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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.

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.

There is limited scientific evidence on the real impact of selective breeding in aquaculture on the medium term, while the composition of aquafeeds is rapidly evolving towards plant-based raw materials. We compared a rainbow trout line selected in freshwater for fillet production (improved growth, carcass yield and fillet fat) for ten generations (G10) with an unselected control line from the same base population (G0). We crossed G10 and G0 neomales to the same G10 females, thus creating a Selected and a Control group expected to diverge by half the true difference between G0 and G10. Those were grown to 1.6 kg, and two feeds were compared across the two lines from 264 to 374 days post-hatching. One was a commercial standard, the second was a “future” feed devoid of fishmeal, fish oil and soy-based products, with microalgae as a source of docosahexaenoic acid (DHA). After doubling the difference between the Selected and the Control to estimate the true performance of G0, we saw that G10 was improved relative to G0 for body weight (+61%), feed conversion ratio (−17 to −20%), fillet fat (+28–53%) and carcass yield (+4.2%), but not for fillet yield. Survival was not affected by selection. Both feeds had a similar performance in terms of growth, but the future feed showed a higher FCR, probably due to a feed intake measurement issue. Fish had a good EPA+DHA content (>1.2 g/100 g wet weight) with both feeds, partly linked to endogenous synthesis of these fatty acids. There was little if any genotype by feed interaction. This study shows that selective breeding can produce fast growing, feed efficient and thus provide opportunity for more sustainable fish culture. We showed that highly nutritious fish can be produced with good growth performance without using any fish meal, fish oil or soy-based product.

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.

Introduction: The sea bass, Dicentrarchus labrax, is an important species for European mariculture, mainly in Mediterranean countries. In this species, females grow faster and reach a higher weight than males. However, most farmed fish batches show a highly male-skewed sex-ratio. The sea bass has a complex sex determination system, combining both genetic (polygenic) and environmental (temperature) influences. Low initial temperatures (<17°C) favor female sex determination. In contrast, temperature in the late post-larval phase has the opposite effect, with cold temperature favoring male differentiation and high temperature (up to 23°C) favoring female differentiation (Clota et al., 2021). However, data on the combined effects of genotype and temperature are lacking. We need to know whether there is genotype-by-environment (GxE) interaction or not, to deploy a strategy towards producing monosex female individuals for production while keeping a balanced sex-ratio for hatchery and selective breeding. Results: Starting at 1 day and using incremental rearing periods at 16°C (31 to 244 days), followed by an increase to 21°C, we first showed that, while 31 days at 16°C led to 26% of females, increased cold exposure promoted the proportion of females, up to 46% after 74 days at 16°C. Conversely, exposure to 16°C for a period longer than 74 days progressively reduced the proportion of females, reaching a minimum of ≈ 10% after 230 days at 16°C. In a second experiment, we demonstrated that after an initial rearing of fish for 90 days at 16°C, a secondary exposure to four different temperatures (19, 21, 23, 25°C) resulted in different sex-ratios, with more females at higher temperatures (from 30% at 19°C to 49% at 25°C). Then, we examined the genotype-by-environment interaction in both periods, by genotyping fish with a 57K SNP chip, comparing 1) two groups reared at 16 or 21°C during the first 60 days and 2) four groups of fish reared at 19, 21, 23 or 25°C after 90 days at 16

Fish sex determination is often considered as governed by either genetic or environmental factors, but the European sea bass (Dicentrarchus labrax) defies this theory. In this species, a polygenic threshold sex determination system was demonstrated (Vandeputte et al. 2007), where the genetic sex tendency is influenced by larval rearing temperature to determine the phenotypic sex (Piferrer et al, 2005). In this study, we applied two thermal treatments during early larval stage, a low temperature protocol (16°C, LT), known to favour balanced sex-ratios and a high temperature masculinizing protocol (21°C, HT). We combined various “-omics” approaches to characterize this temperature-dependent polygenic sex determination of European sea bass. We produced 8 families by mating 8 males with the same female. The progenies were reared in common garden under two thermal treatments (LT, HT) in triplicate. Fish at four different key developmental stages encompassing the temperature sensitive period were sampled. We predicted the genetic sex tendency (eGST) of the animals using a genomic relationship matrix derived from 57K SNPs from the DLabCHIP array (Griot et al., 2021) with a threshold animal model. This was completed by a transcriptomic approach, whole-body energy measurements. The proportion of females was 53.4% at LT and 25.3% at HT, showing a marked masculinization at high temperature. We found that the eGST accurately predicted the future phenotypic sex. We provided evidence that energetic pathways, concerning the regulation of lipids and glucose, are involved in sex determination and could explain why females tend to exhibit higher energy levels and improved growth compared to males. Overall, we describe for the first time a sex determination system resulting from continuous genetic and environmental influences in an animal, which provides significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish

The European sea bass is a gonochoristic species that exhibits sexual size dimorphism in favor of females, the preferred sex in aquaculture, and has a polygenic system of sex determination, where both genetic factors and temperature contribute to population sex ratios. Thus, when reared at temperatures >17ºC, a proportion of the fish which would develop as females under cooler temperature become masculinized (neomales). Epigenetic biomarkers such as DNA methylation changes at specific loci (CpG), which are susceptible to environmental change, hold promise to complement genetic selection of broodstock and could help select fish with desired phenotypic traits resulting from the interplay between genetics and environment. Here, we aim to understand the nature of the epigenetic inheritance and the contribution of the genotype and of the environment to DNA methylation profiles. To this end, we created eight families by crossing one female with eight males which had been reared at different temperature treatments when young: two at low temperature (LT), three at high temperature (HT), and 3 HT neomales (NM). The offspring were also exposed to LT and HT during the thermosensitive period, thus creating a total of 32 groups for analysis (eight parents of three types, two temperatures and two sexes) and gonadal tissues were sampled when fish were over one year old. Based on genotypic (sex tendency) and phenotypic data of the offspring, we selected fish representative of each group by sex, temperature, and sire type. In total, we produced 130 libraries by Reduced Representation Bisulfite sequencing to analyze the DNA methylome of grandparents’ gametes (F0, n=2), sires and dam gametes (F1, n=9) and offspring juvenile gonad (F2, n=119). The obtained dataset generated a matrix of high dimensionality (130 samples x ~1,400,000 CpGs per sample). To make it more manageable, we contemplated several approaches to retain the most informative CpG positions. One included the definition of

The European sea bass is a teleost with polygenic sex determination (PSD), where genetics and environmental factors contribute to sex ratios. However, in farming, many fish that would become females under natural conditions develop as phenotypic males, called neomales. Identifying males that produce progeny resistant to the masculinizing effects of elevated temperature is desirable. However, neomales are indistinguishable genetically from regular females and transcriptomically from regular males. Here, we compared the gonadal epigenome of heat-resistant females (n=23) and neomales (n=24) of six different families obtained from the cross of the same female with six different males. After several data pre-processing steps of more than 1,4 x10^6 CpGs we filtered out the 118,2x10^3 DMCs between testes (n=24) and ovaries (n= 23) to eliminate differences due to tissue. We ended up with 128,1 x10^3 most variable regions of 200 bp each. Then we applied multi-omics factor analysis (MOFA) taking as informative layers promoters, exons, introns and CpG islands (D=1000). The unsupervised model revealed four hidden factors. Factor 1 discriminated neomales from females and allowed the identification of biomarkers such as a CpG in the sfxn2 promoter, the methylation of which was higher in females than in neomales. To our knowledge, this constitutes the first example where epigenetics is used to reveal differences in the susceptibility of the gonads to high temperature in a PSD species