. Fao, Contributing to food security and nutrition for all, 2016.

R. L. Naylor, R. W. Hardy, D. P. Bureau, A. Chiu, M. Elliott et al., Feeding aquaculture in an era of finite resources, Proceedings of the National Academy of Sciences, vol.106, pp.15103-15110, 2009.

M. Jobling, Fish nutrition research: past, present and future, Aquaculture International, vol.24, pp.767-786, 2015.

D. M. Gatlin, F. T. Barrows, P. Brown, K. Dabrowski, T. G. Gaylord et al., Expanding the utilization of sustainable plant products in aquafeeds: a review, Aquaculture Research, vol.38, pp.551-579, 2007.

B. Torstensen, M. Espe, M. Sanden, I. Stubhaug, R. Waagbø et al., Novel production of Atlantic salmon (Salmo salar) protein based on combined replacement of fish meal and fish oil with plant meal and vegetable oil blends, Aquaculture, vol.285, pp.193-200, 2008.

S. Panserat, G. Hortopan, E. Plagnes-juan, C. Kolditz, M. Lansard et al., Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver, Aquaculture, vol.294, pp.123-131, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01193491

G. M. Turchini, B. E. Torstensen, and W. K. Ng, Fish oil replacement in finfish nutrition, Reviews in Aquaculture, vol.1, pp.10-57, 2009.

M. J. Leaver, L. A. Villeneuve, A. Obach, L. Jensen, J. E. Bron et al., Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar), BMC Genomics, vol.9, p.299, 2008.

L. Benedito-palos, J. C. Navarro, A. Sitjà-bobadilla, J. G. Bell, S. Kaushik et al., High levels of vegetable oils in plant protein-rich diets fed to gilthead sea bream (Sparus aurata L.): growth performance, muscle fatty acid profiles and histological alterations of target tissues, The British Journal of Nutrition, vol.100, pp.992-1003, 2008.

D. Santis, C. Bartie, K. L. Olsen, R. E. Taggart, J. B. Tocher et al., Nutrigenomic profiling of transcriptional processes affected in liver and distal intestine in response to a soybean meal-induced nutritional stress in Atlantic salmon (Salmo salar), Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, vol.15, pp.1-11, 2015.

M. Gu, T. M. Kortner, M. Penn, A. K. Hansen, and Å. Krogdahl, Effects of dietary plant meal and soya-saponin supplementation on intestinal and hepatic lipid droplet accumulation and lipoprotein and sterol metabolism in Atlantic salmon (Salmo salar L.), The British Journal of Nutrition, vol.111, pp.432-444, 2014.

J. B. Taggart, J. E. Bron, S. A. Martin, P. J. Seear, B. Høyheim et al., A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray, Journal of Fish Biology, vol.72, p.19125201, 2008.

L. Tacchi, C. J. Secombes, R. Bickerdike, M. A. Adler, C. Venegas et al., Transcriptomic and physiological responses to fishmeal substitution with plant proteins in formulated feed in farmed Atlantic salmon (Salmo salar), BMC Genomics, vol.13, p.363, 2012.

S. Panserat, C. Kolditz, N. Richard, E. Plagnes-juan, F. Piumi et al., Hepatic gene expression profiles in juvenile rainbow trout (Oncorhynchus mykiss) fed fishmeal or fish oil-free diets, The British Journal of Nutrition, vol.100, pp.953-967, 2008.

F. Geay, S. Ferraresso, J. L. Zambonino-infante, L. Bargelloni, C. Quentel et al., Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet, BMC Genomics, vol.12, p.522, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01019771

S. Morais, T. Silva, O. Cordeiro, P. Rodrigues, D. R. Guy et al., Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar), BMC Genomics, vol.13, p.448, 2012.

M. Frøystad, E. Lilleeng, A. Bakke-mckellep, K. Vekterud, G. I. Hemre et al., Gene expression in distal intestine of Atlantic salmon (Salmo salar L.) fed genetically modified soybean meal, Aquaculture Nutrition, vol.14, pp.204-214, 2008.

S. Morais, R. B. Edvardsen, D. R. Tocher, and J. G. Bell, Transcriptomic analyses of intestinal gene expression of juvenile Atlantic cod (Gadus morhua) fed diets with Camelina oil as replacement for fish oil, Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, vol.161, pp.283-293, 2012.

J. A. Calduch-giner, A. Sitjà-bobadilla, G. C. Davey, M. T. Cairns, S. Kaushik et al., Dietary vegetable oils do not alter the intestine transcriptome of gilthead sea bream (Sparus aurata), but modulate the transcriptomic response to infection with Enteromyxum leei, BMC Genomics, vol.13, p.470, 2012.

A. W. Kendall, E. H. Ahlstrom, H. G. Moser, H. G. Moser, W. J. Richards et al., Early life history stages of fishes and their characters, Ontogeny and Systematics of Fishes, vol.1, pp.11-24, 1984.

A. Woynarovich, G. Hoitsy, and T. Moth-poulsen, Small-scale rainbow trout farming: Food and Agriculture Organization of the United Nations. Fisheries and Aquaculture Technical Paper No. 561, 2011.

V. Lazzarotto, G. Corraze, A. Leprevost, E. Quillet, M. Dupont-nivet et al., 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, vol.10, 2015.

. Aoac, Official Methods of Analysis of the AOAC international 17th edition, 2000.

B. V. Mccleary, V. Solah, and T. S. Gibson, Quantitative measurement of total starch in cereal flours and products, Journal of Cereal Science, vol.20, pp.51-58, 1994.

T. Stadtman, Preparation and assay of cholesterol and ergosterol, Methods in enzymology, vol.3, pp.392-394, 1957.

J. Folch, M. Lees, and G. Sloane-stanley, A simple method for the isolation and purification of total lipids from animal tissues, The Journal of Biological Chemistry, vol.226, pp.497-509, 1957.

N. C. Shantha and R. G. Ackman, Nervonic acid versus tricosanoic acid as internal standards in quantitative gas chromatographic analyses of fish oil longer-chain n-3 polyunsaturated fatty acid methyl esters, Journal of Chromatography: Biomedical Applications, vol.533, pp.1-10, 1990.

V. Lazzarotto, G. Corraze, L. Larroquet, D. Mazurais, and F. Médale, Does broodstock nutritional history affect the response of progeny to different first-feeding diets? A whole-body transcriptomic study of rainbow trout alevins, The British Journal of Nutrition, vol.115, pp.2079-2092, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01483272

S. Morais, J. Pratoomyot, B. E. Torstensen, J. B. Taggart, D. R. Guy et al., Diet × genotype interactions in hepatic cholesterol and lipoprotein metabolism in Atlantic salmon (Salmo salar) in response to replacement of dietary fish oil with vegetable oil, The British Journal of Nutrition, vol.106, pp.1457-1469, 2011.

P. A. Olsvik, K. K. Lie, A. Jordal, T. O. Nilsen, and I. Hordvik, Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon, BMC Molecular Biology, vol.6, p.21, 2005.

M. V. Matz, R. M. Wright, and J. G. Scott, No control genes required: Bayesian analysis of qRT-PCR data, PloS One, vol.8, 2013.

D. A. Hosack, G. Dennis, B. T. Sherman, H. C. Lane, and R. A. Lempicki, Identifying biological themes within lists of genes with EASE, Genome Biology, vol.4, 2003.

F. J. Gatesoupe, Z. Infante, J. L. Cahu, C. Bergot, and P. , Ontogeny, development and digestive physiology of fish larvae, pp.197-212, 2001.

L. Boucher, R. Quillet, E. Vandeputte, M. Lecalvez, J. M. Goardon et al., Plant-based diet in rainbow trout (Oncorhynchus mykiss Walbaum): Are there genotype-diet interactions for main production traits when fish are fed marine vs plant-based diets from the first meal, Aquaculture, vol.321, pp.41-48, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000179

M. Li and J. Leatherland, Temperature and ration effects on components of the IGF system and growth performance of rainbow trout (Oncorhynchus mykiss) during the transition from late stage embryos to early stage juveniles, General and Comparative Endocrinology, vol.155, pp.668-679, 2008.

D. Baum, R. Laughton, J. Armstrong, and N. Metcalfe, The effect of temperature on growth and early maturation in a wild population of Atlantic salmon parr, Journal of Fish Biology, vol.67, pp.1370-1380, 2005.

F. Médale and S. Kaushik, Protein sources in feed for farmed fish, Cahiers Agricultures, vol.18, pp.103-111, 2009.

G. Corraze and S. Kaushik, Lipid nutrition and fish oil replacement by vegetable oils in pisciculture, Cahiers Agricultures, vol.18, pp.112-118, 2009.

K. Brix, A. Dunkhorst, K. Mayer, and S. Jordans, Cysteine cathepsins: cellular roadmap to different functions, Biochimie, vol.90, pp.194-207, 2008.

V. Turk, B. Turk, and D. Turk, Lysosomal cysteine proteases: facts and opportunities, The EMBO Journal, vol.20, pp.4629-4633, 2001.

H. A. Chapman, R. J. Riese, and G. Shi, Emerging roles for cysteine proteases in human biology, Annual Review of Physiology, vol.59, pp.63-88, 1997.

L. C. Hsing and A. Y. Rudensky, The lysosomal cysteine proteases in MHC class II antigen presentation, Immunological Reviews, vol.207, pp.229-241, 2005.

R. J. Riese, R. N. Mitchell, J. A. Villadangos, G. Shi, J. T. Palmer et al., Cathepsin S activity regulates antigen presentation and immunity, Journal of Clinical Investigation, vol.101, pp.2351-2363, 1998.

J. Zhou, L. Li, and Z. Cai, Identification of putative cathepsin S in mangrove red snapper Lutjanus argentimaculatus and its role in antigen presentation, Developmental & Comparative Immunology, vol.37, pp.28-38, 2012.

E. Lilleeng, M. H. Penn, Ø. Haugland, C. Xu, A. M. Bakke et al., Decreased expression of TGF-?, GILT and T-cell markers in the early stages of soybean enteropathy in Atlantic salmon, Salmo salar L.). Fish & Shellfish Immunology, vol.27, pp.65-72, 2009.

F. Kokou, S. Adamidou, I. Karacostas, and E. Sarropoulou, Sample size matters in dietary gene expression studies-A case study in the gilthead sea bream (Sparus aurata L.), Aquaculture Reports, vol.3, pp.82-87, 2016.

R. Capasso, I. Matias, B. Lutz, F. Borrelli, F. Capasso et al., Fatty acid amide hydrolase controls mouse intestinal motility in vivo, Gastroenterology, vol.129, pp.941-951, 2005.

Å. Krogdahl, M. Penn, J. Thorsen, S. Refstie, and A. M. Bakke, Important antinutrients in plant feedstuffs for aquaculture: an update on recent findings regarding responses in salmonids, Aquaculture Research, vol.41, pp.333-344, 2010.

S. Panserat, F. Médale, C. Blin, J. Breque, C. Vachot et al., Hepatic glucokinase is induced by dietary carbohydrates in rainbow trout, gilthead seabream, and common carp, American Journal of Physiology-Regulatory, Integrative and Comparative Physiology, vol.278, pp.1164-1170, 2000.

T. Atsumi, T. Nishio, H. Niwa, J. Takeuchi, H. Bando et al., Expression of inducible 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase/PFKFB3 isoforms in adipocytes and their potential role in glycolytic regulation, Diabetes, vol.54, pp.3349-3357, 2005.

C. Brauge, G. Corraze, and F. Médale, Effect of dietary levels of lipid and carbohydrate on growth performance, body composition, nitrogen excretion and plasma glucose levels in rainbow trout reared at 8 or 18?C, Reproduction Nutrition Development, vol.35, pp.277-290, 1995.
URL : https://hal.archives-ouvertes.fr/hal-00899750

A. Couto, P. Enes, H. Peres, and A. Oliva-teles, Effect of water temperature and dietary starch on growth and metabolic utilization of diets in gilthead sea bream (Sparus aurata) juveniles, Comparative Biochemistry and Physiology Part A: Molecular and Integrative Physiology, vol.151, pp.45-50, 2008.

K. M. Phillips, D. M. Ruggio, J. I. Toivo, M. A. Swank, and A. H. Simpkins, Free and esterified sterol composition of edible oils and fats, Journal of Food Composition and Analysis, vol.15, pp.123-142, 2002.

A. Sitjà-bobadilla, S. Peña-llopis, P. Gómez-requeni, F. Médale, S. Kaushik et al., Effect of fish meal replacement by plant protein sources on non-specific defence mechanisms and oxidative stress in gilthead sea bream (Sparus aurata), Aquaculture, vol.249, pp.387-400, 2005.

S. Kaushik, J. Cravedi, J. Lalles, J. Sumpter, B. Fauconneau et al., Partial or total replacement of fish meal by soybean protein on growth, protein utilization, potential estrogenic or antigenic effects, cholesterolemia and flesh quality in rainbow trout, Oncorhynchus mykiss, Aquaculture, vol.133, pp.257-274, 1995.

N. Richard, G. Mourente, S. Kaushik, and G. Corraze, Replacement of a large portion of fish oil by vegetable oils does not affect lipogenesis, lipid transport and tissue lipid uptake in European seabass (Dicentrarchus labrax L.), Aquaculture, vol.261, pp.1077-1087, 2006.

J. S. Morey, J. C. Ryan, and F. M. Van-dolah, Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR, Biological Procedures Online, vol.8, pp.175-193, 2006.

S. Morais, J. Pratoomyot, J. B. Taggart, J. E. Bron, D. R. Guy et al., Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis, BMC Genomics, vol.12, p.255, 2011.

F. W. Allendorf and G. H. Thorgaard, Tetraploidy and the evolution of salmonid fishes, Turner BJ, editor. Evolutionary genetics of fish, pp.1-53, 1984.

U. Limtipsuntorn, Y. Haga, H. Kondo, I. Hirono, and S. Satoh, Microarray analysis of hepatic gene expression in juvenile Japanese flounder Paralichthys olivaceus fed diets supplemented with fish or vegetable oils, Marine Biotechnology, vol.16, p.24052493, 2014.

M. Bell, J. Dick, and A. Porter, Pyloric ceca are significant sites of newly synthesized 22:6 n?3 in rainbow trout (Oncorhynchus mykiss), Lipids, vol.38, pp.39-44, 2003.

J. Fonseca-madrigal, J. G. Bell, and D. R. Tocher, Nutritional and environmental regulation of the synthesis of highly unsaturated fatty acids and of fatty-acid oxidation in Atlantic salmon (Salmo salar L.) enterocytes and hepatocytes, Fish Physiology and Biochemistry, vol.32, pp.317-328, 2006.

B. E. Torstensen and D. R. Tocher, Fish oil replacement and alternative lipid sources in aquaculture feeds, pp.405-438, 2011.

J. Fonseca-madrigal, V. Karalazos, P. J. Campbell, J. G. Bell, and D. R. Tocher, ) influence of dietary palm oil on growth, tissue fatty acid compositions and fatty acid metabolism in liver and intestine in rainbow trout (Oncorhynchus mykiss), Aquaculture Nutrition, vol.11, pp.241-250, 2005.

S. Morais, O. Monroig, X. Zheng, M. J. Leaver, and D. R. Tocher, Highly unsaturated fatty acid synthesis in Atlantic salmon: characterization of ELOVL5-and ELOVL2-like elongases, Marine Biotechnology, vol.11, p.19184219, 2009.

D. R. Tocher, Metabolism and functions of lipids and fatty acids in teleost fish, Reviews in Fisheries Science, vol.11, pp.107-184, 2003.

H. Sprecher, D. L. Luthria, B. Mohammed, and S. P. Baykousheva, Reevaluation of the pathways for the biosynthesis of polyunsaturated fatty acids, Journal of Lipid Research, vol.36, pp.2471-2477, 1995.

G. M. Turchini and D. S. Francis, Fatty acid metabolism (desaturation, elongation and ?-oxidation) in rainbow trout fed fish oil-or linseed oil-based diets, The British Journal of Nutrition, vol.102, pp.69-81, 2009.