Prediction of fatty acids composition in the rainbow trout Oncorhynchus mykiss by using Raman micro-spectroscopy.

The importance of poly-unsaturated fatty acids (PUFAs) in food is crucial for the animal and human development and health. As a complementary strategy to nutrition approaches, genetic selection has been suggested to improve fatty acids (FAs) composition in farmed fish. Gas chromatography (GC) is used as a reference method for the quantification of FAs; nevertheless, the high cost prevents large scale phenotyping as needed in breeding programs. Therefore, a calibration by means of Raman scattering spectrometry has been established in order to predict FA composition of visceral adipose tissue in rainbow trout Onchorhynchus mykiss. FA composition was analyzed by both GC and Raman micro-spectrometry techniques on 268 individuals fed with three different feeds, which have different FA compositions. Among the possible regression methods, the ridge regression method, was found to be efficient to establish calibration models from the GC and spectral data. The best cross-validated R2 values were obtained for total PUFAs, omega-6 (Ω-6) and omega-3 (Ω-3) PUFA (0.79, 0.83 and 0.66, respectively). For individual Ω-3 PUFAs, α-linolenic acid (ALA, C18:3), eicosapentaenoic acid (EPA, C20:5) and docosahexenoic acid (DHA, C22:6) were found to have the best R2 values (0.82, 0.76 and 0.81, respectively). This study demonstrates that Raman spectroscopy could be used to predict PUFAs with good correlation coefficients on adipocytes, for future on adipocytes physiology or for large scale and high throughput phenotyping in rainbow trout.

Genetic architecture and genomic selection of female reproduction traits in rainbow trout.

BACKGROUND: Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits. RESULTS: A pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits. CONCLUSIONS: Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.

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.

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.

Genetics of behavioural adaptation of livestock to farming conditions.

Behavioural adaptation of farm animals to environmental changes contributes to high levels of production under a wide range of farming conditions, from highly controlled indoor systems to harsh outdoor systems. The genetic variation in livestock behaviour is considerable. Animals and genotypes with a larger behavioural capacity for adaptation may cope more readily with varying farming conditions than those with a lower capacity for adaptation. This capacity should be exploited when the aim is to use a limited number of species extensively across the world. The genetics of behavioural traits is understood to some extent, but it is seldom accounted for in breeding programmes. This review summarizes the estimates of genetic parameters for behavioural traits in cattle, pigs, poultry and fish. On the basis of the major studies performed in the last two decades, we focus the review on traits of common interest in the four species. These concern the behavioural responses to both acute and chronic stressors in the physical environment (feed, temperature, etc.) and those in the social environment (other group members, progeny, humans). The genetic strategies used to improve the behavioural capacity for adaptation of animals differ between species. There is a greater emphasis on responses to acute environmental stress in fish and birds, and on responses to chronic social stress in mammals.

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.

Evolution of genetic variability in a population of the edible snail, Helix aspersa Müller, undergoing domestication and short-term selection.

The evolution of genetic variability is studied in six successive generations of a population originating from wild Helix aspersa. During the first three generations (G1 to G3), no artificial selection was applied. During the next three generations (G4 to G6), two lines were reared: a control line (C) and a line (S) selected for increased adult weight. Genetic variability is described by genealogical parameters (inbreeding, number of founders, effective number of founders and ancestors, effective number of remaining genomes) and by the additive genetic variance in adult weight. A large decrease in all parameters was observed between G1 and G2, suggesting strong natural selection: additive genetic variance in adult weight (transformed data) decreased from 0.0119 +/- 3.8 x 10(-3) to 0.0070 +/- 1.7 x 10(-3) (P < 0.05) and effective number of ancestors from 97.4 to 67.0. Selection also caused a large decrease during the first generation: additive genetic variance was 0.0079 +/- 2.1 x 10(-3) in G3 and 0.0040 +/- 1.1 x 10(-3) after the first selection cycle (P < 0.02). At the same time, the effective number of ancestors decreased from 59.2 to 29.5 and 24.2. This decrease is consistent with the theory of selection and the Bulmer effect.

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

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.