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In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual_ feed), standing stock (Qstock), and daily feed distributed (Qdaily_ feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily_ feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily_ feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily_ feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.

In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual-feed), standing stock (Qstock), and daily feed distributed (Qdaily-feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily-feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily-feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily-feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.

In sea cage farming, fish are exposed to seasonal variations of water temperature, and these variations can differ from one location to another. A small increase in water temperature does not only stimulate growth of the fish (until an optimal level) but also lowers dissolved oxygen concentration in water. Dissolved oxygen may then become a rearing constraint during the production cycle if the oxygen requirement of fish is higher than the supply. The impact of this constraint on production parameters (stocking density of cages and/or batch rotation) and thus on economic profit of a farm will depend on both local thermal regime and growth potential of the fish. Increased growth is one of the most important traits in a breeding objective to increase production capacity and profitability. We used a bioeconomic model of seabass reared in cages to calculate the economic value (EV) of increasing thermal growth coefficient (TGC) by selection in different conditions of average temperature (Tm) and amplitude of temperature variation (Ta). Tm and Ta values were taken from different locations in the eastern and western Mediterranean. Results show that increasing TGC has two consequences: (i) fast growing fish reach harvest weight earlier, which increases the number of batches that can be produced per year, and (ii) fast growing fish have higher daily feed intake and, consequently, higher daily oxygen consumption. To balance the oxygen demand and availability in a cage, a farmer might have to reduce the average stocking density, resulting in fewer fish produced per batch. Consequently, EV of TGC is positive when Tm is 19.5 °C or 21 °C, when an increase in number of batches produced compensates for the decrease in stocking density. EV of TGC is negative or null in areas where Tm is closer to 18 °C because the increase in number of batches produced cannot compensate for the decrease in stocking density. Our results show, for the first time, the importance of variation in ambient

World fish farm production is growing rapidly. However, the supply of fishmeal and fish oil, the major ingredients of fish diets, has reached a limit because of the limits in the exploitation of wild fish stocks that cannot be increased to meet a growing demand. The main response, especially in Europe, has been the progressive replacement of fishmeal and fish oil by plant products. However, the strong reduction of growth and sometimes survival of fish fed highly substituted diets has urged research on the genetic potential for adaptation to plant-based diets. Recent results clearly demonstrate that fish can be selected for their capacity to grow when fed plant-based diets, even though the underlying mechanisms remain unknown. Genotype-diet interactions have been shown, indicating that the best performers differ according to the diet. Such interactions may make the management of breeding programmes difficult, as progeny may be reared with a diet differing from the one used to select the breeders. Simulations of the expected genetic gain according to different scenarios can help manage selection programmes for sea bass and rainbow trout, the main farmed species in France. Using both selective breeding and optimized diets provide the opportunity to increase sustainability of fish farming, whilst maintaining product quality., La production mondiale de poissons d’élevage augmente rapidement alors que les principaux ingrédients des aliments pour poissons (huiles et farines de poisson issues de la pêche) sont en quantité désormais insuffisante pour répondre à la demande. Cette situation, en Europe notamment, a conduit au remplacement progressif des produits marins par des matières premières végétales. Mais les taux de substitution élevés provoquent des réductions importantes des performances (croissance, voire survie) chez les espèces d’élevage de haut niveau trophique, à forts besoins en protéines et lipides. L’étude du potentiel d’adaptation de plusieurs de ces espèces à des aliments fortement ou totalement substitués (sans huiles ni farines de poisson) a révélé qu’il est possible de sélectionner au sein des populations d’élevage des individus à forte capacité de croissance avec des régimes à base de végétaux. Les mécanismes à l’origine de cette adaptation restent à identifier. Les analyses montrent aussi que les groupes les plus performants varient en fonction de l’aliment (marin ou substitué). Ces interactions génotype-aliment peuvent compliquer la gestion d’un programme de sélection si les reproducteurs sont sélectionnés avec un aliment différent de celui utilisé pour élever leurs descendants. Des simulations du progrès génétique attendu dans différents scénarios alimentaires permettent d’identifier quelques pistes pour optimiser la sélection chez la truite arcen-ciel et le bar, espèces majeures de la pisciculture d’eau douce et marine en France. La combinaison judicieuse de programmes d’amélioration génétique et de parcours alimentaires raisonnés pourrait aider la filière piscicole à évoluer vers un mode de production moins dépendant des ressources naturelles marines, tout en continuant à fournir des produits de qualité au consommateur

World aquaculture is growing (+ 8% per year) to meet the increasing demand of fish for human consumption that capture by fisheries can no longer cover. Consequently, the need for aquafeed and feedstuffs is rising while volumes of fishmeal and fish oil, the traditional aquafeed ingredients, remain stable. More and more fishmeal and fish oil are substituted by plant products. Between 80 and 95% of fish meal can be replaced by a combination of plant protein sources providing the indispensable amino acids in sufficient quantity to meet the fish needs. Beyond this substitution rate, feed intake, feed efficiency and growth rate decrease and metabolic changes are observed despite the diets containing all the required nutrients. Fish oil can be replaced by a mix of vegetable oils without deleterious effect on fish growth and health, provided that the diet supplies essential fatty acids. Fatty acids requirements vary with species according to their capacity to synthesize EPA and DHA. However, in all species, fish oil substitution results in a reduction in the flesh content of these omega 3fatty acids. Research must continue to further reduce the reliance of aquaculture on fishery resources while ensuring an efficient fish production of high quality products with limited environmental impacts., L'aquaculture mondiale se développe (+ 8% par an) pour répondre à une demande croissante des consommateurs que les captures de pêche ne peuvent plus couvrir. Les besoins en aliments piscicoles et donc en matières premières s’accroissent, alors que les volumes de farines et huiles de poisson, ingrédients traditionnels des aliments aquacoles, ne peuvent augmenter. Selon les espèces, 80 à 95% de la farine de poisson peut être substituée par un mélange de sources protéiques végétales apportant les acides aminés indispensables en quantité suffisante pour couvrir les besoins des poissons. Au-delà de ce taux de remplacement, on observe une baisse de la consommation d'aliment, de l'efficience alimentaire et de la croissance, bien que les aliments contiennent les nutriments nécessaires aux poissons. Quant à l'huile de poisson, elle peut être remplacée jusqu’à 80 ou 100% par des huiles végétales sans effet délétère sur la croissance et la santé des poissons, à condition que le régime apporte en quantité suffisante les acides gras essentiels à la couverture des besoins, qui diffèrent selon l'espèce : contrairement aux poissons marins, les salmonidés disposent en effet d’une relative capacité de synthèse d’acides gras longs polyinsaturés omega 3 à partir de l’acide linoléique. La conséquence majeure est une baisse de la teneur de ces acides gras dans la chair. Les recherches doivent se poursuivre pour affranchir encore davantage l'aquaculture des produits de la pêche, en choisissant des matières premières alternatives qui garantissent une production piscicole efficace, des produits de haute qualité et des impacts environnementaux limités.

Aquaculture of carnivorous species has strongly relied on fish meal and fish oil for feed formulation; however, greater replacement by terrestrial plant-based products is occurring now. This rapid change in dietary environment has been a major revolution and has to be taken into consideration in breeding programs. The present study analyzes potential consequences of this nutritional tendency for selective breeding by estimating genetic parameters of BW and growth rates estimated by the thermal growth coefficient (TGC) over different periods with extremely different diets. European sea bass (Dicentrarchus labrax L.) from a factorial cross (1,526 fish) between 25 sires and 9 dams were used to estimate heritabilities and genotype by diet interaction. Starting 87 d after fertilization (2.5 g), one-half of the sea bass were fed a diet containing marine products (M), and the other one-half were fed a totally plant-based (PB) diet (without any fish meal or fish oil). The fish were individually tagged, reared in a recirculated system, and genotyped at 13 microsatellites to rebuild parentage of individuals. Body weight and TGC were measured for 335 d until fish fed the M diet reached 108.3 g of BW. These traits were significantly less in fish fed the PB diet (P < 0.05) in the very first stages after the dietary shift, but the difference in TGC between diets rapidly disappeared (P > 0.1). Survival was significantly less in fish fed the PB diet (PB = 64.7%, M = 93.7% after 418 d, P < 0.05). This work identified moderate heritabilities (0.18 to 0.46) for BW with both diets and high genetic correlations between diets (0.78 to 0.93), meaning low genotype by diet interactions, although diets were extremely different. Heritabilities of TGC (0.11 to 0.3) were less than for BW as well as genetic correlations between diets (0.43 to 0.64). Using such extremely different diets, predicted BW gains in different scenarios indicated that selecting fish for growth on a marine diet should be

Sustainable aquaculture, which entails proportional replacement of fish-based feed sources by plant-based ingredients, is impeded by the poor growth response frequently seen in fish fed high levels of plant ingredients. This study explores the potential to improve, by means of early nutritional exposure, the growth of fish fed plant-based feed. Rainbow trout swimup fry were fed for 3 weeks either a plant-based diet (diet V, V-fish) or a diet containing fishmeal and fish oil as protein and fat source (diet M, M-fish). After this 3-wk nutritional history period, all V- or M-fish received diet M for a 7-month intermediate growth phase. Both groups were then challenged by feeding diet V for 25 days during which voluntary feed intake, growth, and nutrient utilisation were monitored (V-challenge). Three isogenic rainbow trout lines were used for evaluating possible family effects. The results of the V-challenge showed a 42% higher growth rate (P = 0.002) and 30% higher feed intake (P = 0.005) in fish of nutritional history V compared to M (averaged over the three families). Besides the effects on feed intake, V-fish utilized diet V more efficiently than M-fish, as reflected by the on average 18% higher feed efficiency (P = 0.003). We noted a significant family effect for the above parameters (P,0.001), but the nutritional history effect was consistent for all three families (no interaction effect, P.0.05). In summary, our study shows that an early shortterm exposure of rainbow trout fry to a plant-based diet improves acceptance and utilization of the same diet when given at later life stages. This positive response is encouraging as a potential strategy to improve the use of plant-based feed in fish, of interest in the field of fish farming and animal nutrition in general. Future work needs to determine the persistency of this positive early feeding effect and the underlying mechanisms.

Application of DNA parentage assignment for commercial selection in aquaculture is still rare. An experiment was performed to quantify and to minimize maternal effects on growth in rainbow trout. Six hundred families were reared until 198 day post fertilization (dpf) according to two different procedures. In the first procedure (NORM), all families were pooled at eyed stage. In the second procedure (MIN), where maternal effects due to differences in egg size were expected to be minimal, the spawns were divided into sub-groups with similar mean egg weight at eyed stage. These sub-groups were then pooled when they achieved the same mean body length (147 dpf). Genetic parameters were estimated for body weight, body length and condition factor at 198 dpf, with 2964 fish assigned to their parents using microsatellites. Significant maternal effects were observed in the NORM group for body weight and body length (m(2) = 0.08 +/- 0.03). The heritability of body weight was 0.16 +/- 0.07 in the NORM group and 0.36 +/- 0.06 in the MIN group, in which maternal effects were not significant It is concluded that, when eggs of different females are mixed at eyed stage, maternal effects persist at least until 198 dpf. The proposed procedure efficiently limits maternal effects, substantially increasing the heritability for growth, and therefore the expected selection response. (C) 2012 Elsevier B.V. All rights reserved.

Background There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout. Results A QTL design (5 full-sib families, about 200 F2 progeny each) was produced from a cross between F0 grand-parents previously selected during two generations for a high or a low cortisol response after a standardized confinement stress. When fish were about 18 months old (near 204 g body weight), individual progeny were submitted to two successive hyper-osmotic challenges (30 ppt salinity) 14 days apart. Plasma chloride and sodium concentrations were recorded 24 h after each transfer. After the second challenge, fish were sacrificed and a gill index (weight of total gill arches corrected for body weight) was recorded. The genome scan was performed with 196 microsatellites and 85 SNP markers. Unitrait and multiple-trait QTL analyses were carried out on the whole dataset (5 families) through interval mapping methods with the QTLMap software. For post-challenge plasma ion concentrations, significant QTL (P <0.05) were found on six different linkage groups and highly suggestive ones (P <0.10) on two additional linkage groups. Most QTL affected concentrations of both chloride and sodium during both challenges, but some were specific to either chloride (2 QTL) or sodium (1 QTL) concentrations. Six QTL (4 significant, 2 suggestive) affecting gill index were discovered. Two were specific to the trait, while the others were also identified as QTL for post-challenge ion concentrations. Altogether, allelic effects were consistent for QTL affecting chloride and sodium concentrations but inconsistent for QTL affecting ion concentrations and gill morpho

A QTL design was implemented to investigate the genetic architecture of variation in the plasma cortisol response to an acute confinement stressor. About 1000 F2 progeny (5 full-sib families) were produced from a cross between F0 grand-parents previously selected for two generations for a high or a low cortisol response after a standardized confinement stress. Plasma cortisol concentrations were recorded on 15 month-old juveniles after two successive rounds of confinement stress challenge, at one month interval. Overall, eight and five QTLs (P<0.10) were identified for plasma cortisol concentration after the first and second challenge respectively. The most significant QTLs (P<0.05) were not the same in the two challenges. The results agree with previous studies reporting genetic variation for cortisol response after exposure to a stressor, but emphasize that response to stress is a highly complex trait, and that plasma cortisol may reflect a range of underlying physiological mechanisms.

Little is known about the genetic basis of residual feed intake (RFI) variation in fish, since this trait is highly sensitive to environmental influences, and feed intake of individuals is difficult to measure accurately. The purpose of this work was (i) to assess the genetic variability of RFI estimated by an X-ray technique and (ii) to develop predictive criteria for RFI. Two predictive criteria were tested: loss of body weight during feed deprivation and compensatory growth during re-feeding. Ten heterozygous rainbow trout clones were used. Individual intake and body weight were measured three times at three-week intervals. Then, individual body weight was recorded after two cycles of a three-week feed deprivation followed by a three-week re-feeding. The ratio of the genetic variance to the phenotypic variance was found high to moderate for growth, feed intake, and RFI (VG/VP = 0.63 +/- 0.11, 0.29 +/- 0.11, 0.29 +/- 0.09, respectively). The index that integrates performances achieved during deprivation and re-feeding periods explained 59% of RFI variations. These results provide a basis for further studies on the origin of RFI differences and show that indirect criteria are good candidates for future selective breeding programs.

The overall aims of the project is to identify, in sea bream, sea bass, oyster, and rainbow trout, genes of which expression is associated with disease and stress resistance and to develop genetic approaches that allow characterisation of genetic markers for marker-assisted selective breeding of disease and/or stress resistant individuals. For such project, the following main objectives have to be reached