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Menu Logo Principal AgroParisTech Université Paris-Saclay


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


Recent publications

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.

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

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.

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, 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

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.

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.

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. in press.   

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.


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

Previous publications

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