.
Poster de conférence hal-04178952v1
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GENOME-WIDE ASSOCIATION STUDY OF INFECTIOUS PANCREATIC NECROSIS IN TWO SUCCESSIVE GENERATIONS OF RAINBOW TROUT

Jonathan D’ambrosio , Pierre Patrice , Yoannah François , Thierry Morin , Joëlle Cabon
Aquaculture Europe 2021, Oct 2021, Madeira, Spain
Poster de conférence hal-04385905v1

Estimation de la diversité génétique entre et intra lignées françaises de truite arc en ciel

Jonathan d'Ambrosio , Florence Phocas , Pierrick Haffray , Edwige Quillet , Anastasia Bestin
6. Journées de la Recherche Filière Piscicole, Jul 2019, Paris, France. , 2019, Journées de la Recherche Filière Piscicole
Poster de conférence hal-02264930v1
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Factors of variation of genomic selection accuracy for female reproduction traits with a constant reference population size of rainbow trouts

Jonathan D’ambrosio , Romain Morvezen , Sophie Brard-Fudulea , Anastasia Bestin , Pierrick Haffray
Gordon Research Conference on Quantitative Genetics and Genomics, Feb 2019, Lucca (Barga), France
Poster de conférence hal-04386586v1

Déterminisme génétique et sélection génomique des caractères de reproduction femelle chez la truite arc-en-ciel

J. d'Ambrosio , Romain Morvezen , A. Perez , S. Brard-Fudulea , Anastasia Bestin
6. Journées de la Recherche Piscicole, Jul 2019, Paris, France. , 2019
Poster de conférence hal-02193908v1
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Development of genomic predictions for female reproduction traits in rainbow trout (Oncorhynchus mykiss)

Jonathan D’ambrosio , Romain Morvezen , Sophie Brard-Fudulea , Anastasia Bestin , Pierrick Haffray
Gordon Research Conference on Quantitative Genetics and Genomics, Feb 2019, Lucca (Barga), Italy
Poster de conférence hal-04386578v1
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RAINBOW TROUT RESISTANCE TO Flavobacterium psychrophilum: A GENOME WIDE ASSOCIATION STUDY IN A FRENCH POPULATION AFTER A NATURAL DISEASE OUTBREAK

Clémence Fraslin , S. Brard-Fudulea , Jonathan d'Ambrosio , Anastasia Bestin , Mathieu Charles
AQUA 2018, Aug 2018, Montpellier, France. , 2018, AQUA 2018
Poster de conférence hal-01865605v1