Marc Vandeputte

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.

Physiological mechanisms underlying a trade-off between growth rate and tolerance of feed deprivation in the European sea bass (Dicentrarchus labrax)

SUMMARY The specific growth rate (SGR) of a cohort of 2000 tagged juvenile European sea bass was measured in a common tank, during two sequential cycles comprising three-weeks feed deprivation followed by three-weeks ad libitum re-feeding. After correction for initial size at age as fork length, there was a direct correlation between negative SGR (rate of mass loss) during feed deprivation and positive SGR (rate of compensatory growth) during re-feeding (Spearman rank correlation R=0.388, P=0.000002). Following a period of rearing under standard culture conditions, individuals representing ‘high growth’ phenotypes (GP) and ‘high tolerance of feed deprivation’ phenotypes (DP) were selected from either end of the SGR spectrum. Static and swimming respirometry could not demonstrate lower routine or standard metabolic rate in DP to account for greater tolerance of feed deprivation. Increased rates of compensatory growth in GP were not linked to greater maximum metabolic rate, aerobic metabolic scope or maximum cardiac performance than DP. When fed a standard ration, however, GP completed the specific dynamic action (SDA) response significantly faster than DP. Therefore, higher growth rate in GP was linked to greater capacity to process food. There was no difference in SDA coefficient, an indicator of energetic efficiency. The results indicate that individual variation in growth rate in sea bass reflects, in part, a trade-off against tolerance of food deprivation. The two phenotypes represented the opposing ends of a spectrum. The GP aims to exploit available resources and grow as rapidly as possible but at a cost of physiological and/or behavioural attributes, which lead to increased energy dissipation when food is not available. An opposing strategy, exemplified by DP, is less ‘boom and bust’, with a lower physiological capacity to exploit resources but which is less costly to sustain during periods of food deprivation.

Selective breeding of quantitative traits in the common carp (Cyprinus carpio): a review

The common carp is one of the main aquaculture species in the world. Despite this, most of the production is carried out using unselected strains. Selective breeding for fast growth has not proven to be effective in this species, but other traits (disease resistance, shape) could be successfully selected for. Most heritability estimates in the literature are unreliable due to environmental biases, but complementary results from population genetics and comparison of strains seem to indicate that there should be a potential for selective breeding in this species, including selection for growth rate, provided the base populations are variable enough (e.g. synthetic strains). New techniques such as parentage assignment with microsatellites and use of doubled haploid progenies may help describe much more accurately, without environmental bias, the genetic determination of traits of interest in the carp. This could be a new opportunity to design efficient breeding programs in this important species.

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet.

BackgroundEfforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax).ResultsWe report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies.ConclusionsOverall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies.

Early development and survival in brown trout (Salmo trutta fario L.): indirect effects of selection for growth rate and estimation of genetic parameters

Abstract Some components of the response to selection for growth in the PROSPER program on brown trout (Salmo trutta fario L.) (+30% in three generations) were investigated. A correlated response on growth during yolk-sac resorption was looked for, and we estimated the genetic parameters on growth-related traits at the end of endogenous feeding. For this purpose, a diallel cross between selected and control fish was designed, including 200 full-sib families (20 males×10 females), each of them being represented by four individually recorded fish. A positive-correlated effect of selection was seen on survival and percent weight gain at swim-up, and a negative one was shown on dry weight and dry matter content. No effect was seen on final wet weight. A putative interpretation is that selected individuals have a higher development rate, inducing a higher consumption of yolk reserves by the end of the experiment, and therefore, a decrease in wet weight, dry weight and dry matter content. Significant sire heritabilities were seen for final wet weight and percent weight gain (hs2=0.28±0.13 in both cases). For all traits except percent weight gain, maternal effects were strong, and an important part of them was related to the initial weight of eggs. Significant dominance effects were reported for wet weight, dry weight and percent weight gain.

Regulation of FADS2 expression and activity in European sea bass (Dicentrarchus labrax, L.) fed a vegetable diet

Supplies of marine fish oils are limited, and continued growth in aquaculture production dictates that lipid substitutes in fish diets must be used without compromising fish health and product quality. In this study, the total substitution of a fish meal and fish oil by a blend of vegetable meals (corn, soybean, wheat and lupin) and linseed oil in the diet of European sea bass (Dicentrachus labrax) was investigated. Two groups of European sea bass were fed with fish diet (FD) or vegetable diet (VD) for 9months. VD, totally deprived of eicosapentaenoate (EPA; 20:5n-3) and docosahexaenoate (DHA; 22:6n-3), revealed a nutritional deficiency and affected growth performance. Whilst VD induced a significant increase in fatty acid desaturase 2 (FADS2) and sterol binding regulatory element-binding protein 1 (SREBP-1) mRNA levels, the desaturation rate of [1-(14)C]18:3n-3 into [1-(14)C]18:4n-3, analysed in microsomal preparations using HPLC method, did not show an upregulation of FADS2 activities in liver and intestine of fish fed VD. Moreover Western-blot analysis did not revealed any significant difference of FADS2 protein amount between the two dietary groups. These data demonstrate that sea bass exhibits a desaturase (FADS2) activity whatever their diet, but a post-transcriptional regulation of fads2 RNA prevents an increase of enzyme in fish fed a HUFA-free diet. This led to a lower fish growth and poor muscle HUFA content.

Enhanced individual selection for selecting fast growing fish: the "PROSPER" method, with application on brown trout (Salmo trutta fario)

Growth rate is the main breeding goal of fish breeders, but individual selection has often shown poor responses in fish species. The PROSPER method was developed to overcome possible factors that may contribute to this low success, using (1) a variable base population and high number of breeders (Ne > 100), (2) selection within groups with low non-genetic effects and (3) repeated growth challenges. Using calculations, we show that individual selection within groups, with appropriate management of maternal effects, can be superior to mass selection as soon as the maternal effect ratio exceeds 0.15, when heritability is 0.25. Practically, brown trout were selected on length at the age of one year with the PROSPER method. The genetic gain was evaluated against an unselected control line. After four generations, the mean response per generation in length at one year was 6.2% of the control mean, while the mean correlated response in weight was 21.5% of the control mean per generation. At the 4th generation, selected fish also appeared to be leaner than control fish when compared at the same size, and the response on weight was maximal (≈130% of the control mean) between 386 and 470 days post fertilisation. This high response is promising, however, the key points of the method have to be investigated in more detail.

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.

Viral encephalopathy and retinopathy in aquaculture: a review

Viral encephalopathy and retinopathy (VER), otherwise known as viral nervous necrosis (VNN), is a major devastating threat for aquatic animals. Betanodaviruses have been isolated in at least 70 aquatic animal species in marine and in freshwater environments throughout the world, with the notable exception of South America. In this review, the main features of betanodavirus, including its diversity, its distribution and its transmission modes in fish, are firstly presented. Then, the existing diagnosis and detection methods, as well as the different control procedures of this disease, are reviewed. Finally, the potential of selective breeding, including both conventional and genomic selection, as an opportunity to obtain resistant commercial populations, is examined.

A new SNP-based vision of the genetics of sex determination in European sea bass (Dicentrarchus labrax)

BackgroundEuropean sea bass (Dicentrarchus labrax) is one of the most important farmed species in Mediterranean aquaculture. The observed sexual growth and maturity dimorphism in favour of females adds value towards deciphering the sex determination system of this species. Current knowledge indicates the existence of a polygenic sex determining determination system that interacts with temperature. This was explored by restriction-site associated DNA (RAD) marker analysis in a test panel of 175 offspring that originated from a factorial cross between two dams and four sires from a single full-sib family.ResultsThe first high-density single nucleotide polymorphism (SNP) based linkage map for sea bass was constructed, consisting of 6706 SNPs on 24 linkage groups. Indications for putative sex-determining QTL (quantitative trait loci) that were significant at the genome-wide threshold were detected on linkage groups 6, 11 and 18 to 21, although a genome-wide association study (GWAS) did not identify individual significant SNPs at a genome-wide threshold. A preliminary genomic prediction approach that tested the efficiency of SNP-based selection for female sea bass showed a slight advantage compared to traditional pedigree-based selection. However, when the same models were tested on the same animals for selection for greater length, a clear advantage of the SNP-based selection was observed.ConclusionsOverall, the results of this study provide additional support to the polygenic sex determination hypothesis in sea bass. In addition, identification of sex-ratio QTL may provide new opportunities for sex-ratio control in sea bass.