Alain Vergnet

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.

Physiological mechanisms underlying individual variation in tolerance of food deprivation in juvenile European sea bass, Dicentrarchus labrax

Although food deprivation is a major ecological pressure in fishes, there is wide individual variation in tolerance of fasting, whose mechanistic bases are poorly understood. Two thousand individually tagged juvenile European sea bass were submitted to two ‘fasting/feeding’ cycles each comprising 3 weeks of food deprivation followed by 3 weeks of ad libitum feeding at 25°C. Rates of mass loss during the two fasting periods were averaged for each individual to calculate a population mean. Extreme fasting tolerant (FT) and sensitive (FS) phenotypes were identified that were at least one and a half standard deviations, on opposing sides, from this mean. Respirometry was used to investigate two main hypotheses: (1) tolerance of food deprivation reflects lower mass-corrected routine metabolic rate (RMR) in FT phenotypes when fasting, and (2) tolerance reflects differences in substrate utilisation; FT phenotypes use relatively less proteins as metabolic fuels during fasting, measured as their ammonia quotient (AQ), the simultaneous ratio of ammonia excretion to RMR. There was no difference in mean RMR between FT and FS over 7 days fasting, being 6.70±0.24 mmol h−1 fish−1 (mean ± s.e.m., N=18) versus 6.76±0.22 mmol h−1 fish−1 (N=17), respectively, when corrected to a body mass of 130 g. For any given RMR, however, the FT lost mass at a significantly lower rate than FS, overall 7-day average being 0.72±0.05 versus 0.90±0.05 g day−1 fish−1, respectively (P<0.01, t-test). At 20 h after receiving a ration equivalent to 2% body mass as food pellets, ammonia excretion and simultaneous RMR were elevated and similar in FT and FS, with AQs of 0.105±0.009 and 0.089±0.007, respectively. At the end of the period of fasting, ammonia excretion and RMR had fallen in both phenotypes, but AQ was significantly lower in FT than FS, being 0.038±0.004 versus 0.061±0.005, respectively (P<0.001, t-test). There was a direct linear relationship between individual fasted AQ and rate of mass loss, with FT and FS individuals distributed at opposing lower and upper extremities, respectively. Thus the difference between the phenotypes in their tolerance of food deprivation did not depend upon their routine energy use when fasting. Rather, it depended upon their relative use of tissue proteins as metabolic fuels when fasting, which was significantly lower in FT phenotypes.

Heritability of Boldness and Hypoxia Avoidance in European Seabass, Dicentrarchus labrax

To understand the genetic basis of coping style in European seabass, fish from a full factorial mating (10 females x 50 males) were reared in common garden and individually tagged. Individuals coping style was characterized through behavior tests at four different ages, categorizing fish into proactive or reactive: a hypoxia avoidance test (at 255 days post hatching, dph) and 3 risk-taking tests (at 276, 286 and 304 dph). We observed significant heritability of the coping style, higher for the average of risk-taking scores (h2 = 0.45 ± 0.14) than for the hypoxia avoidance test (h2 = 0.19 ± 0.10). The genetic correlations between the three risk-taking scores were very high (rA = 0.96–0.99) showing that although their repeatability was moderately high (rP = 0.64–0.72), successive risk-taking tests evaluated the same genetic variation. A mild genetic correlation between the results of the hypoxia avoidance test and the average of risk-taking scores (0.45 ± 0.27) suggested that hypoxia avoidance and risk-taking tests do not address exactly the same behavioral and physiological responses. Genetic correlations between weight and risk taking traits showed negative values whatever the test used in our population i.e. reactive individual weights were larger. The results of this quantitative genetic analysis suggest a potential for the development of selection programs based on coping styles that could increase seabass welfare without altering growth performances. Overall, it also contributes to a better understanding of the origin and the significance of individual behavioral differences.

Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)

Abstract Describing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.

How could fully scaled carps appear in natural waters in Madagascar

The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the ‘mirror’ reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.

Potential for Genetic Improvement of the Main Slaughter Yields in Common Carp With in vivo Morphological Predictors

Common carp is a major aquaculture species worldwide, commonly sold alive but also as processed headless carcass or filets. However, recording of processing yields is impossible on live breeding candidates, and alternatives for genetic improvement are either sib selection based on slaughtered fish, or indirect selection on correlated traits recorded in vivo. Morphological predictors that can be measured on live fish and that correlate with real slaughter yields hence remain a possible alternative. To quantify the power of morphological predictors for genetic improvement of yields, we estimated genetic parameters of slaughter yields and various predictors in 3-year-old common carp reared communally under semi-intensive pond conditions. The experimental stock was established by a partial factorial design of 20 dams and 40 sires, and 1553 progenies were assigned to their parents using 12 microsatellites. Slaughter yields were highly heritable (h2 = 0.46 for headless carcass yield, 0.50 for filet yield) and strongly genetically correlated with each other (rg = 0.96). To create morphological predictors, external (phenotypes, 2D digitization) and internal measurements (ultrasound imagery) were recorded and combined by multiple linear regression to predict slaughter yields. The accuracy of the phenotypic prediction was high for headless carcass yield (R2 = 0.63) and intermediate for filet yield (R2 = 0.49). Interestingly, heritability of predicted slaughter yields (0.48–0.63) was higher than that of the real yields to predict, and had high genetic correlations with the real yields (rg = 0.84–0.88). In addition, both predicted yields were highly phenotypically and genetically correlated with each other (0.95 for both), suggesting that using predicted headless carcass yield in a breeding program would be a good way to also improve filet yield. Besides, two individual predictors (P1 and P2) included in the prediction models and two simple internal measurements (E4 and E23) exhibited intermediate to high heritability estimates (h2 = 0.34 – 0.72) and significant genetic correlations to the slaughter yields (rg = |0.39 – 0.83|). The results show that there is a solid potential for genetic improvement of slaughter yields by selecting for predictor traits recorded on live breeding candidates of common carp.

Combining Vitassign and Colony for pedigree reconstruction in a case of factorial mating with missing parental genotypes

Combining VITASSIGN and COLONY for pedigree reconstruction in a case of factorial mating with missing parental genotypes. Aquaculture Europe 2015