Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing

Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs.Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencingpublishedVersio

Potential for genomic selection on feed efficiency in gilthead sea bream (Sparus aurata), based on individual feed conversion ratio, carcass and lipid traits

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

Changes in transcriptomic and behavioural traits in activity and ventilation rates associated with divergent individual feed efficiency in gilthead sea bream (Sparus aurata)

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

Very high genetic fragmentation in a large marine fish, the meagreArgyrosomus regius(Sciaenidae, Perciformes) : impact of reproductive migration, oceanographic barriers and ecological factors

The meagre Argyrosomus regius is a large Sciaenid fish known to reproduce in the eastern Atlantic and Mediterranean Sea in just five distinct and restricted geographic areas: along the Mauritanian coast and at estuary openings (Gironde, Tagus, Guadalquivir and Nile). The biological traits of A. regius (high dispersal capabilities, high fecundity, long larval phase, overlapping generations, reproduction until 40 years of age) are, in principle, favourable to high gene flow, which should lead to genetic homogeneity over large geographic scales. Nevertheless, the high geographic distances between the few reproductive areas leads one ask whether there is genetic differentiation in this species. In the present study, the genetic differentiation of the wild A. regius was investigated across most of its natural range from the Atlantic Ocean (France, Portugal, Spain, Mauritania) to the Mediterranean Sea (Egypt, Turkey), using 11 microsatellite markers previously identified in another Sciaenid, the red drum Sciaenops ocellatus. At least two very distinct groups could be identified, separated by the Gibraltar Strait. Genetic divergences (FST values) were intermediate between the Atlantic samples (0.012–0.041), high between Egypt and the Atlantic (0.06–0.107) or Aegean Sea (0.081) and extremely high between the Aegean Sea and the Atlantic (0.098–0.168). A. regius exhibited a very high level of genetic differentiation rarely reported in marine fishes. These results also demonstrate the existence of a sixth independent spawning area in the Menderes delta (Turkey). Factors potentially involved in this very high genetic fragmentation are discussed, including physical barriers, glaciation pulses and biological traits

Very high genetic fragmentation in a large marine fish, the meagre

The meagre Argyrosomus regius is a large Sciaenid fish known to reproduce in the eastern Atlantic and Mediterranean Sea in just five distinct and restricted geographic areas: along the Mauritanian coast and at estuary openings (Gironde, Tagus, Guadalquivir and Nile). The biological traits of A. regius (high dispersal capabilities, high fecundity, long larval phase, overlapping generations, reproduction until 40 years of age) are, in principle, favourable to high gene flow, which should lead to genetic homogeneity over large geographic scales. Nevertheless, the high geographic distances between the few reproductive areas leads one ask whether there is genetic differentiation in this species. In the present study, the genetic differentiation of the wild A. regius was investigated across most of its natural range from the Atlantic Ocean (France, Portugal, Spain, Mauritania) to the Mediterranean Sea (Egypt, Turkey), using 11 microsatellite markers previously identified in another Sciaenid, the red drum Sciaenops ocellatus. At least two very distinct groups could be identified, separated by the Gibraltar Strait. Genetic divergences (FST values) were intermediate between the Atlantic samples (0.012–0.041), high between Egypt and the Atlantic (0.06–0.107) or Aegean Sea (0.081) and extremely high between the Aegean Sea and the Atlantic (0.098–0.168). A. regius exhibited a very high level of genetic differentiation rarely reported in marine fishes. These results also demonstrate the existence of a sixth independent spawning area in the Menderes delta (Turkey). Factors potentially involved in this very high genetic fragmentation are discussed, including physical barriers, glaciation pulses and biological traits

Development and characterization of a 57K Single Nucleotide Polymorphism array for European sea bass

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Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata)

International audienceDisease 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 effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream

Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57k SNP array DlabChip

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