Search

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.

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

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.

European sea bass (Dicentrarchus labrax) is an important European aquaculture species. Females, performing better than males with later maturation and larger size, are preferred. Unfortunately, in aquaculture conditions, the sex-ratio is typically biased towards males. Thus, deciphering the sex determinism system and finding routes for controlling the sexratio of this species has been a long-lasting challenge to support sea bass production and selective breeding programmes. 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 more balanced sex-ratios, and a high temperature masculinizing protocol (21°C, HT). We used genome-wide SNP genotypes to estimate the genetic parameters and genotype-by-temperature interaction of sex tendency in European sea bass

In most animals, sex determination occurs at conception, when sex chromosomes are segregated following Mendelian laws. However, in multiple reptiles and fishes, this genetic sex can be overridden by external factors after fertilization or birth. In some species, the genetic sex may also be governed by multiple genes, further limiting our understanding of sex determination in such species. We used the European sea bass (Dicentrarchus labrax) as a model and combined genomic (using a single nucleotide polymorphism chip) and transcriptomic (RNA-Sequencing) approaches to thoroughly depict this polygenic sex determination system and its interaction with temperature. We estimated genetic sex tendency (eGST), defined as the estimated genetic liability to become a given sex under a liability threshold model for sex determination, which accurately predicts the future phenotypic sex. We found 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. Besides, early exposure to high-temperature up-regulated sox3, followed by sox9a in individuals with intermediate eGST, but not in individuals showing highly female-biased eGST, providing the most parsimonious explanation for temperature-induced masculinization. This gonadal state was maintained likely by DNA methylation and the up-regulation of several genes involved in histone modifications, including jmjd1c. Overall, we describe a sex determination system resulting from continuous genetic and environmental influences in an animal. Our results provide significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish

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

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 (

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.

In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual_ feed), standing stock (Qstock), and daily feed distributed (Qdaily_ feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily_ feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily_ feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily_ feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.

Fish farming is growing but is also facing challenges regarding economic viability and environmental sustainability. Selective breeding could enhance the sustainability of fish farming by changing animal performances. Thus, our aim was to develop sustainable breeding goals by using economic (EV) or environmental values (ENV) to weigh the traits to improve. EV and ENV represent the economic and environmental impacts of improving a trait. They were calculated using a bioeconomic model combined with a life cycle assessment. We showed that the EV and ENV of traits change with the factor constraining the production of the farm. It suggests that breeding goals should be finely tuned according to the limiting factor to maximize economic or environmental responses. In addition, we showed that improving feed conversion ratio is a major trait to improve because it always increases profit and decreases environmental impacts. We conclude that it is possible to develop breeding programs enhancing the sustainability of fish farming by improving the right trait in the right production system.