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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech


Recent publications

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


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. In press
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.  In press

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

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

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

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

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. Aquacultur. 520, 734986


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


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.


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


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


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

Zou J, Gorgoglione B, Taylor NG, Summathed T, Lee PT, Panigrahi A, Genet C, Chen YM, Chen TY, Ul Hassan M, Mughal SM, Boudinot P, Secombes CJ. 2014. Salmonids have an extraordinary complex type I IFN system: Characterization of the IFN locus in Rainbow trout Oncorhynchus mykiss reveals two novel IFN subgroups. J Immunol. 193, 2273-2286