Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm.

In rainbow trout farming, Flavobacterium psychrophilum, the causative agent of bacterial cold water disease, is responsible for important economic losses. Resistance to F. psychrophilum is heritable, and several quantitative trait loci (QTL) with moderate effects have been detected, opening up promising perspectives for the genetic improvement of resistance. In most studies however, resistance to F. psychrophilum was assessed in experimental infectious challenges using injection as the infection route, which is not representative of natural infection. Indeed, injection bypasses external barriers, such as mucus and skin, that likely play a protective role against the infection. In this study, we aimed at describing the genetic architecture of the resistance to F. psychrophilum after a natural disease outbreak. In a 2000-fish cohort, reared on a French farm, 720 fish were sampled and genotyped using the medium-throughput Axiom™ Trout Genotyping Array. Overall mortality at the end of the outbreak was 25%. Genome-wide association studies were performed under two different models for time to death measured on 706 fish with validated genotypes for 30 060 SNPs. This study confirms the polygenic inheritance of resistance to F. psychrophilum with a few QTL with moderate effects and a large polygenic background, the heritability of the trait being estimated at 0.34. Two new chromosome-wide significant QTL and three suggestive QTL were detected, each of them explaining between 1% and 4% of genetic variance.

Effect of production quotas on economic and environmental values of growth rate and feed efficiency in sea cage fish farming.

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.

Adaptive capacities from survival to stress responses of two isogenic lines of rainbow trout fed a plant-based diet.

The composition of feed for farmed salmonids has strongly evolved during the last decades due to the substitution of fishery-derived fish oil and fishmeal by ingredients of plant origin. Little information is available regarding the effects of this transition on adaptive capacities in fish. Two rainbow trout isogenic lines, known for their divergent ability to grow on a plant-based diet (PBD), were fed for seven months from first feeding either a fully PBD or a control marine-resources diet and were compared for their growing and survival capacities over time and their behavioral and stress responses at similar sizes but different ages. Although fish displayed similar appetitive behaviour, the two lines were highly affected by the PBD translated in decreased growth and apathetic behaviour, but also stronger stress responses displayed by stronger cortisol increases and more stress-related behaviour when isolated. The two lines were found to be similarly sensitive to a PBD for the assessed stress-related parameters, but one line displayed a lower survival during the early rearing period. Overall, these results suggest that a PBD supplied to fish from the alevin stage has strong effects on physiological and behavioural parameters, with possible impairment of fish welfare, but also genome-dependent survival.

Economic values of growth and feed efficiency for fish farming in recirculating aquaculture system with density and nitrogen output limitations: a case study with African catfish (Clarias gariepinus).

In fish farming, economic values (EV) of breeding goal traits are lacking, even though they are key parameters when defining selection objectives. The aim of this study was to develop a bioeconomic model to estimate EV of 2 traits representing production performances in fish farming: the thermal growth coefficient (TGC) and the feed conversion ratio (FCR). This approach was applied to a farm producing African catfish (Clarias gariepinus) in a recirculating aquaculture system (RAS). In the RAS, 2 factors could limit production level: the nitrogen treatment capacity of the biofilter or the fish density in rearing tanks at harvest. Profit calculation includes revenue from fish sales, cost of juveniles, cost of feed, cost of waste water treatment, and fixed costs. In the reference scenario, profit was modeled to zero. EV were calculated as the difference in profit per kilogram of fish between the current population mean for both traits (µt) and the next generation of selective breeding (µt+Δt) for either TGC or FCR. EV of TGC and FCR were calculated for three generations of hypothetical selection on either TGC or FCR (respectively 6.8% and 7.6% improvement per generation). The results show that changes in TGC and FCR can affect both the number of fish that can be stocked (number of batches per year and number of fish per batch) and the factor limiting production. The EV of TGC and FCR vary and depend on the limiting factors. When dissolved NH3-N is the limiting factor for both µt and µt+Δt, increasing TGC decreases the number of fish that can be stocked but increases the number of batches that can be grown. As a result, profit remains constant and EVTGC is zero. Increasing FCR, however, increases the number of fish stocked and the ratio of fish produced per kilogram of feed consumed ("economic efficiency"). The EVFCR is 0.14 €/kg of fish, and profit per kilogram of fish increases by about 10%. When density is the limiting factor for both µt and µt+Δt, the number of fish stocked per batch is fixed; therefore, extra profit is obtained by increasing either TGC, which increases the annual number of batches, or by decreasing FCR, which decreases annual feed consumption. EVTGC is 0.03 €/kg of fish and EVFCR is 0.05-0.06 €/kg of fish. These results emphasize the importance of calculating economic values in the right context to develop efficient future breeding programs in aquaculture.

Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout.

Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full-sib families issued from two rainbow trout lines divergently selected for high or low post-confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post-stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (<10% of phenotypic variance) were detected on 18 chromosomes, strongly supporting the hypothesis that control of the trait is polygenic. Although a core array of QTL controlled cortisol concentrations at both challenges, several QTL seemed challenge specific, suggesting that responses to the first and to a subsequent exposure to the confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol-associated QTL did not support evidence for negative genetic relationships between the two types of traits.

Sex differentiation in an all-female (XX) rainbow trout population with a genetically governed masculinization phenotype.

Sex determination is known to be male heterogametic in the rainbow trout, Oncorhynchus mykiss; however, scattered observations that deviate from this rather strict genetic control have been reported. Here, we provide a detailed morphological and histological characterization of the gonadal differentiation and development (from 43 days postfertilization to 11 months of age) in an all-female (XX) population with a genetically governed masculinization phenotype. In comparison with control males and females, the gonadal differentiation in these animals was characterized by many perturbations, including significantly fewer germ cells. This decrease in germ cells was confirmed by the significantly decreased expression of 2 germ cell maker genes (vasa and sycp3) in the masculinized XX populations as compared with the control females and control males. Although only a proportion of the total adult population was partially or fully masculinized, this early differentiating phenotype affected nearly all the sampled animals. This suggests that the adult masculinization phenotype is the consequence of an early functional imbalance in ovarian differentiation in the entire population. We hypothesize that the lower number of germ cells that we observed in this population could be one cause of their masculinization.

Genotype by diet interactions in European sea bass (Dicentrarchus labrax L.): Nutritional challenge with totally plant-based diets.

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 the most efficient way to increase growth on plant-based diets, meaning that, in this case, indirect selection should be more efficient than direct selection.

Comparison of isogenic lines provides evidence that phenotypic plasticity is under genetic control in rainbow trout Oncorhynchus mykiss.

Comparison of nine isogenic lines of rainbow trout Oncorhynchus mykiss kept in the same environment showed significant genetic determinism of phenotypic plasticity assessed through body mass measurements. Ranking of lines differed between two tested environments.

Selection for growth in brown trout increases feed intake capacity without affecting maintenance and growth requirements.

The correlated responses in feed intake and G:F ratio with selection for increased growth rate were evaluated by comparing selected (S) and control (C) brown trout (Salmo trutta) reared under conditions known to affect feed efficiency: feed restriction and periods of compensatory growth. Nitrogen and energy requirements for maintenance and growth were also measured. Trout were allotted at comparable BW (3.7+/-0.06 and 3.8+/-0.04 g, for C and S respectively) to triplicate groups per treatment. The experiment lasted a total of 198 d, during which animals were successively submitted to a 116-d feeding phase and fed 10, 30, 50, 70, 100, and 140% of their usual daily ration (UDR), a 35-d phase of food deprivation, and a 47-d refeeding phase. The G:F of C and S were comparable in all experimental conditions tested. During the feeding phase, S grew better than C only when fed 100 and 140% UDR (P < 0.001). This was explained by a higher feed intake capacity. The requirements for growth and maintenance were similar among the lines, which is in agreement with their comparable loss of weight (mean energy loss of -53 and -55 kJ/(kg x d) for C and S, respectively; P > 0.38) observed during the feed deprivation phase and the lack of differences in carcass composition (fat, P > 0.35; protein, P > 0.54). During the refeeding phase, growth performance and G:F were high in all groups. The daily growth coefficient was higher in S than in C (P < 0.001) because of a higher feed intake (P < 0.001). An increase in absolute individual variability in final BW and length was associated with the level of food restriction in both lines; however, it always remained lower in S than in C. In conclusion, fish selected for growth under ad libitum conditions will only exhibit growth superiority when fed diets close to ad libitum, and there was no evidence that selection was associated with an improvement in efficiency of maintenance nor in retention of body tissues.

Mutation in a sex-determining gene in rainbow trout: detection and genetic analysis.

In rainbow trout (Oncorhynchus mykiss), the acknowledged sex-determining system is genetic sex determination (GSD) with female homogamety (female symbolXX-male symbolXY). Subsequently, mitotic gynogens are all expected to be females. Unexpected maleness was fortuitously observed in a mitotic gynogenetic family of rainbow trout (13 males out of 27). An equal ratio of males and females suggested the possible segregation of some Mendelian sex-influencing factor. In order to perform a comprehensive analysis of the inheritance and expression of the factor involved, the transmission of maleness was studied across the next three generations, using both conventional and/or meiotic and mitotic gynogenetic offspring. On the whole, males as well as intersexes were observed in crosses between two expected carrier parents, and in gynogenetic offspring of expected carrier females, but not in crosses between one expected carrier parent and one normal XX control. Sex ratios in the different crosses often fitted Mendelian proportions, but not always. Both excess and lack of maleness were observed. The simplest hypothesis consistent with most results is a one-locus model, assuming the existence of a mutation (termed mal) of a sex-determining gene, which is able to override the primary XX mechanism of sex determination and to induce the development of testicular tissue in the gonads of expected XX individuals. The one-locus model requires that the mal mutation usually, but not systematically, behave as a recessive mutation and have a limited penetrance, that is, heterozygous (mal/+) may be sex reversed, homozygous (mal/mal) may remain female, and carrier individuals may undergo partial masculinization alone (many intersexes were recorded). Inconsistency in sex ratios among offspring of parents expected to respond the same way was recorded, indicating that other modifier loci may also be involved. Finally, the occurrence of both males and females in clonal progenies showed that epigenetic factors also likely influence the expression of maleness. The effects of the mal mutation are compared to similar mutations recently described in other fish species. The nature and location of the mal gene (carried by heterochromosomes or an autosomal pair) is briefly discussed in view of the knowledge recently acquired on the subject.

In vitro viral haemorrhagic septicaemia virus replication in excised fins of rainbow trout: correlation with resistance to waterborne challenge and genetic variation.

In vitro viral haemorrhagic septicaemia virus replication in excised fin tissue (VREFT) was investigated as a possible criterion to predict the resistance of groups or individuals to viral haemorrhagic septicaemia virus (VHSV) in rainbow trout. Adipose and rayed fins were compared for VREFT response, and a statistically significant correlation was found. Correlation between VREFT and survival after waterborne viral challenge was estimated on a set of 27 groups of trout, and was highly significant (R = 0.72). A further experiment with fish individually tagged and challenged some time after fin clipping for determination of VREFT confirmed that the mean value of resistant (surviving) fish was significantly lower than the mean value of susceptible (dead) ones, but there was a wide variation within each of these groups. In particular, a large proportion of fish expected to be resistant based on VREFT values died all the same. Using clones, we showed that the correlation between VREFT and survival was dramatically high (R = 0.96). Genetic analyses of the data from the different groups available in the experiment consistently indicated a large amount of genetic determination of VREFT, an encouraging result for selection purposes. Though these results were obtained in experimentally controlled conditions not identical to those in the field, they shed new light on the analysis of defence mechanisms against the virus and on the possibility of performing indirect selection for resistance, using VREFT as the secondary character.

Selection of rainbow trout resistant to viral haemorrhagic septicaemia virus and transmission of resistance by gynogenesis.

In 1984 a programme of selection for resistance to viral haemorrhagic septicaemia virus (VHSV) in rainbow trout was initiated. The progenies of 14 males were submitted to a VHSV waterborne challenge. The mortality ranged from 30 to 95% and the heritability of resistance was estimated to be 0.63 +/- 0.26. One male consistently provided the most resistant offspring, and the second generation was produced from sires and dams selected among these families. The mean resistance improved and several females giving birth to resistant offspring were identified (0-10% mortality while the mortality in the controls was from 70 to 90%). The meiotic gynogenetic progeny of these females also demonstrated high resistance (mortality less than 10%). The role of superficial tissues in the resistance was confirmed and there was a striking difference in the growth of VHSV in fins excised and infected in vitro. The fins from resistant fish replicated the virus poorly as compared with the fins of susceptible fish.

Induced gynogenesis in the rainbow trout: Sex and survival of progenies production of all-triploid populations.

Gynogenesis could be an efficient way for producing inbred lines in commercial fish species. Gamma-irradiation of sperm gives haploid embryos that all die without hatching; in the present study, we optimized heat treatment of the eggs, in order to produce high rates of diploid gynogenetics. When the eggs are heated to 26 °C for 20 min after 25 min of development, 80% of the embryos hatch, and all the resulting fry are diploid; nevertheless, high mortalities are recorded until feeding start. The monosex female constitution of gynogenetic offspring confirms the female homogamety in the rainbow trout.When the eggs are treated with the same heat shock 25 min after a fertilization with functional sperm, alltriploid populations are obtained; their survival until feeding start is not different from the control.