Mathilde Dupont-Nivet

A Polygenic Hypothesis for Sex Determination in the European Sea Bass Dicentrarchus labrax

Polygenic sex determination, although suspected in several species, is thought to be evolutionarily unstable and has been proven in very few cases. In the European sea bass, temperature is known to influence the sex ratio. We set up a factorial mating, producing 5.893 individuals from 253 full-sib families, all reared in a single batch to avoid any between-families environmental effects. The proportion of females in the offspring was 18.3%, with a large variation between families. Interpreting sex as a threshold trait, the heritability estimate was 0.62 ± 0.12. The observed distribution of family sex ratios was in accordance with a polygenic model or with a four-sex-factors system with environmental variance and could not be explained by any genetic model without environmental variance. We showed that there was a positive genetic correlation between weight and sex (rA = 0.50 ± 0.09), apart from the phenotypic sex dimorphism in favor of females. This supports the hypothesis that a minimum size is required for sea bass juveniles to differentiate as females. An evolution of sex ratio by frequency-dependent selection is expected during the domestication process of Dicentrarchus labrax populations, raising concern about the release of such fish in the wild.

Scaling of metabolism in Helix aspersa snails: changes through ontogeny and response to selection for increased size.

SUMMARY Though many are convinced otherwise, variability of the size-scaling of metabolism is widespread in nature, and the factors driving that remain unknown. Here we test a hypothesis that the increased expenditure associated with faster growth increases metabolic scaling. We compare metabolic scaling in the fast- and slow-growth phases of ontogeny of Helix aspersa snails artificially selected or not selected for increased adult size. The selected line evolved larger egg and adult sizes and a faster size-specific growth rate, without a change in the developmental rate. Both lines had comparable food consumption but the selected snails grew more efficiently and had lower metabolism early in ontogeny. Attainment of lower metabolism was accompanied by decreased shell production, indicating that the increased growth was fuelled partly at the expense of shell production. As predicted, the scaling of oxygen consumption with body mass was isometric or nearly isometric in the fast-growing (early) ontogenetic stage, and it became negatively allometric in the slow-growing (late) stage; metabolic scaling tended to be steeper in selected (fast-growing) than in control (slow-growing) snails; this difference disappeared later in ontogeny. Differences in metabolic scaling were not related to shifts in the scaling of metabolically inert shell. Our results support the view that changes in metabolic scaling through ontogeny and the variability of metabolic scaling between organisms can be affected by differential growth rates. We stress that future approaches to this phenomenon should consider the metabolic effects of cell size changes which underlie shifts in the growth pattern.

Setting up a strain-testing design for the seabass, Dicentrarchus labrax: a simulation study

The seabass, Dicentrarchus labrax L., is a leading species in European marine aquaculture, but its genetic characteristics necessary to set up breeding programmes are still unknown. New tools, such as genomic markers, now allow to carry out strain testings and estimations of genetic parameters in reasonable scale experimental facilities. However, because of the high cost of genotyping, the total number of fish to be measured will be limited and mating designs (type of cross, number of sires and dams) must be optimised. An optimisation trial is done in this study by simulation of a quantitative trait for two different strains of fish according to a polygenic model with additive, dominance, maternal and residual effects. The phenotypic coefficient of variation and the difference between crosses means (D=10%) were also included in the model. For technical limitations due to the species, the mating design chosen was a factorial cross between sires of both strains with dams from one strain (topcross). Different combinations of size of progeny sample (500–4000), number of sires (10–120/strain) and dams (4–16) were studied. Various mixed models (SAS®, proc Mixed, option REML) were used to estimate D, the power for detecting D, heritability (h2) and their standard error (S.E.) over 1000 repetitions. Incomplete factorials were also tested as well as the effect of differential survival between dam families. In strictly additive models (no dominance or maternal effects), D and h2 estimates were unbiased. The number of dams did not noticeably affect the precision of estimates, whatever the number of sires. A joint optimisation of sample size and number of sires led to a consensus value of 40 sires/strain with a sample size of 2000 progenies, which gave good precisions for D and h2. It was also shown that a mixed model (fixed strain effect+random sire effect) gave more accurate results than a simple fixed model (strain effect only). The inclusion of maternal and dominance effects did not markedly bias nor affect the precision of D and h2 estimates in a full factorial design, but could lower the precision (up to 40% increase S.E.) in incomplete factorial design. Variance in dam family sizes (due to differential survivals) did not affect the results in full factorials when set at values observed in seabass. It is then concluded that a factorial cross of 40 sires/strain with 8 dams and a sample size of 2000 progenies (on average 1000/strain) is appropriate for comparing seabass strains (power >0.8 for detecting a 20% difference between strains means) and jointly estimating heritability.

The Positive Impact of the Early-Feeding of a Plant-Based Diet on Its Future Acceptance and Utilisation in Rainbow Trout

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 swim-up 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 short-term 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.

Selection for Adaptation to Dietary Shifts: Towards Sustainable Breeding of Carnivorous Fish

Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss) after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively). Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.

Optimization of factorial mating designs for inference on heritability in fish species

Abstract Microsatellites allow pedigrees to be redrawn in groups of mixed families. However, genotyping costs are still high and experiments deserve new optimizations based on total number of genotyped offspring. Using stochastic simulations, this paper compares and optimizes three factorial or partly factorial mating designs for inference on heritability: FF: full factorial: s sires, each mated with s dams ( s 2 families) FD: s sires, each mated with two dams (2 s families) BH: described by Berg and Henryon [A comparison of mating designs for inference on genetic parameters in fish. Proceedings of the Sixth World Congress on Genetic Applied to Livestock Production, Armidale, Australia, 11–16th January, 27, 115.]: s sires mated with s dams: sire 1 with dams 1, 2; sire 2 with dams 2, 3…sire S with dams 1, S (2 s families). A quantitative trait is simulated according to a strictly additive, polygenic model. Two levels for number of genotyped offspring (NO=300 or 1000) and three levels for true heritability ( h 2 =0.1, 0.25 and 0.5) are considered. For each NO– h 2 combination, all possible couples number of families (NF)/family size were studied to find the one giving the most precise estimation of heritability. Standard deviation of heritability was calculated over 5000 repetitions in each situation. In most cases, FF designs are less interesting than FD and BH ones. FD designs are more precise than BH designs, except for NO=1000 and h 2 =0.5. Optimum family size is similar for FD and BH designs and both NOs: 3–5 offspring per family for h 2 =0.5, 5–8 offspring per family for h 2 =0.25 and 12–20 offspring per family for h 2 =0.1.

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

Terrestrial plant resources are increasingly used as substitutes for fish meal and fish oil in fish feed in order to reduce the reliance of aquaculture on marine fishery resources. Although many studies have been conducted to assess the effects of such nutritional transition, no whole breeding cycles of fish fed diets free from marine resources has been reported to date. We therefore studied the reproductive performance of trout after a complete cycle of breeding while consuming a diet totally devoid of marine ingredients and thus of n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs) that play a major role in the formation of ova. Two groups of female rainbow trout were fed from first feeding either a commercial diet (C, marine and plant ingredients), or a 100% plant-based diet (V, blend of plant proteins and vegetable oils). Livers, viscera, carcasses and ova were sampled at spawning and analyzed for lipids and fatty acids. Although the V-diet was devoid of n-3 LC-PUFAs, significant amounts of EPA and DHA were found in livers and ova, demonstrating efficient bioconversion of linolenic acid and selective orientation towards the ova. Some ova were fertilized to assess the reproductive performance and offspring survival. We observed for the first time that trout fed a 100% plant-based diet over a 3-year breeding cycle were able to produce ova and viable alevins, although the ova were smaller. The survival of offspring from V-fed females was lower (-22%) at first spawning, but not at the second. Our study showed that, in addition to being able to grow on a plant-based diet, rainbow trout reared entirely on such a diet can successfully produce ova in which neo-synthesized n-3 LC-PUFAs are accumulated, leading to viable offspring. However, further adjustment of the feed formula is still needed to optimize reproductive performance.

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.

Assessment of Genetic Variability of Fish Personality Traits using Rainbow Trout Isogenic Lines

The study of inter-individual variability of personality in fish is a growing field of interest but the genetic basis of this complex trait is still poorly investigated due to the difficulty in controlling fish genetic origin and life history. When available, isogenic lines that allow performing independent tests on different individuals having identical genotype constitute a very relevant experimental material to disentangle the genetic and environmental components of behavioural individuality. We took advantage of heterozygous isogenic lines to investigate the personality in rainbow trout through the analysis of their reactions to different experimental situations. To this end, seven to ten rainbow trout isogenic lines were screened for their spatial exploratory behaviour, their flight response toward a stressor and their risk taking behaviour. Results showed that some lines seemed less sensitive to new events or environmental changes and could be defined as low responsive, while others were very sensitive and defined as high responsive. The use of isogenic lines highlighted the importance of genetic factors, in combination with life history, in the expression of personality in domesticated fish.

Direct and correlated responses to individual selection for large adult weight in the edible snail Helix aspersa Müller.

A selection experiment for large adult weight based on individual performance was conducted for three generations in Helix aspersa aspersa. A second line was kept as an unselected control line. Direct response measured as deviation from the control line was 3.55 g after three generations of artificial selection, which averaged 13%. Realized heritability was 0.38 +/- 0.04. Correlated responses to selection showed a significant increase in weight after hibernation, mean egg weight and mean weight of newly-hatched snails with selection. For adult age, egg number, and hatching rate, no significant change correlated to selection was found, but this is to be confirmed.