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The development of sustainable aquaculture relies on replacing marine raw materials like fish meal (FM) and fish oil (FO). Emerging alternatives, such as single-cell proteins and alternative lipids, offer promise. This study explored the effects of partially substituting FM with 10% bacterial protein (Methylococcus capsulatus) and completely replacing FO with a blend of poultry oil (PO) and DHA-rich microalgae oil in European sea bass (Dicentrarchus labrax) of unselected (WT) and selected (HG) genotypes. The results indicated that bacterial protein had no adverse impact on fish growth. The HG group demonstrated better growth and feed conversion due to genetic selection. This study also analysed the dietary and genotype effects on body lipid composition and fatty acid profiles. Notably, the HG fish had lower levels of major fatty acids (EPA, DHA, n-3 FAs, and n-3 LC-PUFAs) in their fillets, but not in their whole-body composition. These differences influenced sensory and qualitative aspects. Electronic sensory analyses (the first e-sensory profiling conducted for genetic purposes in fish) showed more significant differences due to diet in the WT group, with a less variable pattern in the e-tongue score in for the HG group. The volatile profiles showed no significant differences. In summary, combining selected fish genotypes with innovative feeds is a step forward in aquaculture. It maximizes nutrient utilization, enhances fish growth, and improves product quality. This approach becomes increasingly important in scenarios with limited FM/FO availability, promoting sustainability in aquaculture.

The sustainable development of the aquaculture industry relies on the use of alternative conventional and emergent raw materials that contributes to a circular economy and to reduce the dependency on fish meals and fish oils coming from oceanic fish populations. Additionally, the genetic selection of farmed fish that can display higher growth and feed utilization when fed alternative feeds, is pointed out to be a complementary valuable tool to facilitate the implementation of circular economy approaches. The main purpose of the present study was to determine the effectiveness of genetic selection for growth in European sea bass, in response to a challenge with an alternative diet that aimed to partially replaced fishmeal (FM) by poultry meal (PM) and totally replace fish oil (FO) by a blend of poultry oil (PO) with a novel microalgae oil. The two families of fish juveniles were obtained by in vitro fertilization of selected for a multi-trait including high growth (genetically selected, GS) or non-selected (wild type, WT) broodstocks and then were nutritionally challenged with a control diet that mirrored a standard commercial diet with fishmeal (20%) and fish oil (7%), or a Future diet that partially replaced the FM by PM and totally replaced the FO by a blend of rapeseed oil, PO, and a novel DHA rich-algal oil. From the second month of feeding until the end of the trial, European sea bass that was selected since for 7 generations performed better in terms of growth than the wild-type genotype, possibly related with an apparent favored feed and nutrient utilization. Furthermore, selection decreased the perivisceral fat and increased the nutritional value of flesh by increasing DHA (in g/ 100 g flesh) and ARA contents. In contrast, the dietary treatment showed little effect on fish growth performance, denoting the successful partial replacement of FM by PM and the total replacement of FO by a blend of poultry oil and an emergent microalgal oil. However, Future diet t

Background Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. Results We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. Conclusions We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in

Feed conversion ratio (FCR) is an important trait to target in fish breeding programs, and the aim of the present study is to underline how the genetic improvement of FCR in gilthead sea bream (Sparus aurata) drives to changes in transcriptional and behavioural patterns. Groups of fish with high (FCR+) and low (FCR-) individual FCR were established at the juvenile stage (161–315 dph) by rearing isolated fish on a restricted ration. Fish were then grouped on the basis of their individual FCR and they grew up until behavioural monitoring and gene expression analyses were done at 420 dph. The AEFishBIT datalogger (externally attached to operculum) was used for simultaneous measurements of physical activity and ventilation rates. This allowed discrimination of FCR+ and FCR- groups according to their different behaviour and energy partitioning for growth and locomotor activity. Gene expression profiling of liver and white muscle was made using customized PCR-arrays of 44 and 29 genes, respectively. Up to 15 genes were differentially expressed in liver and muscle tissues highlighting a different metabolic scope of FCR+ and FCR- fish. Hepatic gene expression profile of FCR- fish displayed a lower lipogenic activity that was concurrent with a down-regulation of markers of mitochondrial activity and oxidative stress, as well as a reallocation of body fat depots with an enhanced flux of lipids towards skeletal muscle. Muscle gene expression profile of FCR- fish matched with stimulatory and inhibitory growth signals, and an activation of energy sensors and antioxidant defence as part of the operating mechanisms for a more efficient muscle growth. These new insights contribute to phenotype the genetically mediated differences in fish FCR thanks to the combination of transcriptomic and behavioural approaches that contribute to better understand the mechanisms involved in a reliable FCR improvement of farmed gilthead sea bream.

Eight juvenile European seabass were exposed to two thermal ramping protocols with different levels of aerobic activity and tolerance endpoint: the critical thermal maximum for swimming (CTSmax) while exercising aerobically until fatigue, and the critical thermal maximum (CTmax) under static conditions until loss of equilibrium (LOE). In the CTSmax, warming caused a profound increase in oxygen uptake rate (M˙O2) culminating in a gait transition, from steady aerobic towards unsteady anaerobic swimming, then fatigue at 30.3±0.4°C (mean±SE). Gait transition and fatigue presumably indicate an oxygen limitation, an inability to meet the combined demands of swimming plus warming. The CTmax also elicited an increase in M˙O2, culminating in LOE at 34.0±0.4°C, significantly warmer than fatigue at CTSmax. The maximum M˙O2 achieved in the CTmax was, however, less than 30% of that achieved in the CTSmax. Therefore, the static CTmax did not exploit full cardiorespiratory capacity for oxygen supply, indicating that LOE was not caused by systemic oxygen limitation. Consequently, systemic oxygen supply can be significant for tolerance of acute warming in seabass but this depends upon the physiological context and the endpoint used.

Genetic improvement of feed efficiency is key to improve the economic and environmental sustainability of fish farming. However, it requires individual phenotypes of feed efficiency, which are difficult if not impossible to obtain when fish are reared in tanks or cages. Here, we applied and validated on gilthead sea bream a method to evaluate individual feed efficiency based on individual rearing of fish in aquariums under restricted feeding. We collected individual phenotypes of feed efficiency in aquariums on 538 sea bream (average weight = 54.50 g). Based on these individual phenotypes, fish (average weight = 174.6 g) were reared in groups of divergent phenotypes (high or low feed efficiency), validating that individual feed efficiency had an impact on group feed efficiency at a later stage. All 538 fish, their parents as well as 794 sibs reared in cages in a production environment, were genotyped on a 57k SNP array to estimate genomic heritability and correlations between traits. We showed that feed efficiency was heritable but did not find significant associated QTLs. We also showed that feed efficiency was negatively genetically correlated to viscera yield, indicating that the most efficient fish had less viscera than the least efficient ones. Altogether, these results support that measuring individual feed efficiency in aquariums under restricted feeding may be used as a reliable phenotyping method to genetically improve feed efficiency, despite the bias intrinsically linked to individual rearing.

In this study, we aimed to investigate the relationship between cortisol and the determination of sexual fate in the commercially important European sea bass (Dicentrarchus labrax). To test our hypothesis, we designed two temperature-based experiments (19 ℃, 21 ℃ and 23 ℃, experiment 1; 16 ℃ and 21 ℃, experiment 2) to assess the effects of these thermal treatments on European sea bass sex determination and differentiation. In the fish from the first experiment, we evaluated whether blood cortisol levels and expression of stress key regulatory genes were different between differentiating (149 to 183 dph) males and females. In the second experiment, we assessed whether cortisol accumulated in scales over time during the labile period for sex determination as well as the neuroanatomical localisation of brain cells expressing brain aromatase (cyp19a1b) and corticotropin-releasing factor (crf) differed between males and females undergoing molecular sex differentiation (117 to 124 dph). None of the gathered results allowed to detect differences between males and females regarding cortisol production and regulatory mechanisms. Altogether, our data provide strong physiological, molecular and histochemical evidence, indicating that in vivo cortisol regulation has no major effects on the sex of European sea bass.

Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K–60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51–0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL e

In European sea bass (Dicentrarchus labrax), as in many other fish species, temperature is known to influence the sex of individuals, with more males produced at relatively high temperatures. It is however unclear to what extent growth or stress are involved in such a process, since temperature is known to influence both growth rate and cortisol production. Here, we designed an experiment aiming at reducing stress and affecting early growth rate. We exposed larvae and juveniles originating from both captive and wild parents to three different treatments: low stocking density, food supplemented with tryptophan and a control. Low stocking density and tryptophan treatment respectively increased and decreased early growth rate. Each treatment influenced the stress response depending on the developmental stage, although no clear pattern regarding the whole-body cortisol concentration was found. During sex differentiation, fish in the low-density treatment exhibited lower expression of gr1, gr2, mr, and crf in the hypothalamus when compared to the control group. Fish fed tryptophan displayed lower crf in the hypothalamus and higher level of serotonin in the telencephalon compared to controls. Overall, fish kept at low density produced significantly more females than both control and fish fed tryptophan. Parents that have been selected for growth for three generations also produced significantly more females than parents of wild origin. Our findings did not allow to detect a clear effect of stress at the group level and rather point out a key role of early sexually dimorphic growth rate in sex determination.

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stocky supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and filletcharacteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass: 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables eff

The European sea bass (Dicentrarchus labrax) exhibits female-biased sexual size dimorphism (SSD) early in development. New tagging techniques provide the opportunity to monitor individual sex-related growth during the post-larval and juvenile stages. We produced an experimental population through artificial fertilization and followed a rearing-temperature protocol (~16°C from hatching to 112 days post-hatching, dph; ~20°C from 117 to 358 dph) targeting a roughly balanced sex ratio. The fish were tagged with microchips between 61 and 96 dph in five tagging trials of 50 fish each; individual standard length (SL) was recorded through repeated biometric measurements performed between 83 to 110 dph via image analyses. Body weight (BW) was modelled using the traits measured on the digital pictures (i.e. area, perimeter and volume). At 117 dph, the fish were tagged with microtags and regularly measured for SL and BW until 335 dph. The experiment ended at 358 dph with the sexing of the fish. The sex-ratio at the end of the experiment was significantly in favor of the females (65.6% vs. 34.4%). The females were significantly longer and heavier than the males from 103 dph (~30 mm SL, ~0.44 g BW) to 165 dph, but the modeling of the growth curves suggests that differences in size already existed at 83 dph. A significant difference in the daily growth coefficient (DGC) was observed only between 96 and 103 dph, suggesting a physiological or biological change occurring during this period. The female-biased SSD pattern in European sea bass is thus strongly influenced by very early growth differences between sexes, as already shown in previous studies, and in any case long before gonadal sex differentiation has been started, and thus probably before sex has been determined. This leads to the hypothesis that early growth might be a cause rather than a consequence of sex differentiation in sea bass.

Viral Nervous Necrosis (VNN, also called viral encephalo- and retinopathy (VER)), is a widespread disease of marine aquaculture caused by betanodavirus (or nervous necrosis virus - NNV), a segmented positive sense RNA virus, member of the nodaviridae family. VNN affects predominantly marine fish and cause significant losses to the Mediterranean fish farming industry, including the production of European sea bass (Dicentrarchus labrax). Of the four circulating genotypes of betanodavirus, red-spotted grouper NNV (RGNNV) and the reassortant genotype red-spotted grouper/striped jack NNV (RG/SJNNV) are most prevalent in the Mediterranean. Inheritable resistance against VNN has been detected in sea bass, and selective breeding could be a mean to limit this untreatable disease. In the current study, we compare resistance to disease among three populations from the Atlantic Ocean (AT), Eastern Mediterranean (EM) and Western Mediterranean (WM), by challenge trials using both a highly pathogenic isolate of RGNNV and a lower pathogenic reassortant isolate of RG/SJNNV. The survival of the three populations were modelled with a logistic regression, and the odds ratio (OR) of surviving was calculated. The challenge with RG/SJNNV reduced the odds of surviving three-fold (OR = 0.29 [0.07-0.87]), whereas the challenge with RGNNV reduced the odds of surviving 100-fold (OR = 0.01 [0.00-0.03]). Overall, the EM population had 3.32 (1.92–5.86) times higher odds of surviving the challenge than the AT and WM stocks. All survivors were harboring viral RNA in the brain, as demonstrated by RT-qPCR. However, viral RNA levels were in average lower in survivors from the EM population in both challenges, though only significantly lower in the challenge with RG/SJNNV (p < 0.01). The survival results combined with the RT-qPCR results indicate that the EM sea bass population has a natural resistance to disease caused by RGNNV, possibly associated with limited viral entry into and/or replication in t

Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic species. Recent developments of high throughput genotyping technology now enable the implementation of genomic selection, a method aiming to predict the breeding value of candidates based on their genotype at genome-wide markers. In this review article, we review the state of the arts, challenges and prospects for the application of genomic selection in aquaculture species. The particular focus is on the status of genomic selection in several major aquaculture species of International Council for the Exploration of the Sea (ICES) member countries: Atlantic salmon, rainbow trout, Atlantic cod, American catfish, Pacific oyster, European sea bass and gilthead sea bream. While the potential of genomic selection is clear, tailored species-specific applications will be needed to maximise its benefit for the aquaculture sector.

Introduction and importance Osteopetrosis is a poorly known and probably underdiagnosed pathology. It is caused by various genetic abnormalities resulting in osteoclast dysfunction. Functional and aesthetic consequences have a major impact on the patient’s quality of life. Ten percent of osteopetrosis cases develop osteomyelitis that usually involves the mandible. Management of this complication remains complex and often unsatisfactory. Case presentation We report a case of a 62-year-old woman with osteopetrosis, complicated by mandibular osteomyelitis with intra-oral bone exposure and submental fistulas. Management was performed with antibiotic therapy and surgical necrotic resection. This cured the fistulas but the bone exposure persisted. Discussion This case report highlights the difficulty of achieving complete healing of osteomyelitis in osteopetrosis. Antibiotic therapy, surgical management, or even hyperbaric oxygen therapy are required, but must be adapted to the case. A free flap procedure is undesirable but, when it is necessary, a bone marrow transplant could be considered to restore osteoclast function. Conclusion The management of mandibular osteomyelitis in patients with osteopetrosis must adapt to the situation and severity. To avoid most cases of osteomyelitic complications in patients suffering from osteopetrosis, we propose that a preventive strategy of better dental care should be considered.

Feed efficiency (FE) is the amount of body weight gain for a given feed intake. Improving FE through selective breeding is key for sustainable finfish aquaculture but its evaluation at individual level is technically challenging. We therefore investigated whether individual routine metabolic rate (RMR) was a predictor of individual FE in the European sea bass Dicentrarchus labrax, a major species in European mariculture. The European sea bass has three genetically distinct populations across its geographical range, namely Atlantic Ocean (AT), West Mediterranean (WM) and East Mediterranean (EM). We compared FE and RMR of fish from these three populations at 18°C or 24°C. We held 200 fish (62 AT, 66 WM and 72 EM) in individual aquaria and fed them from ad libitum down to fasting. Feed efficiency was assessed for an ad libitum feeding rate and for a fixed restricted ration (1% of metabolic body weight.day -1, with metabolic body weight = body weight 0.8). After being refed 12 weeks in a common tank, individual RMR was measured over 36h by intermittent flow respirometry. There was a significant effect of temperature whereby fish at 18°C had greater mean FE (P < 0.05) and lower RMR (P < 0.001). There was also a significant effect of population, where AT fish had lower FE (P < 0.05) and greater RMR (P < 0.001) than WM and EM, at both temperatures. Despite these differences in temperature and population means, individual FE and RMR were not significantly correlated (P > 0.05). Therefore, although the results provide evidence of an association between metabolic rate and FE, RMR was not a predictor of individual FE, for reasons that require further investigation.

Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event betweenD. labraxandD. punctatusis responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages ofD. labrax. An exception to this was found within regions involved in RI between the twoD. labraxlineages. In those regions, archaic tracts originating fromD. punctatuslocally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred betweenD. punctatusand theD. labraxAtlantic lineage, while Atlantic and MediterraneanD. labraxlineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the twoD. labraxlineages.

The European seabass (Dicentrarchus labrax) is a species of particular ecological and economic importance. Stock assessments have recently revealed the worrying state of the “Northern stock”, probably due to overfishing and a series of poor recruitments. The extent to which these poor recruitments are due to environmental variability is difficult to assess, as the processes driving the seabass life cycle are poorly known. Here we investigate how food availability and temperature may affect the growth and survival of wild seabass at the individual scale. To this end, we developed a bioenergetics model based on the Dynamic Energy Budget (DEB) theory. We applied it to seabass population of the Northeast Atlantic region (Bay of Biscay – English Channel area) throughout their entire life cycle. We calibrated the model using a combination of age-related length and weight datasets: two were from aquaculture experiments (larvae and juveniles raised at 15 and 20°C) and one from a wild population (juveniles and adults collected during surveys or fish market sampling). By calibrating the scaled functional response that rules the ingestion of food and using average temperature conditions experienced by wild seabass (obtained from tagged individuals), the model was able to reproduce the duration of the different stages, the growth of the individuals, the number of batches and their survival to starvation. We also captured one of the major differences encountered in the life traits of the species: farmed fish mature earlier than wild fish (3 to 4 years old vs. 6 years old on average for females, respectively) probably due to better feeding conditions and higher temperature. We explored the growth and survival of larvae and juveniles by exposing the individuals to varying temperatures and food levels (including total starvation). We show that early life stages of seabass have a strong capacity to deal with food deprivation: the model estimated that first feeding larvae could survi

Using breeding programs to improve feed efficiency, the ratio between fish body weight gain (BWG) and feed intake (FI), could increase aquaculture sustainability through reduced feed costs and environmental impact. To this end, individual phenotypic information is required. Individual FI can be measured by isolating each fish. Under these conditions, restricting the feeding rate has proved relevant to improve feed efficiency indirectly by selecting faster-growing animals. Moreover, a restricted feeding rate reduces the work load of collecting uneaten pellets after each meal. The approach assumes the most efficient fish at high and low feeding rates are the same, but this assumption remains untested. In European sea bass (Dicentrarchus labrax), feed efficiency is likely to be impacted also by population, temperature, and their interaction, as already demonstrated for growth in this species. To investigate these issues, 200 European sea bass from three wild populations, Atlantic (AT), West Mediterranean (WM) and East Mediterranean (EM), were reared individually at two temperatures, 18°C and 24°C. Their BWG and FI were measured at six different feeding rates, from ad libitum (100% ADL) down to fasting. A trade-off between performance at 100% ADL and at fasting was observed: more efficient fish at 100% ADL showed a stronger decrease in BWG (standardized to metabolic weight) when the feeding rate was progressively lowered and lost more weight at fasting. The most efficient fish were not the same depending on the feeding rate, suggesting the feeding rate used to phenotype fish in selective breeding programs must be the same as that used in commercial practices. The slope in the linear relationship between BWG and FI (both standardized to metabolic weight) was similar among populations and temperatures. However, EM fish had a higher intercept than others, suggesting this population grew more and thus was more efficient for an equal feeding rate. Similarly, fish reared at 1

In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood‐based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user‐defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN) on a real European seabass (Dicentrarchus labrax) SNP data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user‐set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy‐to‐use and reliable software for parentage assignment, even when up to 50% of sires are missing.

Measuring individual feed intake of fish in farms is complex and precludes selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content that were possibly linked to FCR. The 588 fish were derived from a full factorial mating between parental lines divergently selected for high (F+) or low (F–) weight loss at fasting. The pedigree was known back to the great grand-parents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs which allowed to calculate the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h2 = 0.47 and 0.76, respectively) and strongly genetically correlated (−0.98) meaning that, under restricted feeding, faster growing fish were more efficient. FCR and growth rate in aquariums were also significantly better for fish with both parents from F– (1.38), worse for fish with two parents F+ (1.51) and intermediate for cross breed fish (F+/F– or F–/F+ at 1.46). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, selecting for higher growth rate in aquarium, lower weight loss during fasting and fatter fish could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed experimentally that groups composed of fish with good individual FCR were significantly more efficient. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, improving FCR in aquarium and weight loss during fasting is promising to improve FCR of fish in groups but a selection response experiment needs to be done. Finally, we showed that the reliability of estimated breeding values was higher (

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.

Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW−) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23−) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW− and E8/E23− (Both−), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both− (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while He

Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). We found less females than males in the progeny, both in the global dataset (32.5%) and within each paternal group (from 25.1% for NEM to 39.0% for WEM), with significant variation among populations, dams, and sires. Sex, body weight (BW), and body length (BL) showed moderate heritability (0.52 ± 0.17, 0.46 ± 0.17, 0.34 ± 0.15, respectively) and sex was genetically correlated with BW and BL, with rAsex/BW = 0.69 ± 0.12 and rA sex/BL = 0.66 ± 0.13. A weighted GWAS performed both on the global dataset and within each paternal group revealed a different genetic architecture of sex determination between Atlantic and Mediterranean populations (9 QTLs found in NAT, 7 in WEM, 5 in NEM, and 4 in SEM, with a cumulated variance explained of 27.04%, 21.87%, 15.89%, and 12.10%, respectively) and a more similar genetic architecture among geographically close populations compared to geographically distant populations, consistent with the hypothesis of a population-specific evolution of polygenic sex determination systems in different environments.

We estimated genetic parameters of feed conversion ratio (FCR) and daily growth coefficient (DGC) using individual phenotypes measured in aquariums under a restricted feeding regime and genomic information on 2,722 SNP markers. The results showed a moderate heritability of both traits (0.26 for FCR and 0.41 for DGC) as well as close to unity negative genetic correlation between them. Thus, FCR of fish in aquariums could be improved by selecting fish for higher DGC. Nevertheless, these results must be taken with caution until we know whether individual FCR measured in aquariums also reflects the FCR of fish reared in groups.

Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unrelated to speciation can interfere. Here we use haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. Local ancestry patterns show that genomic islands first emerged in allopatry through linked selection acting on a heterogeneous recombination landscape. Then, upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we find that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.

The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of vertebrate sex, and we report the evidence of such relationship only below a methylation threshold, similar to 80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-beta 2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-beta 2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with similar to 90% accuracy and discuss possible applications.

Background: European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach. Results: We used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29-0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of 'chromosome' 25) 3, 20 and 25 (P < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability. Conclusions: Genome-wide significant QTL were identified but each with

Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30–70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE. Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.

The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.

Viral Nervous Necrosis (VNN) disease is considered as one of the most serious threats for European sea bass cultured in Mediterranean Sea, with no simple and effective procedures to treat this disease. In this study, 1472 offspring resulting from artificial full factorial mating of western Mediterranean dams with sires from four different wild populations of European sea bass (Northern Atlantic, NAT; Western Mediterranean, WEM; Northern-East Mediterranean, NEM; and Southern-East Mediterranean, SEM) were challenged by experimental infection to W80 betanodavirus strain in order to evaluate genetic variations for VNN resistance among populations and genetic correlations between VNN resistance and production traits. The results showed a large variation of VNN resistance between the four populations tested as well as between sire families within strain. The survivals between pure wild populations SEM, NEM, WEM and NAT were estimated at 99%, 94%, 62%, and 44%, respectively. A moderate intra-population heritability of VNN resistance, calculated based on liability scale with sire model, was recorded for the first time in European sea bass (h2u = 0.26 ± 0.11). Finally, moderate negative genetic correlations between VNN resistance and daily growth coefficient (DGC) and body weight (BW) were also demonstrated (− 0.28 ± 0.20, − 0.35 ± 0.14, respectively) while the genetic correlation between resistance to VNN and fillet adiposity (FA) was weakly negative and not significant (− 0.13 ± 0.19). These results give good prospects of selective breeding of European sea bass for improved resistance to VNN disease.

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.

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.