2023

1. Basso, B, Bertrand, C., Boudry, P., Bouffartigue, B., Charvolin-Lemaire, E., Danvy, S. Duclos, D., Ducos, A., Gourdine, J-L., Haffray, P., Hazard, D., Journaux, L., Laloë, D., Lauvie, A., Lenoir, H., Naves, M., Rouger, R., Vandeputte, M., Verrier, E., 2023. Étude concernant l’actualisation, la définition et les exemples de valorisation des races locales, rustiques, menacées. Volet 1 – Races menacées : Actualisation des listes de races menacées, extension de la réflexion aux abeilles et aux espèces aquacoles. INRAE, Etude Races locales, Volet 1 – Races menacées, janvier 2023. https://agriculture.gouv.fr/races-menacees-dabandon-pour-lagriculture
2. Montero, D., Carvalho, M., Terova, G., Fontanillas, R., Serradell, A., Ginés, R., Tuset, T., Acosta, F., Rimoldi, R., Bajek, A., Haffray, P., Allal, F., Torrecillas, S., 2023. Nutritional innovations in superior European sea bass (Dicentrarchus labrax) genotypes: implication on fish performance and feed utilization. Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739486
3. 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 as a strong candidate gene for VNN resistance in European sea bass. Genet Sel Evol 55, 30. https://doi.org/10.1186/s12711-023-00805-2
4. Jourdan, A., Morvezen, R., Enez, F., Haffray, P., Lange, A., Vétois, E., Allal, F., Phocas, F., Bugeon, J., Degremont, L., Boudry, P., 2023. Potential of genomic selection for production and quality traits in mixed-family breeding designs for the Pacific oyster Crassostrea gigas. Aquaculture. https://doi.org/10.1016/j.aquaculture.2023.739878 
5. Lagarde, H., Lallias, D., Patrice, P., Prchal, M., François, Y., D’Ambrosio, J., Segret, E., Perez-Acin, A., Cachelou, F., Haffray, P., Dehaullon, A., Dupont-Nivet, M., Phocas, F., 2022. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits. GSE, 55-39. https://doi.org/10.1186/s12711-023-00811-4
6. Torrecillas, S., Rimoldi, R., Montero, D., Serradell, A., Acosta, F., Fontanillas, R., Allal, F., Haffray, P., Bajek, A., 2023. Genotype x nutrition interactions in European sea bass (Dicentrarchus labrax): effects on intestinal microbiota and gut health. Accepted in Animals. https://doi.org/10.1016/j.aquaculture.2023.739639
7. Serradell, A., Montero, D., Terova., G, Rimoldi, S., Makol, A., Acosta, F., Bajek, A., Haffray, P., Allal, F., Torrecillas, S., 2023. Functional additives in selected European sea bass (Dicentrarchus labrax) genotype : Effects on stress response and gill antioxidant response to hydrogen proxide (H2O2) treatment. Animals, 13(14), 2265.  https://doi.org/10.3390/ani13142265
8. Rimoldi, S., Montero, D., Torrecillas, S., Serradell, A., Acosta, F., Haffray, P., Hostins, B., Fontanillas, R., Allal, F., Bajek, A., Terova, G., 2023. Genetically superior European sea bass (Dicentrarchus labrax) and nutritional innovations: Effects of functional feeds on fish immune response, disease resistance, and gut microbiota. Aquaculture Reports 33, 101747. https://doi.org/10.1016/j.aqrep.2023.101747
9. ​​​​​​​Kuhl, H., Euclide, P.T., Klopp, C., Cabau, C., Zahm, M., Roques, C., Iampietro, C., Kuchly, C., Donnadieu, C., Feron, Parrinello, H., Poncet, C., Jaffrelo, L., Confolent, C., Wen, M., Herpin, A., Jouanno, E., Bestin, A., Haffray, P., Morvezen, R., Rocha de Almeida, T., Lecocq, T., Schaerlinger, B., Chardard, D., Żarski, D., Larson, W., Postlethwait, J.H., Timirkhanov, S., Kloas, W., Wuertz, S., Stöck, M., Guiguen, Y., 2023. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. bioRxiv preprint doi: https://doi.org/10.1101/2023.11.13.566804

2022

1.  Anthony Estienne, Ophélie Bernardi, Christelle Ramé, Maxime Reverchon, Serge Tricoire, Pascal Froment, Joëlle Dupont;, 2022. The influence of selection in wild pheasant (Phasianus colchicus) breeding on reproduction and the involvement of the chemerin system. Poult. Sci. DOI: 10.1016/j.psj.2022.102248
2. Bernardi O., Reverchon M., Estienne A., Baumard Y., Ramé C., Brossaud A., Combarnous Y., Froment P. et Dupont J.; 2022, Chicken white egg chemerin as a tool for genetic selection for egg weight and hen fertility, Frontiers, doi: 10.3389/fphys.2022.1012212
3. Besson, M., Rombout, N., Salou, G., Vergnet, A., Cariou, S., Bruant, J-S., 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, Volume 24, 101132. https://doi.org/10.1016/j.aqrep.2022.101132
4. Charrier, M., Lumineau, S., Georgelin, M., Meurisse, M., Palme, R., Angelier, F., Cornilleau, F., Constantin, P., Coustham, V., Nicolle, C., Bertin, A., Darmaillacq, A.-S., Dickel, L., Guémené, D., Calandreau, L., Houdelier, C., 2022. Prenatal maternal stress is associated with behavioural and epigenetic changes in Japanese quail. Psychoneuroendocrinology. https://doi.org/10.1016/j.psyneuen.2022.105661
5. 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., 2022. Whole‐genome sequencing identifies interferon induced protein IFI6 as a strong candidate gene for VNN resistance in European sea bass. bioRxiv, https://doi.org/10.1101/2022.05.31.494209
6. Duclos R., Delanoue E., Dockes AC., Journaux L., Sourdioux M., Bidanel JP., 2022. Les modifications ciblées du génome appliquées aux animaux d'élevage : à la croisée des controverses. INRAE Prod. Anim. 35 (1), 61-72. https://doi.org/10.20870/productions-animales.2022.35.1.5524
7. Fauchet, L., Bosc, S., Bestin, A., Haffray, P., Menchi, O., Evanno, G., Vandeputte, M., 2022. Large scale application of DNA parentage assignment to monitor the Atlantic salmon (Salmo salar) reintroduction program in the Garonne-Dordogne basin. Submitted to Conservation Genetics.
8. Restoux, G., Rognon, X., Vieaud, A., Guémené, D., Petitjean, F., Rouger, R., Brard-Fudulea, S., Lubac-Paye, S., Chiron, G., Tixier-Boichard, M., 2022. Managing genetic diversity in breeding programs of small populations : the case of French local chicken breeds. Genetics Selection Evolution. 54:56. https://doi.org/10.1186/s12711-022-00746-2
9. Vandeputte, M., Corraze, C., 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. Submitted to Aquaculture Reports

2021

1. 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 characterized using three imaging technologies in rainbow trout, Oncorhynchus mykiss. Front. Genet. 12:639223. http://doi.org/10.3389/fgene.2021.639223
2. 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, 788. https://doi.org/10.1186/s12864-021-08062-7
3. Bernardi O, Estienne A, Reverchon M, Bigot Y, Froment P, Dupont J. Adipokines in metabolic and reproductive functions in birds: An overview of current knowns and unknowns. Mol Cell Endocrinol. 2021 Aug 20;534:111370. doi: 10.1016/j.mce.2021.111370. Epub 2021 Jun 23. PMID: 34171419
4. Bestin, A., Brunel, O., Malledant, A., Debeuf, B., Benoît, P., 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 Siberia sturgeon Acipenser baerii. Aquaculture. 540:736725. https://doi.org/10.1016/j.aquaculture.2021.736725
5. Boudry, P., Allal, F., Aslam, M.L., Bargelloni, L., Beane, T.P., Brard-Fudulea, S., Brieuc, M.S.O., Calbolih, F.C.F., Gilbey, J., Haffray, P., Lamy, J.B., Morvezen, R., Purcell, C., Prodöhl, P.A., Vandeputte, M., Waldbiesern, G.C., Sonesson, A.K., Houston, R.D., 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 Reports, 20. https://doi.org/10.1016/j.aqrep.2021.100700
6. De Verdal, H., Haffray, P., Douchet, V., Vandeputte, M., 2021. Impact of a divergent selective breeding programme on individual feed conversion ratio in Nile tilapia Oreochromis niloticus measured in groups by video-recording. Aquaculture 548. https://doi.org/10.1016/j.aquaculture.2021.737572 Agritrop
7. Estienne A, Reverchon M, Partyka A, Bourdon G, Grandhaye J, Barbe A, Caldas-Silveira E, Rame C, Niżański W, Froment P, Dupont J. Chemerin Impairs In Vitro Testosterone Production, Sperm Motility, and Fertility in Chicken: Possible Involvement of Its Receptor CMKLR1. Cells. 2020 Jul 1;9(7):1599. doi: 10.3390/cells9071599. PMID: 32630345; PMCID: PMC7408590. Pubmed
8. Geffroy, B., Besson, M., Sánchez-Baizán, N., Clota, F., Goikoetxea, A., Sadoul, B., Ruelle, F., Blanc, M.-O., Parrinello, H., Hermet, S., 2021. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system. Proceedings of the National Academy of Sciences 118. Pubmed
9. 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. Optimisation 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. 12:665920. https://doi.org/10.3389/fgene.2021.665920 Pubmed
10. Griot, R., Phocas, F., Brard-Fudulea, S., Morvezen, R., Bestin, A., Haffray, P., François, Y., Morin, T., Poncet, C., Vergnet, A., Cariou, S., Brunier, J., Bruant, J-S., Peyrou, B., Vandeputte, M., 2021. Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a 57K SNP chip. Aquaculture. https://doi.org/10.1016/j.aquaculture.2020.735930 ResearchGate
11. Katy, P., 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. https://doi.org/10.1111/eva.13308 ResearchGate
12. Kuhl, H., Guiguen, Y., Höhne, C., Kreuz, E., Du, K., Klopp, C., Lopez-Roques, C., Yebra-Pimentel, E.S., Ciorpac, M., Gessner, J., Holostenco, D., Kleiner, W., Kohlmann, K., Lamatsch, D.K., Prokopov, D., Bestin, A., Bonpunt, E., Debeuf, B., Haffray, P., Morvezen, R., Patrice, P., Suciu, R., Dirks, R., Wuertz, S., Kloas, W., Schartl, M., Stöck, M. 2021. A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. Philosophical Transactions B. 376 : 20200089.20200089. https://doi.org/10.1098/rstb.2020.0089 pubmed
13. Ledoré, Y., Bestin, A., Haffray, P., Morvezen, R., Alix, M., Schaerlinger, B., Fontaine, P., Chardard, D., 2021. Sex identification in Eurasian perch (Perca fluviatilis) using ultrasonography. Aquaculture Research, 52, 6046-6051  https://doi.org/10.1111/are.15465 ResearchGate
14. Prado, E., Eklouh-Molinier, C., Enez, F., Causeur, D., Blay, C., Dupont-Nivet, M., Labbé, L., Petit, V., Moreac, A., Taupier, G., Haffray, P., Bugeon, J., Corraze, G., Nazabal, V., 2021. Prediction of fatty acids composition in the rainbow trout Oncorhynchus mykiss by using Raman micro-spectroscopy. Analytica Chimica Acta., https://doi.org/10.1016/j.aca.2021.339212 Dumas
15. Rodde, C., de Verdal, H., Vandeputte, M., Allal, F., Nati, J., Besson, M., Blasco, F.R., Benzie, J.A., McKenzie, D.J., 2021. An investigation of links between metabolic rate and feed efficiency in European sea bass Dicentrarchus labrax. Journal of Animal Science 99, skab152. WorldFish
16. Saura, M., Caballero, A., Santiago, E., Fernández, A., Morales-González, E., Fernández, J., Cabaleiro, S., Martínez, P., Millán, A., Palaiokostas, C., Kocour, M., Aslam, L., Houston, R., Prchal, M., Bargelloni, L., Tzokas; K., Bruant, J-S., Haffray, P, Villanueva, B., 2021. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selection programmes. Genet Sel Evol 53, 85. https://doi.org/10.1186/s12711-021-00680-9
17. Vandeputte, M., Bestin, A., Fauchet, L., Allamellou, J-M., 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. Aquatic Living Resources, 34 (7). https://doi.org/10.1051/alr/2021008 ResearchGate

2020

1. Allal, F., Grio, R., Phocas, F., Brard-Fudulea, S., Morvezen, R., Bestin, A., Haffray, P., François, Y., Morin, T., Ponce, C., Vergnet, A., Cariou, S., Brunier, J., Bruant, J-S., Peyrou, B., Gagnaire, P-A., Vandeputte, M., 2020. Genotyping of 4 European sea bass families with the DlabCHIP SNPs genotyping array. SEANOE. https://doi.org/10.17882/75696
2. Allal, F., Griot, R., Phocas, F., Brard-Fudulea, S., Morvezen, R., Bestin, A., Haffray, P., François, Y., Morin, T., Ponce, C., Vergnet, A., Cariou, S., Brunier, J., Bruant, J-S., Peyrou, B., Gagnaire, P-A., Vandeputte, M., 2020. Axiom DlabCHIP, a 57K SNPs genotyping array for European sea bass (Dicentrarchus labrax): array design and genetic map. SEANOE. https://doi.org/10.17882/75680
3. D’Ambrosio, J., Morvezen, R., Brard-Fudulea, S., Bestin, A., Poncet, C., Haffray, P., Dupont-Nivet, M., Phocas, F., 2020. Genetic architecture and genomic selection of female reproduction traits in rainbow trout. BMC Genomics, 21:558,  https://doi.org/10.1186/s12864-020-06955-7
4. Feron, R., Zahm, M., Cabau, C., Klopp, C., Roques, C., Bouchez, O., Eché, C., Valière, S., Donnadieu, C., Haffray, P., Bestin, A., Morvezen, R., Acloque, H., Euclide, P., Wen, M., Jouanno, E., Schartl, M., Postlethwait, J. H., Schraidt, C., Christie, M., Larson, W., Herpin, A., Guiguen, Y., 2020.  Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. Molecular Ecology Resources. 20:531–543.
5. 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. Submitted to Scientific Reports.https://doi.org/10.1101/2020.04.28.057240.
6. Griot, R., Phocas, F., Brard-Fudulea, S., Morvezen, R., Bestin, A., Haffray, P., François, Y., Morin, T., Poncet, C., Vergnet, A., Cariou, S., Brunier, J., Bruant, J-S., Peyrou, B., Vandeputte, M., 2020. Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a 57K SNP chip. Aquaculture. https://doi.org/10.1016/j.aquaculture.2020.735930
7. Kuhl, H., Guiguen, Y., Höhne ; K., Kreuz, E., Du, K., Klopp, K., Lopez-Roques, C., Yebra-Pimentel, E. S., Ciorpac, M., Gessner ; J., Holostenco, D., Kleiner, W., Kohlmann, K., Lamatsch, D. D., Prokopov, D., Bestin, A., Bonpunt, E., Deboeuf S., Haffray, P., Morvezen, R., Patrice, P., Suciu, R., Dirks, R., Wuertz, S., Kloas, W., Schartl, M., Stöc, M., 2020. A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosome. Phil. Trans. R. Soc. B.
8. Piégu, B., Arensburger, P., Beauclair, L., Chabault, M., Raynaud, E., Coustham, V., Brard, S., Guizard, S., Burlot, T., Le Bihan-Duval, E., Bigot, Y., 2020. Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species. Genomics 112, 1660–1673. https://doi.org/10.1016/j.ygeno.2019.10.004 Pubmed
9. Prchal, M., Kocour, K., 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. DOI: 10.1016/j.aquaculture.2020.734993
10. Smits, M., Enez, F., Ferraresso, S., Dalla Rovere, G., Vétois, E., Auvray, J-F., Genestout, L., Mahla, R., Arcangeli, G., Paillard, C., Haffray, P., Bargelloni, L., 2020. Potential for genetic improvement of resistance to Perkinsus olseni in the manilla clam Ruditaped Philippinarum, using DNA-parentage assignment and mass spawning. Front. Vet. Sci..  doi: 10.3389/fvets.2020.579840
11. 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 for the estimation of genetic gain. Aquaculture, 519, 1-11, https://doi.org/10.1016/j.aquaculture.2019.734877 
12. Zhao, J., Prchal, M., Palaiokostas, C., Houston, R., Kause, A., Bugeon, J., Vandeputte, M., Vergnet, A., Bestin, A., Vesely, T., Pokorova, D., Piackova, V., Pojezdal, L., Genestout, L., Gela, D., Kroupova, H., Kocour, M., 2020. Genetic relationship between koi herpesvirus disease resistance and production traits inferred from sibling performance in Amur mirror carp. Aquaculture. 520: 734986. ResearchGate

2019

1. 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 1 effective size of experimental and commercial rainbow trout lines undergoing selective breeding. Genet Sel Evol (2019) 51:26. https://doi.org/10.1186/s12711-019-0468-4
2. Feron, R., Zahm, M., Cabau, C., Klopp, C., Roques, C., Bouchez, O., Eché, C., Valière, S., Donnadieu, C., Haffray, P., Bestin, A., Morvezen, R., Acloque, H., Euclide, P., Wen, M., Jouanno, E., Schartl, M., Postlethwait, J.H., Schraidt, C., Christie, M., Larson, W., Herpin, A., Guiguen, Y., 2019. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. Molecular Ecology Resources Resources. DOI: 10.1111/1755-0998.13133
3. 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 QTL identified after a natural disease outbreak in a French farm. Anim Genet. doi.org/10.1111/age.12777
4. Griot R., Allal F., Brard-Fudulea S., Morvezen R., Haffray P., Phocas F., Vandeputte M., 2019. APIS: An Auto-Adaptive Parentage Inference Software tolerant to missing parents. Molecular Ecology Resources, volume 2 (20), 579-590 : doi.org/10.1111/1755-0998.13103
5. Leroy, G., Gicquel, E., Boettcher, P., Besbes, B., Furre, S., Fernandez, J., Danchin-Burge, C., Alnahhas, N., Baumung, R. 2019. Coancestry rate’s estimate of effective population size for genetic variability monitoring. Conservation Genetics Resources. June 2019. DOI: 10.1007/s12686-019-01092-0
6. Piégu, B., Arensburger, P., Beauclair, L., Chabault, M., Raynaud, E., Coustham, V., Brard-Fudulea, S., Guizard, S., Burlot, T., Le Bihan-Duval, E., Bigot, Y., 2020. Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species. Genomics 112, 1660–1673. https://doi.org/10.1016/j.ygeno.2019.10.00
7. Thélie, A., Bailliard, A., Seigneurin, F., Zerjal, T., Tixier-Boichard, M., Blesbois, E., 2019. Chicken semen cryopreservation and use for the restoration of rare genetic resources. Poultry Science 98(1), 447–455, https://doi.org/10.3382/ps/pey360. A correction has been published: Poultry Science 98(1), Volume 98, p 500, https://doi.org/10.3382/ps/pey441
8. Vandeputte, M., Bugeon, J., Bestin, A., Desgranges, A., Allamellou, J-M., Tyran, A-S, Allal, F., Dupont-Nivet, M., Haffray, P., 2019. First evidence of realized selection response on fillet yield in fish: a demonstration in rainbow trout Oncorhynchus mykiss, using indirect or sib selection. Frontiers in Genetics, 10: 1-13. https://doi.org/10.3389/fgene.2019.01225
9. Vignal, A., Boitard, S., Thébault, N., Guiguigbaza‐Kossigan Dayo, Yapi‐Gnaore, V. Issaka Youssao Abdou, K., Berthouly‐Salazar, C., Pálinkás‐Bodzsár, N., Guémené, D., Thibaud‐Nissen, F., Warren, W-C., Tixier‐Boichard, M., Rognon, X., 2019. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Molecular Ecology Resources. 00: 1–18. doi.org/10.1111/1755-0998.13017

2018

1. Aslam, M. L., Carraro, R., Bestin, A., Sophie Cariou, S., Sonesson, A. K., Bruant, J.-S., Haffray, P., and Luca Bargelloni, L. M., T. H. E. (2018). Genetics of resistance to pasteurellosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. BMC genetics 19 (1), 43. doi.org/10.1186/s12863-018-0631-x.
2. 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. 2018 Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding. (Genetics Selection Evolution.)
3. Fraslin, C., Dechamp, N., Bernard, M., Krieg, F., Hervet, C., Guyomard, R., Esquerré, D., Barbieri, J., Kuchly, C., Duchaud, E., Boudinot., Rochat, T., Bernardet J.F., Quillet E., Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions. 2018. Genetics Selection Evolution. 16; 50(1):60. doi: 10.1186/s12711-018-0431-9.
4. 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. 486:175-183.
5. 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 QTL identified after a natural disease outbreak in a French farm. 2019. Anim Genet. https://doi.org/10.1111/age.12777
6. Haffray, P., Enez, F., Bugeon, J., Chapuis, H., Chatain, B., Dupont-Nivet, M., 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.
7. Harney, E., Lachambre, S., Roussel, S., Huchette, S., Enez, F., Morvezen, R., Haffray, P., Boudry, P., 2018. Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone (Haliotis tuberculata). Aquaculture 491, 105–113.
8. Labbe, C., Haffray, P., Mingant, C., Quittet, B., Diss, B., Tervit, R., Adams, S., Rimond, F., Suquet, M., 2018. Cryopreservation of Pacific oyster (Crassostrea gigas) larvae: revisiting the practical limitations and scaling up the procedure for application to hatchery. Aquaculture, 488, 227-234. doi.org/10.1016/j.aquaculture.2018.01.023.
9. Leroy, G., Gicquel, E., Boettcher, P., Besbes, B., Furre, S., Fernandez, J., Danchin-Burge, C., Alnahhas, N., Baumung, R. 2018. Coancestry rate’s estimate of effective population size for genetic variability monitoring. Conservation Genetics Resources (In Press, accepted at the 17/09/2018).
10. Palaiokostas, C., Cariou, S., Bestin, A., Bruant, J.-S., Haffray, P., Morin, T., Cabon, J., Allal, F., Vandeputte, M., Houston, R., 2018. Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing. Genetics Selection Evolution. 8;50(1):30.  doi.org/10.1186/s12711-018-0401-2.
11. Prchal, M., Bestin, A., Bugeon, J., Vandeputte, M., 2018. The genetics of overwintering performance in two-year old common carp and its relation to performance until market size. Plos One.
12. Prchal, M., Bugeon, J., Vandeputte, M., Kause, A., Vergnet, A., Zhao, J., 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. Frontiers in Genetics. 9:283
13. Prchal, M, Bugeon, J, Vandeputte, M, Vergnet, A, Haffray, P. Zhao, J, Gela, D, Genestout, L, Bestin, A. , Kause, A, Kocour, M. 2018. Investigation of indirect selection criteria for genetic improvement of slaughter yields in market size common carp. Front. Genet. 9:283, Genet. 9:283, doi: 10.3389/fgene.2018.00283.
14. Rouger, R., Brard-Fudulea, S., Thébault, N., Pitel, F., Vignal, A., Bed’hom, B., Rognon, X., Lumineau, S., Guémené, D. 2019. Développement d’un panel de marqueurs SNP pour détecter l’hybridation entre la Caille des Blés et la Caille Japonaise. XIIIème Journées de la Recherche Avicole (20-21 Mars 2019, Tours) https://doi.org/10.3382/ps/pey441
15. Thélie, A., Bailliard, A., Seigneurin, F., Zerjal, T., Tixier-Boichard, M., Blesbois, E., 2019. Chicken semen cryopreservation and use for the restoration of rare genetic resources. Poultry Science 98(1), 447–455. https://doi.org/10.3382/ps/pey360. A correction has been published: Poultry Science 98(1), Volume 98, p 500 https://doi.org/10.3382/ps/pey441
16. Vignal, A., Boitard, S., Thébault, N., Guiguigbaza‐Kossigan Dayo, Yapi‐Gnaore, V. Issaka Youssao Abdou, K., Berthouly‐Salazar, C., Pálinkás‐Bodzsár, N., Guémené, D., Thibaud‐Nissen, F., Warren, W-C., Tixier‐Boichard, M., Rognon, X., 2019. A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Molecular Ecology Resources. 00: 1–18. doi.org/10.1111/1755-0998.13017

2017

1. Alnahhas, N.,Berri, C., Chabault, M., Bourin, M., Arnould, C., Le Bihan-Duval, E. 2017. Combined effect of divergent selection for breast muscle ultimate pH and dietary amino acids on chicken performance, physical activity and meat quality. Animal. 11(2): 335 –344.
2. Doan Q.K., Vandeputte M., Chatain B., Haffray P.,Vergnet A., Breuil G., Allal 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
3. Fraslin, C.,Dupont-Nivet, M., Haffray, P., Bestin, A.,and Vandeputte, M., 2018. How to genetically increase fillet yield in fish: New insights from simulations based on field data. Aquaculture 486, 175-183.
4. Guinand, B., Vandeputte, M., Dupont-Nivet, M., Vergnet, A., Haffray, P.,Chavanne, H., Chatain, B., 2017. Metapopulation patterns of additive and non-additive genetic variance in the sea bass (Dicentrarchus labrax). Ecology and Evolution. DOI:10.1002/ece3.2832.
5. Harney, E., Lachambre, S., Roussel, S., Huchette, S., Enez, F., Morvezen, R., Haffray, P., Boudry, P., 2018. Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata. Aquaculture 491, 105–113.
6. Nolasco-Alzaga, H.R., Perez-Enriquez, R., Palacios-Mechetnov, E., Haffray, P.,2017. Quantitative genetic parameters for growth and fatty acid content in the hemolymph of Litopenaeus vannamei. Aquaculture, 482, 17-23. DOI: doi: 10.1016/j.Aquaculture.2017.09.015
7. Vandeputte, M., Puledda, A., Tyran, A. S., 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 470, 40-49.

2016

1. Alnahhas, N.,Berri, C., Chabault, M., Chartrin, P., Boulay, M.,Bourin, MC., Le Bihan-Duval, E. 2016. Genetic parameters of white striping in relation to body weight, carcass composition, and meat quality traits in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle. BMC Genet. 19; 17:61.
2. Alnahhas, N.,Berri, C., Chabault, M., Bourin, M., Arnould, C., Le Bihan-Duval, E. 2017. Combined effect of divergent selection for breast muscle ultimate pH and dietary amino acids on chicken performance, physical activity and meat quality. Animal.11(2): 335 –344.
3. Bohling, J., Haffray, P., Berrebi, P., 2016. Genetic diversity and population structure of domestic brown trout (Salmo trutta) in France. Aquaculture.Volume 462, 1-9.
4. Chapuis H.,Pincent, C., Colleau, J-J., 2016. Optimizing selection with several constraints in poultry breeding. Journal of Animal Breeding and Genetics, 133: 3-12.
5. Chavanne, H., Janssen, K., Hofherr, J., Contini, F., Haffray, P., Aquatrace Consortium, Komen, H., Nielsen, E.E., Bargelloni, L.2016. A comprehensive survey on selective breeding programs and seed market in the European aquaculture fish industry. Aquaculture International, dOI 10.1007/s10499-016-9985-0.

2015

1. Broquet, T., Barranger, A., Billard, E., Bestin, A., Berger, R., Honnaert G., Viard, F., 2015. The Size Advantage Model of Sex Allocation in the Protandrous Sex-Changer Crepidula fornicata: Role of the Mating System, Sperm Storage, and Male Mobility. The American Naturalist. 186 (3), 404-420.
2. Chapuis H.,Pincent, C., Colleau, J-J., 2016. Optimizing selection with several constraints in poultry breeding. Journal of Animal Breeding and Genetics, 133: 3-12.
3. Nguyen,TMD., Seigneurin,F.,Froment P, Combarnous Y, Blesbois, E., 2015) The 5’-AMP-Activated ProteinKinase (AMPK) Is Involved in the Augmentation of Antioxidant Defenses in Cryopreserved Chicken Sperm. PLoS ONE 10(7): e0134420. doi:10.1371/journal.pone.0134420
4. Verrier E., Audiot A., Bertrand C., Chapuis H.,Charvolin E.,Danchin-Burge C.Danvy S., Gourdine J.L., Gaultier P., Guémené D.,Laloë D., Lenoir H., Leroy G., Naves M., Patin S., Sabbagh, M.2015. Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to 10 species. Animal Genetic Resources. AGR150417. 57: 105-118.

2014

1. Verrier E., Audiot A., Bertrand C., ChapuisH.,Charvolin E.,Danchin-Burge C.Danvy S., Gourdine J.L., Gaultier P., Guémené D.,Laloë D., Lenoir H., Leroy G., Naves M., Patin S., Sabbagh, M.2015. Assessing the risk status of livestock breeds: a multi-indicator method applied to 178 French local breeds belonging to 10 species. Accepté pour publication dans Animal Genetic Resources. AGR150417.
2. Vandeputte, M., Garouste, R., Dupont-Nivet, M., Haffray, P.,Vergnet, A., Chavanne, H., Laureau, S., Ron, T.B., Pagelson, G., Mazorra, C., Ricoux, R., Marques, P., 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.
3. Guatteo, R., Guémené, D.2014. Sources of known and/or potential pain in farm animals. Advances in Animal Biosciences, (2014), 5:3, pp 319–332. & The Animal Consortium 2014
4. Lapègue, S., Harrang, E., Heurtebise, S., Flahauw, E., Donnadieu, C., Gayral., G., Ballenghien, M., Genestout., L., Barbotte, L., Mahla, R., Haffray, P., Klopp, C,2014. Development of SNP genotyping arrays in two non-model shellfish species. Mol. Ecol. Resources, 14, 820–830. doi: 10.1111/1755-0998.12230.
5. Le Roy, P., Chapuis, H., Guémené, D.2014. Sélection génomique : quelles perspectives pour les filières avicoles ? INRA Prod. Anim., 27 (5), 331-336.
6. Suquet M, Labbé C, Puyo S, Mingant C, Quittet B,et al. (2014) Survival, Growth and Reproduction of Cryopreserved Larvae from a Marine Invertebrate, the Pacific Oyster (Crassostrea gigas). PLoS ONE 9(4): e93486. doi:10.1371/journal.pone.0093486.
7. 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. Frontiers in Genetics, Livestock Genomics, 5, Article 432. doi: 10.3389/fgene.2014.00432.

2013

1. Collewet, G., Bugeon, J., Idier, J., Quellec, S., Quittet, B.,Cambert, M., Haffray, P.2013. Rapid quantification of muscle fat content and subcutaneous adipose tissue in fish using MRI. Food Chemistry,138, 2008–2015.
2. Haffray, P.,Bugeon, J, Rivard, Q., Quittet, B., Puyo, S., Allamelou, 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 imageryin large rainbow trout (Oncorhynchus mykiss). Aquaculture.410-411, 236-244.
3. Karahan Nomm 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. 289-299
4. Kileh-Wais, M., Elsen, J.M., Vignal, A., Vignoles, F., Feves, K., Fernandez, X., Manse, H., Davail, S., Andre, J.M., Bastianelli, D., Bonnal, L., Filangi, O., Baéza, E.;Guémené, D., Genêt, C., Bernadet, M.D., Dubos, F., Marie-Etancelin, C. 2013. Detection of QTL controlling metabolism, meat quality, and liver quality traits of the overfed interspecific hybrid mule duck. Journal of Animal Science. Vol. 91, 588-604
5. Seigneurin, F.,Grasseau, I., Chapuis, H.,Blesbois, E. 2013. An Efficient Method of Guinea Fowl Sperm Cryopreservation. Poultry Science. 92, 2988-2996.

2012

1. Chabault M., Baéza E., Gigaud V., Chartrin P., Chapuis H., Boulay M., Arnould C., D’Abbadie F., Berri C., Le Bihan-Duval E., 2012. Analysis of a slow-growing line reveals wide genetic variability of carcass and meatquality-related traits. BMC Genetics, 13:90.
2. Fauvel, C., Boryshpolets, S., Cosson, J., Leedy, J.W., Labbé, C., Haffray, P., Suquet, M., 2011. Improvement of seabass sperm chilled conservation by the use of a cell culture medium. J. Appl. Ichthyol., 28, 961–966.
3. Guatteo, R.; Levionnois, O.; Fournier, D.; Guémené, D.; Latouche, K.; Leterrier, C.; Mormede, P.; Prunier, A.; Servière, J.; Terlouw, C.; Le Neindre, P.; 2012. Minimising pain in farm animals: the 3S approach- 'Suppress, Substitute, Soothe' . Animal , Vol. 6 (8) , 1261-1274.
4. Haffray, P., Malha, R., Ould Taleb Sidi, M., Prista, N., Hassan, M., Castelnaud, G., Karahan-Nomm, B., Gamsiz, K., Sadek, S., Bruant, JS., Balma, P., Bonhomme, F., 2012. Very high genetic fragmentation in a large marine fish, the meagre Argyrosomus regius (Sciaenidae, Perciformes): Impact of reproductive migration, oceanographic barriers and ecological factors. Aquat. Living Resour., 25, 173–183.
5. Haffray, P., Pincent, C., Chapuis, H., Mazeiraud, E., Petit, V., Rault, P., Bugeon, J., Chatain, B., Vandeputte, M., Dupont-Nivet, M., 2012. Negative genetic correlations between production traits and head or bony tissues in large all-female rainbow trout (Oncorhynchus mykiss). Aquaculture, 368–369, 145-152.
6. Haffray, P., Vandeputte, M., Petit, V., Pincent, P., Chatain, B., Chapuis, H., Coudurier, B., Quillet, E., Dupont-Nivet, M., 2012. Minimizing non-genetic maternal effect in salmonid families mixed since eyed stages and a posteriori DNA-pedigreed. Livestock Science, 150, 170-178.
7. Hocquette, J.F.; Capel, C.; David, V.; Guémené, D.; Bidanel, J.; Ponsart, C.; Gatinel, P.L.; Le Bail, P.Y.; Monget, P.; Mormede, P.; Barbezant, M.; Guillou, F.; Peyraud, J.L.; 2012. Objectives and applications of phenotyping network set-up for livestock. Animal Science Journal , Vol. 83 (7) , 517-528; open access : doi : 10.1111/j.1740-0929.2012.01015.x.
8. Kileh-Wais, M.; Elsen, J.M.; Vignal, A.; Vignoles, F.; Feves, K.; Fernandez, X.; Manse, H.; Davail, S.; Andre, J.M.; Bastianelli, D.; Bonnal, L.; Filangi, O.; Baéza, E.; Guémené, D.; Genêt, C.; Bernadet, M.D.; Dubos, F.; Marie-Etancelin, C.; 2013. Detection of QTL controlling metabolism, meat quality, and liver quality traits of the overfed interspecific hybrid mule duck. Journal of Animal Science , Vol. 91, 588-604.
9. Le Boucher R., Dupont-Nivet M., Vandeputte M., Kerneïs T., Goardon L., Labbé L., Chatain B., Borthaire M.- J., Larroquet L., Médale F., Quillet E. 2012. From Individual Foraging Diversity to Breeding to Adapt to Dietary Shifts in Carnivorous Fish Farming. PLoS ONE 7(9): e44898. doi:10.1371/journal.pone.0044898.
10. Suquet, M., Cosson, J., Donval, A., Labbé, C., Boulais, M., Haffray, P., Bernard, I., Fauvel, C., 2012. Marathon vs sprint racers: an adaptation of sperm characteristics to the reproductive strategy of Pacific oyster, turbot and seabass. J. Appl. Ichthyol. 28, 956–960.
11. Suquet, M., Le Mercier, A., Rimond, F., Mingant, C., Haffray, P., Labbe, C., 2012. Setting tools for the early assessment of the quality of thawed Pacific oyster (Crassostrea gigas) trochophores and D-larvae. Theriogenology 78, 462–467.

2011

1. De Jong, I.C., Guémené, D., 2011. Major welfare issues in broiler breeders. World's Poultry Science Journal, 67: 73-81.
2. Fauvel, C., Boryshpolets, S., Cosson, J., Leedy, J.W., Labbé, C., Haffray, P., Suquet, M., 2011. Improvement of seabass sperm chilled conservation by the use of a cell culture medium. Submitted to Journal of Applied Ichthyology.
3. Guatteo, R., Levionnois, O., Fournier, D., Guémené, D., Latouche, K., Leterrier, C., Mormède, P., Prunier, A., Servière, J., Terlouw, C., Le Neindre, P., 2011. Minimising Pain in Farm Animals: the 3S Approach: “Suppress, Substitute, Soothe”. Accepté pour publication dans Animal.
4. Guémené, D., Shi, Z., Guy, G., 2012. Chapter 8 : Waterfowl production and housing systems worldwide. In : Alternative systems for poultry – Health, welfare and Productivity. Edt Sandiland, V., & Hocking, P.M. www.cabi.org. 128 – 154.
5. Hocquette, J.F., Capel, C., David, V., Guémené, D., Bidanel, J., Barbezant, M., Gastinel, P.L., Le Bail, P.Y., Monget, P., Mormède, P., Ponsart, C., Guillou, F., Peyraud J.L., 2011. The objectives and applications of an organized network of phenotyping for livestock. Accepté pour publication dans Animal.
6. Kansaku, N., Guémené, D., Nakamura, A., Uchida, M., 2011. Sequence Characterization of K-gene Linked Region in Various Chicken Breeds Japanese. Poult. Sci., Vol. 48: 181-186.

2010

1. Arnaud, I.; Gardin, E.; Sauvage, E.; Bernadet, M.D.; Couty, M.; Guy, G.; Guémené, D.; 2010. Behavioral and adrenal responses to various stressors in mule ducks from different commercial genetic selection schemes and their respective parental genotypes. Poultry Science, Vol. 89, 1097-1109.
2. Bugeon, J., Lefèvre, F., Cardinal, M., Uyanik, A., Davenel, A., Haffray, P., 2010. Flesh quality in large rainbow trout with high or low fillet yield. J. Muscle Foods 21, 702-721.
3. Calandreau, L.; Constantin, P.; Bertin, A.; Desmedt, A.; Arnould, C., Guémené, D.; Nowak, R.; Boissy, A.; Leterrier, C.; 2010. Enhancement of spatial reversal learning following one week of stress in Japanese quail. Behavioural Brain Research, 217: 104-110.
4. Dupont-Nivet, M., Chevassus, B., Mauger, S., Haffray, P., Vandeputte, M., 2010. Side effects of sexual maturation on heritability estimates in rainbow trout (Oncorhynchus mykiss). Aquaculture Research, 41, e878-e880.
5. Dupont-Nivet, M., Karahan-Nomm, B., Vergnet, A., Merdy, O., Haffray, P., Chavanne, H., Chatain, B., Vandeputte, M., 2010. Genotype by Environment interactions for growth in European seabass (Dicentrarchus labrax) are large when growth rate rather than weight is considered. Aquaculture 306, 365-368.
6. Guibert, F.; Richard-Yris, M.A.; Lumineau, S.; Kotrschal, K.; Guémené, D.; Bertin, A.; Mostl, E.; 2010. Social Instability in Laying Quail: Consequences on Yolk Steroids and Offspring\'s Phenotype. Plos One , Vol. 5 (11) ; open access : ://000284467200006.
7. Moe, R.O.; Guémené, D.; Bakken, M.; Larsen, H.J.S.; Shini, S.; Lervik, S.; Skjerve, E.; Michel, V.; Tauson, R.; 2010. Effects of housing sconditions during the rearing and laying period on adrenal reactivity, immune response and heterophil to lymphocyte (H/L) ratios in laying hens ; 4: 10. Animal , 1709-1715.
8. Peruzzi, S., Wiborg-Dahle, S., Haffray, P., Chatain, B., Primicerio, R., 2010. Body shape variation in meiotic gynogenetic and triploid sea bass, Dicentrarchus labrax. Aquatic Living Resource, 23 (3), 297-302.
9. Suquet M., Labbé C., Brizard R., Donval A., Le Coz J.R., Quere C., Haffray P., 2010. Changes of motility, ATP content, morphology and fertilisation capacity during the movement phase of diploid and tetraploid Pacific oyster (Crassostrea gigas) sperm. Theriogenology, 74 (1), 111-117.