Recent publications
Fujiwara-Nagata E, Rochat T, Lee B-H, Lallias D, Rigaudeau D, Duchaud E. 2024. Host specificity and virulence of Flavobacterium psychrophilum: a comparative study in ayu (Plecoglossus altivelis) and rainbow trout (Oncorhynchus mykiss) hosts. Vet Res https://doi.org/10.1186/s13567-024-01326-6
2024
Basso B., Kistler T., Phocas F. Genetic parameters, trends and inbreeding in a honeybee breeding program for royal jelly production and behavioral traits. Apidologie. https://doi.org/10.1007/s13592-023-01055-3
Basso B, Kistler T, Phocas F. 2024. Genetic parameters, trends, and inbreeding in a honeybee breeding program for royal jelly production and behavioral traits. Apidologie. https://doi.org/10.1007/s13592-023-01055-3
Clota F, Goikoetxea A, Vergnet A, Blanc MO, Lallement S, Ruelle F, Leitwein M, Allal F, Geffroy B, Vandeputte M. 2024. Post-larval exposure to warm temperature enhances female ratio, while starvation and photoperiod do not: The case of European seabass, Dicentrarchus labrax. Aquaculture. https://doi.org/10.1016/j.aquaculture.2024.740758
El Kamouh M, Brionne A, Sayyari A, Lallais D, Labbé C, Laurent A. 2024. Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case‑study on rainbow trout spermatozoa. Fish Physiol Biochem. https://doi.org/10.1007/s10695-024-01326-5
Kistler T, Brascamp EW, Basso B, Bijma P, Phocas F. 2024. Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters. Gen Sel Evol. https://doi.org/10.1186/s12711-024-00898-3
Kistler T, Kouchner C, Brascamp EW, Mondet F, Vignal A, Basso B, Bijma P, Phocas F. Heritability and correlations for production, handling ease and resilience traits in a French honeybee population. Apidologie https://doi.org/10.1007/s13592-024-01088-2
Lefevre F, Bugeon J, Goardon L, Kernéis T, Labbé L, Panserat S, Médale F, Quillet E. Seven generations of selection for muscle fat content greatly affect rainbow trout flesh quality and muscle fiber size. Aquaculture reports. https://doi.org/10.1016/j.aqrep.2024.102343
Nagata E, Rochat T, Lee B-H, Lallias D, Rigaudeau D, Duchaud E. Host specificity and virulence of Flavobacterium psychrophilum: a comparative study in ayu (Plecoglossus altivelis) and rainbow trout (Oncorhynchus mykiss) hosts. Veterinary Research.
Paul K, Restoux G, Phocas F. 2024. Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss). Gen Sel Evol. https://doi.org/10.1186/s12711-024-00884-9
Pouil S, Besson M, Phocas F, Aubin J. Assessing the environmental impacts of conventional and organic scenarios of rainbow trout farming in France. Journal of Cleaner Production. https://doi.org/10.1016/j.jclepro.2024.142296
Pouil S, Harté E, Marchand M, Goardon L, Terrenne T, Labbé L, Dupont-Nivet M, Leguen I, Lallias D. 2024. Cold temperature during embryonic development and its influence on responses to acute confinement and hyperthermia challenges in juvenile rainbow trout. Aquaculture. https://doi.org/10.1016/j.aquaculture.2024.741318
Pouil S, Slembrouck J, Wilfart A, Caruso D, Arifin OZ, Favalier N, Samsudin R, Kristanto AH, Aubin J. 2024. The potential of floating macrophytes as feed and phytoremediation resources to improve the environmental performance of giant gourami production in Indonesia: A life cycle assessment. Aquaculture https://doi.org/10.1016/j.aquaculture.2023.740181
Roche J, Besson M, Allal F, Haffray P, Patrice P, Vandeputte M, Phocas F. 2024. GenoTriplo: A SNP genotype calling method for triploids. 2024. Plos Comp Biol. https://doi.org/10.1371/journal.pcbi.1012483
Roche J, Griot R, Allal F, Besson M, Haffray P, Patrice P, Phocas F, Vandeputte M. 2024. APIS: an updated parentage assignment software managing triploids induced from diploid parents. G3. https://doi.org/10.1093/g3journal/jkae143
2023
Calduch-Giner J, Rosell-Moll E, Besson M, Vergnet A, Bruant J-S, Clota F, Holhorea PG, Allal F, Vandeputte M, Perez-Sanchez J. 2023. Changes in transcriptomic and behavioural traits in activity and ventilation rates associated with divergent individual feed efficiency in gilthead sea bream (Sparus aurata) AQUACULTURE REPORTS.
Caruso D, Lusiastuti AM, Pouil S, Samsudin R, Arifin OZ, Slembrouck J. 2023. Can Azolla filiculoides be a complementary feed resource for ecological intensification in small-scale fish farming? Biological effects on giant gourami (Osphronemus goramy. Aquat. Living Resour.
Delpuech E, Vandeputte M, Morvezen R, Bestin A, Besson M, Brunier J, Bajek A, Imarazene B, François Y, Bouchez O, Cousin X, Poncet C, Morin T, Bruant J-S, Chatain B, Haffray P, Phocas F, Allal F. 2023. Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass. Genet Sel Evol.
Guichard M, Phocas F, Neuditschko M, Basso B, Dainat B. 2023. An overview od selection concepts applied to honey bees. Bee World
Jourdan A, Morvezen R, Enez F, Haffray P, Lange A, Vétois E, Allal F, Phocas F,Bugeon J, Dégremont L, Boudry P. 2023. Potential of genomic selection for growth, meat content and colour traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas. Aquaculture.
Lagarde H, Lallias D, Patrice P, Dehaullon A, Prchal M, Francois Y, D'Ambrosio J, Segret E, Acin-Perez A, Cachelou F, Haffray P, Dupont-Nivet M, Phocas F. 2023. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits. Genet Sel Evol.
Lagarde H, Lallias D, Phocas F, Goardon L, Bideau M, Guyvarc'h F, Labbé L, Dupont-Nivet M, Cousin X. 2023. Links between behaviour and resistances to acute hyperthermia and hypoxia using rainbow trout isogenic lines. BioRXIV https://doi.org/10.1101/2023.10.19.563047v1
Lee B-H, Quillet E, Rigaudeau D, Dechamp N, Duchaud E, Bernardet J-F, Boudinot P, Rochat T. 2023. Interplay between a bacterial pathogen and its host in rainbow trout isogenic lines with contrasted susceptibility to Cold Water Disease. Micorbes and Infection.
Lokesh J, Delaygues M, Defaix R, Le Bechec M, Pigot T, Dupont Nivet M, Kerneis T, Labbe L, Goardon L, Terrier F, Panserat S, Ricaud K. 2023. Interaction between genetics and inulin affects host metabolism in rainbow trout fed a sustainable all plant-based diet. British j nut
Paul K, Pélissier P, Goardon L, Dechamp N, Danon J, Jaffrelo L, Poncet C, Dupont-Nivet M, Phocas F. 2023. Maternal and genetic effects on embryonic survival from fertilization to swim up stage and reproductive success in a farmed rainbow trout line. Aqua Rep
Pouil S, Kernéis T, Quillet E, Labbé L, Lallias D, Phocas F, Dupont-Nivet M. 2023. Isogenic lines of rainbow trout (Oncorhynchus mykiss) as a tool to assess how growth and feeding behaviour are correlated to feed efficiency in fish. Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739904
Prchal M, D'Ambrosio J, Lagarde H, Lallias D, Patrice P, François Y, Poncet C, Desgranges A, Haffray P, Dupont-Nivet M, Phocas F. 2023. Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout. Aquaculture.
Roques S, Deborde C, Skiba-Cassy S, Médale F, Dupont-Nivet M, Lefevre F, Bugeon J, Labbé L, Marchand Y, Moing A, Fauconneau B. 2023. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition : a metabolomics appraisal. Scientific reports https://doi.org/10.1038/s41598-023-46809-2
2022
Akian DD, Yao K, Parmentier E, Clota F, Baroiller JF, Begout ML. 2021. Familiarity reduces aggression but does not modify acoustic communication in pairs of Nile tilapia (Oreochromis niloticus) and black-chinned tilapia (Sarotherodon melanotheron). J Fish Biol.
Bernard M, Dehaullon A, Gao G, Paul K, Lagarde H, Charles M, Prchal M, Danon J, Jaffrelo L, Poncet C, Patrice P, Haffray P, Quillet E, Dupont-Nivet M, Palti Y, Lallias D, Phocas F. 2022. Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping. Front Genetics
Bertho S, Herpin A, Jouanno E, Yano A, Bobe J, Parrinello H, Journot L, Guyomard R, Muller T, Swanson P, McKinney G, Williamson K, Meek M, Schartl M, Guiguen Y. 2022. A nonfunctional copy of the salmonid sex-determining gene (sdY) is responsible for the apparent XY females in Chinook salmon, Oncorhynchus tshawytscha. G3.
Besson M, Rombout N, Salou G, Vergnet A, Cariou S, Bruant JS, Izquierdo M, Bestin A, Clota F, Haffray P, Allal F, Vandeputte M. 2022. Potential for genomic selection on feed efficiency in gilthead sea bream (Sparus aurata), based on individual feed conversion ratio, carcass and lipid traits. AQUACULTURE REPORTS.
Castro R, Navelsaker S, Collet B, Jouneau L, Bochet P, Quillet E, Evensen O, Sunyer JO, Fillatreau S, Bruhns P, Rose T, Huetz F, Boudinot P. 2021. Cutting Edge: Neutralizing Public Antibody Responses Are an Ancient Form of Defense Conserved in Fish and Mammals. J Immunol. 207, 371-375
Calduch-Giner J, Holhorea PG, Ferrer MA, Naya-Català F, Rosell-Moll E , Vega García C, Prunet P, Espmark Å, Leguen I, Kolarevic J, Vega A, Kerneis T, Goardon L, Afonso JM, Pérez-Sánchez J. 2022. Revising the Impact and Prospects of Activity and Ventilation Rate Bio-Loggers for Tracking Welfare and Fish-Environment Interactions in Salmonids and Mediterranean Farmed Fish. Front Marine Science.
De Oliveira J, Chadili E, Turies C, Maillot-Maréchal E, Brion F, Cousin X, Hinfray N. 2021. A comparison of behavioral and reproductive parameters between wild-type, transgenic and mutant zebrafish: Could they all be considered the same “zebrafish” for reglementary assays on endocrine disruption? Comp Biochem Phys Cl. 239, 108879
de Verdal H, Haffray P, Douchet V, Vandeputte M. Impact of a divergent selective breeding programme on individual feed conversion ratio in Nile tilapia Oreochromis niloticus measured in groups by video-recording. Aquaculture.
Geffroy B, Besson M, Sanchez-Baizan N, Clota F, Goikoetxea A, Sadoul B, Ruelle F, Blanc MO, Parrinello H, Hermet S, Blondeau-Bidet E, Pratlong M, Piferrer F, Vandeputte M, Allal F. 2021. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system. PNAS
Lagarde H, Phocas F, Pouil S, Goardon L, Bideau M, Guyvarc'h F, Labbé L, Dechamp N, Prchal M, Dupont-Nivet M, Lallias D. 2022. Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines ? Aquaculture
Marandel L, Heraud C, Veron V, Laithier J, Marchand M, Quillet E, Callet T, Dupont-Nivet M, Medale F. 2022. A plant-based diet differentially affects the global hepatic methylome in rainbow trout depending on genetic background. EPIGENETICS
Phocas F. 2022. Genotyping, the Usefulness of Imputation to Increase SNP Density, and Imputation Methods and Tools. Chapter 4 in: Complex Trait Prediction. Ahmadi N. and Bartholomé J. (eds), Springer Protocols. 113-138
Prado E, Eklouh-Molinier C, Enez F, Causeur D, Blay C, Dupont-Nivet M, Labbe L, Petit V, Moreac A, Taupier G, Haffray P, Bugeon J, Corraze G, Nazabal V. 2022. Prediction of fatty acids composition in the rainbow trout Oncorhynchus mykiss by using Raman micro-spectroscopy. Analytica Chimica Acta.
Vandeputte M, Corraze G, Doerflinger J, Enez F, Clota F, Terrier F, Horat M, Larroquet L, Petit V, Haffray P, Skiba-Cassy S, Dupont-Nivet M. 2022. Realised genetic gains on growth, survival, feed conversion ratio and quality traits after ten generations of multi-trait selection in rainbow trout Oncorhynchus mykiss, fed a standard diet or a “future” fish-free and soy-free diet. Aquaculture Reports
2021
Barsoe S, Allal F, Vergnet A, Vandeputte M, Olesen NJ, Schmidt JG, Larsen CA, Cuenca A, Vendramin N. 2021. Different survival of three populations of European sea bass (Dicentrarchus labrax) following challenge with two variants of nervous necrosis virus (NNV). Aquaculture Report. 19.
Blanc M, Antczak P, Cousin X, Grunau C, Scherbak N,Rüegg J,Keiter SH. 2021. The insecticide permethrin induces transgenerational behavioral changes linked to transcriptomic and epigenetic alterations in zebrafish (Danio rerio). Sci Total Environ. 779, 146404
Blay C, Haffray P, D’Ambrosio J, Prado E, Dechamp N, Nazabal V, Bugeon J, Enez F, Causeur D, Eklouh-Molinier C, Petit V, Phocas F, Corraze G, Dupont-Nivet M. 2021. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout. BMC Genomics. 22
Bestin A, Brunel O, Malledant A, Debeuf B, Benoit P, Mahla R, Chapuis H, Guémené D, Vandeputte M, Haffray P. 2021. Genetic parameters of caviar yield, color, size and firmness using parentage assignment in an octoploid fish species, the Siberian sturgeon Acipenser baerii. Aquacul. 540, 736725.
Blanc M, Alfonso S, Begout ML, Barrachina C, Hyotylainen T, Keiter SH, Cousin X. 2021. An environmentally relevant mixture of polychlorinated biphenyls (PCBs) and polybrominated diphenylethers (PBDEs) disrupts mitochondrial function, lipid metabolism and neurotransmission in the brain of exposed zebrafish and their unexposed F2 offspring. Sci Total Environ. 754, 142097
Blay C, Haffray P,Bugeon J, D’Ambrosio J, Dechamp N, Collewet G, Enez F, Petit V, Cousin X, Corraze G, Phocas F, Dupont-Nivet M. 2021. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss’. Front Genet. 12, 639223
Boudry P, Allal F, Aslam ML, Bargelloni L, Bean TP, Brard-Fudulea S, Brieuc MSO, Calboli FCF, Gilbey J, Haffray P, Lamy JB, Morvezen R, Purcell C, Prodohl PA, Vandeputte M, Waldbieser GC, Sonesson AK, Houston RD. 2021. 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. Aquaculture Report. 20, 100700
Callet T, Dupont-Nivet M, Danion M, Burel C, Cluzeaud M, Surget A, Aguirre P, Kerneis T, Labbe L, Panserat S, Quillet E, Geurden I, Skiba-Cassy S, Medale F. 2021. Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines. Front Physiol. 12
Cormier B, Gambardella C, Tato T, Perdriat Q, Costa E, Veclin C, Le Bihanic F, Grassl B, Dubocq, Karrman A, Van Arkel K, Lemoine S, Lagarde F, Morin B, Garaventa F, Faimali M, Cousin X, Begout ML, Beiras R, Cachot J. 2021. Chemicals sorbed to environmental microplastics are toxic to early life stages of aquatic organisms. Ecotoxicol Environ Saf. 208, 111665
Cormier B, Le Bihanic F, Cabar M, Crebassa JC, Blanc M, Larsson M, Dubocq F, Yeung L, Clérandeau C, Keiter SH, Cachot J, Bégout ML, Cousin X. 2021. Chronic feeding exposure to virgin and spiked microplastics disrupts essential biological functions in teleost fish. J Haz Mat. 125626
De Oliveira J, Chadili E, Turies C, Brion F, Cousin X, Hinfray N. 2021. A comparison of behavioral and reproductive parameters between wild-type, transgenic and mutant zebrafish: Could they all be considered the same "zebrafish" for reglementary assays on endocrine disruption? Comp Biochem Physiol C Toxicol Pharmacol. 239, 108879
Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. 2021. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immun. 12
Faggion S, Vandeputte M, Vergnet A, Clota F, Blanc M-O, Sanchez P, Ruelle F, Allal F. 2021. Sex dimorphism in European sea bass (Dicentrarchus labrax L.): New insights into sex-related growth patterns during very early life stages. PlosOne
Gefroy B, Gesto M, Clota F, Aerts J, Darias MF, Blanc M-O, Ruelle F, Allal F, Vandeputte M. 2021. Parental selection for growth and early‑life low stocking density increase the female‑to‑male ratio in European sea bass. Scient Report.
Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Bestin A, Haffray P, François Y, Morin T, Poncet C, Vergnet A, Cariou S, Brunier J, Bruant JS, Peyrou B, Gagnaire PA, Vandeputte M. 2021. Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57k SNP array DlabChip. Aquaculture. 530, 735930
Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Haffray P, François Y, Morin T, Bestin A, Bruant J-S, Cariou S, Peyrou B, Brunier J, Vandeputte M. 2021. 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). Front Genet. 12
Kistler T, Basso B, Phocas F. 2021. A simulation study of a honeybee breeding scheme accounting for polyandry, direct and maternal effects on colony performance. Genet Sel Evol. 53
Pan Q, Feron R, Jouanno E, Darras H, Herpin A, Koop B, Rondeau E, Goetz FW, Larson WA, Bernatchez L, Tringali M, Curran SS, Saillant E, Denys GPJ, von Hippel FA, Chen S, Lopez JA, Verreycken H, Ocalewicz K, Guyomard R, Eche C, Lluch J, Roques C, Hu H, Tabor R, DeHaan P, Nichols KM, Journot L, Parrinello H, Klopp C, Interesova EA, Trifonov V, Schartl M, Postlethwait J, Guiguen Y. 2021. The rise and fall of the ancient northern pike master sex-determining gene. eLife. 10, e62858
Paul K, D'Ambrosio J, Phocas F. 2021. Temporal and region-specific variations in genome-wide inbreeding effects on female size and reproduction traits of rainbow trout. Evolutionary Applications
Prakoso VA, Pouil S, Cahyanti W, Sundari S, Arifin OZ, Subagja J, Kristanto AH, Slembrouck J. 2021. Fluctuating temperature regime impairs growth in giant gourami (Osphronemus goramy) larvae. Aquaculture, 539
Rodde C, de Verdal H, Vandeputte M, Allal F, Nati J, Besson M, Blasco FR, Benzie JAH, McKenzie DJ. 2021. An investigation of links between metabolic rate and feed efficiency in European sea bass Dicentrarchus labrax. J Anim Sci. 99
Sadoul B, Alfonso S, Cousin X, Prunet P, Begout ML, Leguen I. 2021. Global assessment of the response to chronic stress in European sea bass. Aquaculture. 544
Sardi AE, Begout ML, Cousin X, Labadie P, Loizeau V, Budzinski H. 2021. A review of the effects of contamination and temperature in Solea solea larvae. Modeling perspectives in the context of climate change. J Sea Res
Vandeputte M, Bestin A, Fauchet L, Allamellou JM, Bosc S, Menchi o, Haffray P. 2021. Can we identify wild-born salmon from parentage assignment data? A case study in the Garonne-Dordogne rivers salmon restoration programme in France. Aquat Living Resour.
Zhao JF, Prchal M, Kause A, Vandeputte M, Gela D, Kroupova HK, Piackova V, Sauer P, Steinbach C, Allamellou JM, Palaiokostas C, Houston RD, Kocour M. 2021. The role of energy reserves in common carp performance inferred from phenotypic and genetic parameters. Aquaculture. 541
2020
Alfonso S, Peyrafort M, Cousin X, Bégout ML. 2020. Zebrafish, Danio rerio, show behavioural cross-context consistency at larval and juvenile stages but no consistency between stages. J Fish Biol. 96, 1411-1421
Alfonso S, Sadoul B, Cousin X, Bégout ML. 2020. Spatial distribution and activity patterns as welfare indicators in response to water quality changes in European sea bass, Dicentrarchus labrax. Appl Anim Behav Sci. 104974
Besson M, Komen H, Rose G, Vandeputte M. 2020. The genetic correlation between feed conversion ratio and growth rate affects the design of a breeding program for more sustainable fish production. Genet sel Evol. 52, 5
Blanc M, Cormier B, Hyotylainen T, Krauss M, Scherbak N, Cousin X, Keiter SH. 2020. Multi- and transgenerational effects following early-life exposure of zebrafish to permethrin and coumarin 47: Impact on growth, fertility, behavior and lipid metabolism. Ecotoxicol Environ Saf. 205, 111348
Cousin X, Batel A, Bringer A, Hess S, Begout ML, Braunbeck T. 2020. Microplastics and sorbed contaminants - Trophic exposure in fish sensitive early life stages. Mar Environ Res. 161, 105126
D’Ambrosio J, Morvezen2 R, Brard-Fudulea S, Bestin A, Acin Perez A, Guéméné D, Poncet C, HaffrayP, Dupont-Nivet M, Phocas F. 2020. Genetic architecture and genomic selection of female reproduction traits in rainbow trout. BMC Genomics. 21, 558
De Oliveira J, Chadili E, Piccini B, Turies C, Maillot-Maréchal E, Palluel O, Pardon P, Budzinski H, Cousin X, Brion F, Hinfray N. 2020. Refinement of an OECD test guideline for evaluating the effects of endocrinedisrupting chemicals on aromatase gene expression and reproduction using novel transgenic cyp19a1a-eGFP zebrafish. Aquat Toxicol. 220, 105403
Faggion S, Sanchez P, Vandeputte M, Clota F, Vergnet A, Blanc MO, Allal F. 2020. Evaluation of a European sea bass (Dicentrarchus labrax L.) post-larval tagging method with ultra-small RFID tags. Aquaculture. 520, 734945
Fraslin C, Phocas F, Bestin A, Charles M, Bernard M, Krieg F, Dechamp N, Ciobotaru C, Hozé C, Petitprez F, Milhes M, Lluch J, Bouchez O, Poncet C, Hocdé P, Haffray P, Guiguen Y, Quillet E. 2020. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing. Sci Rep. 10, 17693
Fraslin C, Quillet E, Rochat T, Dechamp N, Bernardet JF, Collet B, Lallias D, Boudinot P. 2020. Combining multiple approaches and models to dissect the genetic architecture of resistance to infections in fish. Front Genet. 11, 677
Griot R, Allal F, Brard‐Fudulea S, Morvezen R, Haffray P, Phocas F, Vandeputte M. 2020. APIS: An auto‐adaptive parentage inference software that tolerates missing parents. Mol Ecol Ressour. 20, 579-590
Lallias D, Bernard M, Ciobotaru C, Dechamp N, Labbé L, Goardon L, Le Calvez JM, Bideau M,Fricot A, Prézelin A, Charles M, Moroldo M, Cousin X, Bouchez O, Roulet A, Quillet E, Dupont-Nivet M. 2020. Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background. Epigenetics. in press.
Le Bihanic F, Clerandeau C, Cormier B, Crebassa JC, Keiter SH, Beiras R, Morin B, Begout ML, Cousin X, Cachot J. 2020. Organic contaminants sorbed to microplastics affect marine medaka fish early life stages development. Mar Pollut Bull. 158, 111059
Prchal M, Kocour M, Vandeputte M, Kause A, Vergnet A,Zhao J, Gela D, Kašpar V, Genestout L, Bestin A, Haffray P, Bugeon J. 2020. Morphological predictors of slaughter yields using 3D digitizer and their use in a common carp breeding program. Aquaculture. 520, 734993
Rodde C, Chatain B, Vandeputte M, Trinh TQ, Benzie JAH, de Verdal H. 2020. Can individual feed conversion ratio at commercial size be predicted from juvenile performance in individually reared Nile tilapia Oreochromis niloticus? Aquacult Rep. 17, 100349
Rodde C, de Verdal H, Lefebvre S, Menniti C, Vandeputte M, Clota F, Allal F, McKenzie DJ, Benzie JAH, Nahon S. 2020. Variations in isotope incorporation rates and trophic discrimination factors of carbon and nitrogen stable isotopes in scales from three European sea bass (Dicentrarchus labrax) populations. J Exp Mar Biol Ecol. 533, 151468
Rodde C, Vandeputte M, Allal F, Besson M, Clota F, Vergnet A, Benzie JAH, de Verdal H. 2020. Population, temperature and feeding rate effects on individual feed efficiency in European sea bass (Dicentrarchus labrax). Front Mar Sci. 7, 578976
Vandeputte M, Clota F, Sadoul B, Blanc MO, Blondeau‐Bidet E, Bégout ML, Cousin X, Geffroy B. 2020. Low temperature has opposite effects on sex determination in a marine fish at the larval/postlarval and juvenile stages. Ecol Evol. 10, 13825-13835
Vandeputte M, Fraslin C, Haffray P, Bestin A, Allal F, Kocour M, Prchal M, Dupont-Nivet M. 2020. How to genetically increase fillet yield in fish: Relevant genetic parameters and methods to predict genetic gain. Aquaculture. 519, 737-877
Zhao J, Prchal M, Palaiokostas C, Houston RD, Kause A, Vandeputte M, Vergnet A, Bugeon J, Bestin A, Veselý T, Pokorová D, Piačková V, Pojezdal L, Genestout L, Gela D, Kroupová HK, Kocour M. 2020. Genetic relationship between koi herpesvirus disease resistance and production traits inferred from sibling performance in Amur mirror carp. Aquaculture. 520, 734986
2019
Alfonso S, Blanc M, Joassard L, Keiter SH, Munschy C, Loizeau V, Bégout ML, Cousin X. 2019. Examining multi- and transgenerational behavioral and molecular alterations resulting from parental exposure to an environmental PCB and PBDE mixture. Aquat Toxicol. 208, 29-38
Besson M, Allal F, Chatain B, Vergnet A, Clota F, Vandeputte M. 2019. Combining individual phenotypes of feed intake with genomic data to improve feed efficiency in sea bass. Front Genet. 10, 219
Cormier B, Batel A, Cachot J, Begout ML, Braunbeck T, Cousin X, Keiter SH. 2019. Multi-laboratory hazard assessment of contaminated microplastic particles by means of enhanced fish embryo test with the zebrafish (Danio rerio). Front Environ Sci. 7, 135
D'Ambrosio J, Phocas F, Haffray P, Bestin A, Brard-Fudulea S, Poncet C, Quillet E, Dechamp N, Fraslin C, Charles M, Dupont-Nivet M. 2019. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding. Genet Sel Evol. 51, 26
de Verdal H, O'Connell CM, Mekkawy W, Vandeputte M, Chatain B, Begout ML, Benzie JAH. 2019. Agonistic behaviour behaviour and feed efficiency in juvenile Nile tilapia Oreochromis niloticus. Aquaculture. 505, 271-279
Eckart V, Yamaguchi T, Franzke K, Bergmann SM, Boudinot P, Quillet E, Kawanobe M, de Haro NA, Fischer U. 2019. New cell lines for efficient propagation of koi herpesvirus and infectious salmon anaemia virus. J Fish Dis. 42, 181-187
Faggion S, Vandeputte M, Chatain B, Gagnaire PA, Allal F. 2019. Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L. Heredity. 122, 612-621
Fraslin C, Brard-Fudulea S, D’Ambrosio J, Bestin A, Charles M, Haffray P, Quillet E, Phocas F. 2019. Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm. Anim Genet. 50, 293-297
George PBL, Lallias D, Creer S, Seaton FM, Kenny JG, Eccles RM, Griffiths RI, Lebron I, Emmett BA, Robinson DA, Jones DL. 2019. Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems. Nat Commun. 10, 1107
Le Roy P, Ducos A, Phocas F. 2019. What performance for tomorrow’s animals? Breeding goals and selection methods. INRA Prod Anim. 32, 233-246
Magadan S, Krasnov A, Hadi-Saljoqi S, Afanasyev S, Mondot S, Lallias D, Castro R, Salinas I, Sunyer O, Hansen J, Koop BF, Lefranc MP, Boudinot P. 2019. Standardized IMGT (R) nomenclature of salmonidae IGH genes, the paradigm of Atlantic Salmon and Rainbow Trout: From genomics to repertoires. Front Immunol. 10, 2541
Navelsaker S, Magadan S, Jouneau L, Quillet E, Olesen NJ, Munang'andu HM, Boudinot P, Evensen Ø. 2019. Sequential immunization with heterologous viruses does not result in attrition of the B cell memory in Rainbow trout. Front Immunol. 10, 2687
Savilammi T, Primmer CR, Varadharajan S, Guyomard R, Guiguen Y, Sandve SR, Vollestad LA,Papakostas S, Lien S. 2019. The chromosome-level genome assembly of European grayling reveals aspects of a unique genome evolution process within Salmonids. G3 (Bethesda). 9, 1283-1294
Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y. 2019. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genet. 15, e1008013
Vandeputte M, Gagnaire PA, Allal F. The European sea bass: a key marine fish model in the wild and in aquaculture. Anim Genet. 50, 195-206
Vandeputte M, Bugeon J, Bestin A, Desgranges A, Allamellou JM, Tyran AS, Allal F, Dupont-Nivet M, Haffray PY. 2019. First evidence of realized selection response on fillet yield in rainbow trout Oncorhynchus mykiss, using sib selection or based on correlated ultrasound measurements. Front Genet. 10, 1225
Yamaguchi T, Quillet E, Boudinot P, Fischer U. 2019. What could be the mechanisms of immunological memory in fish? Fish Shellfish. Immunol. 85, 3-8
Zhu T, Corraze G, Plagnes-Juan E, Montfort J, Bobe J, Quillet E, Dupont-Nivet M, Skiba-Cassy S. 2019. MicroRNAs related to cholesterol metabolism affected by vegetable diet in rainbow trout (Oncorhynchus mykiss) from control and selected lines. Aquaculture. 498, 132-142
2018
Anastasiadi D, Vandeputte M, Sánchez-Baizán N, Allal F, Piferrer F. 2018. Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination. Epigenetics. 13, 988-1011
Beiras R, Bellas J, Cachot J, Cormier B, Cousin X, Engwall M, Gambardella C, Garaventa F, Keiter S, Le Bihanic F, Lopez-Ibanez S, Piazza V, Rial D, Tato T, Vidal-Linan L. 2018. Ingestion and contact with polyethylene microplastics does not cause acute toxicity on marine zooplankton. J Hazard Mater. 360, 452-460
Borey M, Paroissin C, Quillet E, Terrier F, Maunas P, Burel C, Lauga B. 2018. Acute hypoxia reveals diverse adaptation strategies to fully substituted plant-based diet in isogenic lines of the carnivorous rainbow trout. Aquaculture. 490, 288-296.
Callet T, Dupont-Nivet M, Cluzeaud M, Jaffrezic F, Laloë D, Kerneis T,Labbe L, Quillet E, Geurden I, Mazurais D, Skiba-Cassy S, Medale F. 2018. Detection of new pathways involved in the acceptance and the utilisation of a plant- based diet in isogenic lines of rainbow trout fry. PLoS One. 13, e0201462
Carballo C, Berbel C, Guerrero-Cozar I, Jimenez-Fernandez E, Cousin X, Begout ML, Manchado M. 2018. Evaluation of different tags on survival, growth and stress response in the flatfish Senegalese sole. Aquaculture. 494, 10-18
de Verdal H, Komen H, Quillet E, Chatain B, Allal F, Benzie JAH Vandeputte M. 2018. Improving feed efficiency in fish using selective breeding: a review. Rev Aquacult. 10, 833-851
de Verdal H, Vandeputte M, Mekkawy W, Chatain B, Benzie JAH. 2018. Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus. BMC Genet. 19, 105
Fraslin C, Dechamp N, Bernard M, Krieg F, Hervet C, Guyomard R, Esquerré D, Barbieri J, Kuchly C, Duchaud E, Boudinot P, Rochat T, Bernardet JF, Quillet E. 2018. Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions. Genet Sel Evol. 50, 60
Fraslin C, Dupont-Nivet M, Haffray P, Bestin A, Vandeputte M. 2018. How to genetically increase fillet yield in fish: New insights from simulations based on field data. Aquaculture, 486, 175-184
Haffray P, Enez F, Bugeon J, Chapuis H, Dupont-Nivet M, Chatain B, Vandeputte M. 2018. Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss. Aquaculture. 490, 350-354
Horri K, Alfonso S, Cousin X, Munschy C, Loizeau V, Aroua S, Bégout ML, Ernande B. 2018. Fish life-history traits are affected after chronic dietary exposure to an environmentally realistic marine mixture of PCBs and PBDEs. Sci Total Environ. 610-611, 531-545.
Legradi JB Di Paolo C, Kraak MHS, van der Geest HG, Schymanski EL, Williams AJ Dingemans, MML Massei, R, Brack W, Cousin X, Begout ML, van der Oost R, Carion A, Suarez-Ulloa V, Silvestre F, Escher BI, Engwall M, Nilen G, Keiter SH, Pollet D, Waldmann, P, Kienle C; Werner I, Haigis AC, Knapen D, Vergauwen L, Spehr M, Schulz W, Busch W, Leuthold D, Scholz S, vom Berg CM, Basu N, Murphy CA, Lampert, A, Kuckelkorn J, Grummt T, Hollert H. 2018. An ecotoxicological view on neurotoxicity assessment. Environ Sci Eur. 30, 46
Magadan S, Jouneau L, Touzel MP, Marillet S, Chara W, Six A, Quillet E, Mora T, Walczak AM, Cazals F, Sunyer O, Fillatreau S, Boudinot P. 2018. Origin of public pemory B cell clones in fish after antiviral vaccination. Front Immunol. 9, 2115
Nascimento FJA, Lallias D, Bik HM, Creer S. 2018. Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing. Sci Rep. 8, 11737
Palaiokostas C, Cariou S, Bestin A, Bruant JS, Haffray P,Morin T, Cabon J, Allal F, Vandeputte M, Houston RD. 2018. Genome‑wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing. Genet Sel Evol. 50-30.
Prchal M, Bugeon J, Vandeputte M, Kause A, Vergnet A, Zhao JF, Gela D, Genestout L, Bestin A, Haffray P, Kocour M. 2018. Potential for genetic improvement of the main slaughter yields in common carp with in vivo morphological predictors. Front Genet. 9, 283
Prchal M, Kause A, Vandeputte M, Gela D, Allamellou JM, Kumar G, Bestin A, Bugeon J, Zhao J, Kocour M. 2018. The genetics of overwintering performance in two-year old common carp and its relation to performance until market size. PLoS One, 13-e0191624.
Prchal M, Vandeputte M, Gela D, Doležal M, Buchtová H, Rodina M, Flajšhans M, Kocour M. 2018. Estimation of genetic parameters of fatty acids composition in flesh of market size common carp (Cyprinus carpio L.) and their relation to performance traits revealed that selective breeding can ndirectly affect flesh quality. Czech J Anim Sci. 63, 280-291
Song X, Marandel L, Dupont-Nivet M, Quillet E, Geurden I, Panserat S. 2018. Hepatic glucose metabolic responses to digestible dietary carbohydrates in two isogenic lines of rainbow trout. Biol Open. 7, bio032896.
Song X, Marandel L, Skiba-Cassy S, Corraze G, Dupont-Nivet M, Quillet E, Geurden I, Panserat S. 2018. Regulation by dietary carbohydrates of intermediary metabolism in liver and muscle of two isogenic lines of Rainbow trout. Front Physiol. 9, 1579
Verrier ER, Genet C, Laloë D, Jaffrezic F, Rau A, Esquerre D, Dechamp N, Ciobotaru C, Hervet H, Krieg F, Jouneau L, Klopp C, Quillet E, Boudinot P. 2018. Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout. BMC Genomics. 19,482.
Zhu T, Corraze G, Plagnes-Juan E, Quillet E, Dupont-Nivet M, Skiba-Cassy S. 2018. Regulation of genes related to cholesterol metabolism in rainbow trout (Oncorhynchus mykiss) fed a plant-based diet. Am J Physiol Regul Integr Comp Physiol. 314, R58-R70.
2017
Besson M, de Boer IJM, Vandeputte M, Van Arendonk JAM, Quillet E, Komen H, Aubin J. 2017. Effect of production quotas on economic and environmental values of growth rate and feed efficiency in sea cage fish farming. PLoS One. 12, e0173131
Bista I, Carvalho GR, Walsh K, Seymour M, Hajibabaei M, Lallias D, Christmas M, Creer S. 2017. Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat Commun. 8, 14087
Callet T, Médale F, Larroquet L, Surget A, Aguirre P, Kerneis T, Labbé L, Quillet E, Geurden I, Skiba-Cassy S, Dupont-Nivet M. 2017. Successful selection of rainbow trout (Oncorhynchus mykiss) on their ability to grow with a diet completely devoid of fishmeal and fish oil, and correlated changes in nutritional traits. PLoS One. 12, e0186705.
de Verdal H, Komen H, Quillet E, Chatain B, Allal Benzie JA, Vandeputte M. 2017. Improving feed efficiency in fish using selective breeding: a review. Rev Aquacult. early view.
de Verdal, H, Mekkawy W, Lind CE, Vandeputte M, Chatain B, Benzie AH. 2017. Measuring individual feed efficiency and its correlations with performance traits in Nile tilapia, Oreochromis niloticus. Aquaculture. 468, 489-495
Doan KQ, Vandeputte M, Chatain B, Haffray P, Vergnet A, Breuil G, Allala F. 2017. Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European sea bass (Dicentrarchus labrax). Aquaculture. 478, 1-8.
Doan QK, Vandeputte M, Chatain B, Morin T, Allal F. 2017. Viral encephalopathy and retinopathy in aquaculture: a review. J Fish Dis. 40, 717-742.
Guinand B, Vandeputte M, Dupont-Nivet M, Vergnet A, Haffray P, Chavanne H, Chatain B. 2017. Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax). Ecol Evol. 7.
Hillen JEJ, Coscia I, Vandeputte M, Herten K, Hellemans B, Maroso F, Vergnet A, Allal F, Maes GE, Volckaert FAM. 2017. Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass. Aquaculture. 479, 742-749.
Janssen K, Berentsen P, Besson M, Komen H. 2017. Derivation of economic values for production traits in aquaculture species. Genet Sel Evol. 49, 5. GenAqua
Oral M, Colléter J, Bekaert M, Taggart JB, Palaiokostas C, McAndrew BJ, Vandeputte M, Chatain B, Kuhl H, Reinhardt R, Peruzzi S, Penman DJ. 2017. Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics. 18.
Vandeputte M, Puledda A, Tyran AS, Bestin A, Coulombet C, Bajek A, Baldit G, Vergnet A, Allal F, Bugeon J, Haffray P. 2017. Investigation of morphological predictors of fillet and carcass yield in European sea bass (Dicentrarchus labrax) for application in selective breeding. Aquaculture. in press
Vignet C, Trenkel V, Vouillarmet A, Bricca G, Bégout ML, Cousin X. 2017. Changes in brain monoamines underlie behavioural disruptions after zebrafish diet exposure to polycyclic aromatic hydrocarbons environmental mixtures. Int J Mol Sci. 18, 560.
ZhuT, Corraze G, Plagnes-Juan E, Quillet E, Dupont-Nivet M, Skiba-Cassy S. 2017. Regulation of genes related to cholesterol metabolism in rainbow trout (Oncorhynchus mykiss) fed plant-based diet. Am J Physiol. in press
2016
Andria-Mananjara DE, Rasamoelina H, Vandeputte M. 2016. Comparison of rearing performances and intermuscular bone number in the mirror and nude genotypes of common carp (Cyprinus carpio L.) in a controlled field test in Madagascar. Aquacult Rep. 3, 77-81
Balasubramanian MN, Panserat S, Dupont-Nivet M, Quillet E, Montfort J, Le Cam A, Medale F, Kaushik SJ, Geurden I. 2016. Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure. BMC Genomics. 17, 449
Besson M, Aubin J, Komen H, Poelman M, Quillet E, Vandeputte M, van Arendonk JAM, de Boer, IJM. 2016. Environmental impacts of genetic improvement of growth rate and feed conversion ratio in fish farming under rearing density and nitrogen output limitations. J Cleaner Prod. 116, 100-109
Besson M, Vandeputte M , van Arendonk JAM, Aubin J, de Boer IJM, Quillet E, Komen H. 2016. Influence of water temperature on the economic value of growth rate in fish farming: The case of sea bass (Dicentrarchus labrax) cage farming in the Mediterranean. Aquaculture. 462, 47-55
Doan QK, Vandeputte M, Chatain B, Morin T, Allal F. 2016. Viral encephalopathy and retinopathy in aquaculture: a review. J Fish Dis. early online
Ferrari S, Horri K, Allal F, Vergnet, A, Benhaim D, Vandeputte M, Chatain B, Bégout ML. 2016. Heritability of boldness and hypoxia avoidance in European seabass, Dicentrarchus labrax. PLoS One. 11, e0168506
Grade A, Chairi H, Lallias D, Power DM, Ruano F, Leitao A, Drago T, King JW, Boudry P, Batista FM. 2016. New insights about the introduction of the Portuguese oyster, Crassostrea angulata, into the North East Atlantic from Asia based on a highly polymorphic mitochondrial region. Aquat Living Resour. 29, 404
Hubert JN, Allal F, Hervet C, Ravakarivelo M, Jeney Z, Vergnet A, Guyomard R, Vandeputte M. 2016. How could fully scaled carps appear in natural waters in Madagascar ? Proc Royal Soc Biol Sci. 283, 1-8
Sadoul B, Foucard A, Valotaire C, Labbe L, Goardon L, LeCalvez JM, Medale F, Quillet E, Dupont-Nivet M, Geurden I, Prunet P, Colson V. 2016. Adaptive capacities from survival to stress responses of two isogenic lines of rainbow trout fed a plant-based diet. Sci Rep. 6, 35957.
Vandeputte M, Porte JD, Auperin B, Dupont-Nivet M, Vergnet A, Valotaire C, Claireaux G, Prunet P, Chatain, B. 2016. Quantitative genetic variation for post-stress cortisol and swimming performance in growth-selected and control populations of European sea bass (Dicentrarchus labrax). Aquaculture. 455, 1-7
Veron V, Panserat S, Le Boucher R, Labbé L, Quillet E, Dupont-Nivet M, Médale F. 2016. Long-term feeding a plant-based diet devoid of marine ingredients strongly affects certain key metabolic enzymes in the rainbow trout liver. Fish Physiol Biochem. 42, 771-785
Historique
Acosta-Alba I, Aubin J, Cariou S, Haffray P, Quittet B, Vandeputte M. 2015. The FilDor programme: combining genetic selection and environmental impact assessment of fish breeding farms. Courrier de l'Environnement de l'INRA. 65, 49-57
Benhaim D, Guyomard R, Chatain B, Quillet E, Begout ML. 2013. Effect of domestication history on behavioural traits in juvenile brown trout (Salmo trutta L.). Appl Anim Behav Sci. 147, 235-242.
Berthelot, Bernard M, Boussasha M, Quillet E, Guyomard R, Genet C, Guiguen Y. 2014. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 5, 3657
Besson M., Komen H., Aubin J., de Boer I.J.M., PoelmanM., Quillet E., Vancoillie C., Vandeputte M., van Arendonk J.A.M. 2014. Economic values of growth and feed efficiency in fish farming under density and nitrogen output limitations: an African catfish case study. J Anim Sci. 92, 5394-5405
Canario L., Mignon-Grasteau S., Dupont-Nivet M., Phocas F. 2013. Genetics of behavioural adaptation of livestock to farming conditions. Animal 7, 357-377
Canario L, Mignon-Grasteau S, Dupont-Nivet M, Phocas F. 2013. Génétique de l'adaptation comportementale des animaux aux conditions d'élevage: le cas des productions bovines, porcines, avicoles et aquacoles. INRA Productions Animales 26, 35-50
Castro R, Takizawa F, Chaara W, Lunazzi A, Dang TH, Koellner B, Quillet E, Six A, Fischer U, Boudinot P. 2013. Contrasted TCRβ diversity of CD8(+) and CD8(-) T cCells in rainbow trout. Plos One 8, e60175
Castro R., Jouneau L., Pham HP., Bouchez O., Giudicelli V., Lefranc MP., Quillet E., Benmansour A., Cazals F., Six A., Fillatreau S., Sunyer O., Boudinot P. 2013. Teleost Fish Mount Complex Clonal IgM and IgT Responses in Spleen upon Systemic Viral Infection. Plos Pathogens 9, e1003098
Cosson JF, Galan M, Bard E, Razzauti M, Bernard M, Morand S, Brouat C, Dalecky A, Bâ K, Charbonnel N, Vayssier-Taussat M. 2015. Detection of Orientia sp. DNA in rodents from Asia, West Africa and Europe. Parasit Vectors. 8, 172
Costa C., F. Antonucci, C. Boglione, P. Menesatti, M. Vandeputte, B. Chatain. 2013. Automated sorting for size, sex and skeletal anomalies of cultured seabass using external shape analysis. Aquacultural Engineering, 52, 58-64
Costa C., Negretti P., Vandeputte M., Pallottino F., Antonucci F., Aguzzi J., Bianconi G., Menesatti P. 2014. Innovative automated landmark detection for food processing: the backwarping approach. Food and Bioprocess Technology. 7, 2291-2298
Costa C, Vandeputte M, Antonucci F, Boglione C, de Verdal H, Chatain B. 2015. Are trunk lateral line anomalies and disoriented scale pattern in European seabass (Dicentrarchus labrax L.) influenced by genetics ? Aquaculture. 448, 38-42
Daulé S, Vandeputte M, Vergnet A, Guinand B, Grima L, Chatain B. 2014. Effect of selection for fasting tolerance on feed intake, growth and feed efficiency in the European sea bass Dicentrarchus labrax. Aquaculture. 420-421, S42-S49
de Verdal H, Rosario W, Vandeputte M , Muyalde N , Morissens P, Baroiller JF, Chevassus B. 2014. Response to selection for growth in an interspecific hybrid between Oreochromis mossambicus and O-niloticus in two distinct environments. Aquaculture. 430, 159-165
de Verdal H, Vandeputte M, Pepey E, Vidal MO, Chatain B. 2014. Individual growth monitoring of Europena sea bass larvae by image analysis and microsatellite genotyping. Aquaculture. 434, 470-475
Ferrari S, Chatain B, Cousin X, Leguay D, Vergnet A, Vidal MO, Vandeputte M, Bégout ML. 2014. Early individual electronic identification of sea bass using RFID microtags: a first example of early phenotyping of sex-related growth. Aquaculture. 426-427, 165-171
Geurden I, Borchert P, Balasubramanian MN, Schrama JW, Dupont-Nivet M, Quillet E, Kaushik SJ, Panserat S, Médale F. 2013. The positive impact of the early-feeding of a plant-based diet on its future acceptance and utilisation in rainbow trout. Plos One 8, e83162
Haffray P., Bugeon J., Rivard Q., Quittet B., Puyo S., Allamellou J.M., Vandeputte M., Dupont-Nivet M. 2013. Genetic parameters of in-vivo prediction of carcass, head and fillet yields by internal ultrasound and 2D external imagery in large rainbow trout (Oncorhynchus mykiss). Aquaculture. 410–411, 236-244
Karahan B., Chatain B., Chavanne H., Vergnet A., Bardon A., Haffray P., Dupont-Nivet M.,Vandeputte M. 2013. Heritabilities and correlations of deformities and growth-related traits in the European sea bass (Dicentrarchus labrax, L) in four different sites. Aquaculture Research 44, 289-299
Kileh-Wais M., Elsen JM., Vignal A., Feves K., Vignoles F., Fernandez X., Manse H., Davail S., André JM., Bastianelli D., Bonnal L., Filangi O., Baéza E., Guéméné D., Genêt C., Bernadet MD., Dubos F., Marie-Etancelin C. 2013. Detection of QTL controlling metabolism, meat and liver quality traits of the overfed interspecific hybrid mule duck. Journal of Animal Science 91, 588-604
Lazzarotto V, Corraze G, Leprevost A, Quillet E, Dupont-Nivet M, Médale F. 2015. Three-year breeding cycle of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet, totally free of marine resources: consequences for reproduction, fatty acid composition and progeny survival. PLoS One. 10, e0117609
Le Boucher R, Vandeputte M, Dupont-Nivet M, Quillet E, Ruelle F, Vergnet A, Kaushik S, Allamellou JM, Médale F, Chatain B. 2013. Genotype by diet interactions in European sea bass (Dicentrarchus labrax L.): Nutritional challenge with totally plant-based diets. J Anim Sci. 91, 44-56
Le Boucher R., Dupont-Nivet M., Laureau S., Labbé L., Geurden I., Médale F., Chatain B., Vandeputte M., Quillet E. 2013 Transitions alimentaires en pisciculture : l’amélioration génétique peut faciliter l’utilisation d’aliments à base de végétaux. INRA Productions Animales 26, 317-326
Lefrevre F, Cardinal M, Bugeon J, Labbe L, Médale F, Quillet E. 2015. Selection for muscle fat content and triploidy affect flesh quality in pan-size rainbow trout, Oncorhynchus mykiss. Aquaculture. 448, 569-577
McKenzie DJ, Vergnet A, Chatain B, Vandeputte M, Desmarais E, Steffensen JF5, Guinand B. 2014. Physiological mechanisms underlying individual variation in tolerance of food deprivation in juvenile European sea bass, Dicentrarchus labrax. J Exp Biol. 217, 3283-3292
Médale F, Le Boucher R, Dupont-Nivet M, Quillet E, Aubin J, Panserat S. 2013. Des aliments à base de végétaux pour les poissons d’élevage. Productions animales. 26, 303- 316
Millot S, Péan S, Labbé L, Kerneis T, Quillet E, Dupont-Nivet M, Bégout ML. 2014. Assessment of genetic variability of fish personality traits using rainbow trout isogenic lines. Behav Genet. 44, 383-393
Palaiokostas C, Bekaert M, Taggart JB, Gharbi K, McAndrew BJ, Chatain B, Penman DJ, Vandeputte M. 2015. A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax). Genet Sel Evol. 47, 68
Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet E, Yao J, Thorgaard GH, Salem M, Rexroad CEIII. 2013. A resource of single-nucleotide polymorphisms in rainbow trout generated byRAD tag sequencing of doubled haploids. Molecular Ecology Resources.14, 588-596
Perrier C, Bagliniere JL, Evanno G. 2013. Understanding admixture patterns in supplemented populations: a case study combining molecular analyses and temporally explicit simulations in Atlantic salmon. Evol Applic. 6, 218-230
Perrier C, Guyomard R, Bagliniere JL, Nikolic N, Evanno G. 2013. Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency. Ecol Evol. 3, 2334-2349
Phocas F, Agabriel J , Dupont-Nivet M, Geurden I, Médale F, Mignon-Grasteau S, Gilbert H, Dourmad J-Y. 2014. Phenotyping for feed efficiency and its components, a need to improve the efficiency of livestock production. INRA Prod Anim. 27, 235-247
Quillet E, Krieg F, Dechamp N, Hervet C, Bérard A, Le Roy P, Guyomard R, Prunet P, Pottinger TG. 2014. QTL for magnitude of the plasma cortisol response to confinement in rainbow trout. Animal Genetics. 45, 223-234
Valdivia K, Jouanno E, Volff J-N, Galiana-Arnoux D, Guyomard R, Helary L, Mouro B, Fostier A, Quillet E, Guiguen Y. 2014. High temperature increases the masculinization rate of the all-female (XX) rainbow trout "mal" population governed masculinized phenotype. PLoS ONE. 9, e113355
Valdivia K., Mourot B., Jouanno E., Volff J-N., Galiana-Arnoux D., Guyomard R., Cauty C., Collin B., Rault P., Helary L., Fostier A., Quillet E., Guiguen Y. 2013. Sex differentiation in an all-female (XX) rainbow trout population with a genetically governed masculinization phenotype. Sexual Development 7, 196-206
Vandeputte M, Haffray P. 2014. Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals. Front Genet. 5, 432
Vandeputte M, Garouste R., Dupont-Nivet M., Haffray P., Vergnet A., Chavanne H., Laureau S., Ron T.B., Pagelson G., Mazorra C., Ricoux R., MarquesP., Gameiro M., Chatain B. 2014. Multi-site evaluation of the rearing performances of 5 wild populations of European sea bass (Dicentrarchus labrax). Aquaculture. 424-425, 239- 248
Verrier ER., Dorson M., Mauger S., Torhy C., Ciobotaru C., Hervet C., Dechamp N., Genêt C., Boudinot P., Quillet E. 2013. Resistance to a Rhabdovirus (VHSV) in Rainbow Trout: Identification of a Major QTL Related to Innate Mechanisms. Plos One 8, e55302
Verrier ER, Ehanno A, Biacchesi S, Le Guillou S, Dechamp N, Boudinot P, Bremont M, Quillet E. 2013. Lack of correlation between the resistances to two rhabdovirus infections in rainbow trout. Fish Shellfish Immunol. 35, 9-17
Yano A, Nicol B, Jouanno E, Quillet E, Fostier A, Guyomard R, Guiguen Y. 2013. The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids. Evol Applic. 6, 486-496
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