Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)

Development of the First Microsatellite Multiplex PCR Panel for Meagre (Argyrosomus regius), a Commercial Aquaculture Species

In this study, a microsatellite-based multiplex PCR panel for meagre (Argyrosomus regius) was developed as a useful and single tool in parental assignment and population studies. Twenty-one specific and interspecific microsatellites from different aquaculture species of meagre (Argyrosomus regius), Japanese meagre (A. japonicus), red drum (Sciaenops ocellatus) and yellow meagre (Acoupa weakfish) were assessed for genetic variability, allelic range and genotype reliability. Finally, a SuperMultiplex for Argyrosomus regius (SMAr) was designed with only the best eight microsatellite markers. The panel assessment was performed using a batch of brood stock from one company and a sample of 616 offspring. It was possible to assign 95% of the offspring to a single pair of parents using the exclusion method. It is therefore considered an easy procedure, and a powerful and low-cost tool for parental assignment to support companies’ breeding programs and to exchange information between research groups.

Phenotypic and Genetic Components for Growth, Morphology, and Flesh-Quality Traits of Meagre (Argyrosomus regius) Reared in Tank and Sea Cage

Simple Summary

Meagre is an emergent species in aquaculture, due to its fast growth rate, low feed conversion ratio, and the high quality of the product. Although advances have been achieved in its management, reproduction, and feeding, breeding programs have not yet been developed. For this reason, this study aimed to provide information about the genetic variations in growth, morphology traits, and flesh chemical composition to be included in a selective breeding program, studied in two different housing systems (cage and tank). Heritabilities for growth and morphology traits, and for fillet fat percentage were medium, revealing those traits as a possible selection criterion in a breeding program. Image analysis provided a great amount of objective information regarding the different morphological traits of the fish, where a positive and high correlation with growth traits was observed. Positive phenotypic correlation between fillet fat percentage and body weight was observed, so a selection process to improve growth rate could lead to a fish with higher fillet fat percentage.

Abstract

Meagre (Argyrosomus regius) plays an important role in the aquaculture system, with the potential for diversification of European aquaculture, and is characterized by its fast growth rate, low feed conversion ratio, and the high quality of the product. Focusing on the relevance of meagre, the aim of the study was to analyze growth performance, fish morphology, and flesh composition phenotypically and genetically to be considered as a strategy in a breeding program. For this purpose, 633 fish were raised in two different housing systems, in sea cages or in a continental tank, and when they reached harvest size, manual growth traits, automatic morphology by the image analysis program IMAFISH_ML, and flesh chemical composition (fat, protein, moisture, and collagen percentages) were measured. The fish reared in the cages showed a higher body weight and fillet fat percentage than those in the tank. Heritabilities for growth and morphology traits, and for fillet fat percentage were medium, revealing these traits as a possible selection criterion in a breeding program. Phenotypic and genetic correlations between growth and morphology traits were positive and high. Phenotypic correlations between growth or morphology traits with fillet fat percentage were positive and medium; genetic correlations were not estimated accurately.

Genetic Analysis of the Fatty Acid Profile in Gilthead Seabream (Sparus aurata L.)

Simple Summary

Humans require essential fatty acids in their diet and marine fish are a source of them, especially omega3 fatty acids that present high benefits on diverse vascular diseases and the immune system. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, that could lead to fish with a higher fillet fat content and a fatty acid profile with a lower polyunsaturated fatty acids percentage. Fillet fat content and its fatty acids profile have been revealed as heritable traits. Therefore, further studies to go deeper in the selection process are advisable.

Abstract

The gilthead seabream is one of the most valuable species in the Mediterranean basin both for fisheries and aquaculture. Marine fish, such as gilthead seabream, are a source of n3 polyunsaturated fatty acids, highly appreciated for human food owing to their benefits on the cardiovascular and immune systems. The aim of the present study was to estimate heritability for fatty acid (FA) profile in fillet gilthead seabream to be considered as a strategy of a selective breeding program. Total of 399 fish, from a broodstock Mediterranean Sea, were analysed for growth, flesh composition and FA profile. Heritabilities for growth traits, and flesh composition (fat, protein, and moisture content) were medium. Heritability was moderate for 14:0, 16:0 and 18:1n9 and for sum of monounsaturated FA and n6/n3 ratio, and it was low for 20:1n11 and 22:6n3 and the ratio unsaturated/saturated FA. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, other quality traits, such as fillet fat content and its fatty acids profile should be considered, since they are very important traits for the consumer, from a nutritional point of view and the benefits for the health.

Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.

Reproductive performance of gilthead seabream (Sparus aurata) broodstock showing different expression of fatty acyl desaturase 2 and fed two dietary fatty acid profiles

Previous studies have shown that it is possible to nutritionally program gilthead seabream offspring through fish oil (FO) replacement by vegetable oils (VO) in the broodstock diet, to improve their ability to grow fast when fed low fish meal (FM) and FO diets during grow-out phase. However, in those studies broodstock performance was reduced by the VO contained diet. Therefore, the present study aimed to determine if it is possible to replace FO by a mixture of FO and rapeseed oil (RO) with a specific fatty acid profile in broodstock diets, without altering gilthead seabream broodstock reproductive performance. Besides, the study also aimed to evaluate the reproductive performance of broodstock with different expression of fatty acid desaturase 2 gene (fads2) a key enzyme in synthesis of long chain polyunsaturated fatty acids. For that purpose, broodfish having either a high (HD) or low (LD) expression of fads2 were fed for three months during the spawning season with two diets containing different fatty acid profiles and their effects on reproductive hormones, fecundity, sperm and egg quality, egg biochemical composition and fads2 expression were studied. The results showed that blood fads2 expression in females, which tended to be higher than in males, was positively related to plasma 17β-estradiol levels. Moreover, broodstock with high blood fads2 expression showed a better reproductive performance, in terms of fecundity and sperm and egg quality, which was correlated with female fads2 expression. Our data also showed that it is feasible to reduce ARA, EPA and DHA down to 0.43, 6.6 and 8.4% total fatty acids, respectively, in broodstock diets designed to induce nutritional programming effects in the offspring without adverse effects on spawning quality. Further studies are being conducted to test the offspring with low FM and FO diets along life span.

Heritability Estimates and Genetic Correlation for Growth Traits and LCDV Susceptibility in Gilthead Sea Bream (Sparus aurata)

The lymphocystis disease (LCD) is a viral infection with a high economic impact in gilthead sea bream aquaculture. In this study, genetic estimates associated with lymphocystis disease virus (LCDV) disease susceptibility and growth were determined in sea bream juveniles. Two fish batches (named batch 1 and batch 2) were built from mass spawning and reared under industrial conditions until disease outbreak. At the moment of the sampling (n = 500 specimens for each batch), all animals had the typical LCDV lesions in the skin. For phenotyping, animals were weighted and photographed for image analysis (surface covered and lesion intensity). LCDV DNA copies were quantified in the liver by qPCR. Batch 1 had a higher surface covered and lesion intensity than batch 2, and the body caudal region was the lowest affected region in both batches. The average LCDV DNA copies in liver were higher in the batch 1 than batch 2, and they were positively correlated with severity index (SI) categories (r2 = 0.90–0.94). The total number of families evaluated were 150 and 128 for batch 1 and batch 2, respectively, with a high bias in offspring contribution by family and broodstock. Heritabilities for weight and length were 0.18 and 0.14 in batch 1 and 0.06 and 0.05 in batch 2, respectively. Heritability for the number of viral DNA copies was low (<0.08) in both batches. Heritabilities for SI in binary scale were 0.32/0.33 and 0.21/0.24 (underlying liability/Bayesian approach) for batch 1 and batch 2, respectively. Genetic correlations were very high and positive when growth traits (weight and length) or disease traits (LCDV DNA copies and SI) were compared. In contrast, the genetic correlations between growth and disease traits were moderate–high and positive in the batch 1 but negative in batch 2. These results indicate the genetic selection for LCDV susceptibility and growth is feasible in sea bream juveniles, although estimates are highly dependent on the age. The information provided is relevant to designing selective breeding programs in sea bream.

Spatial connectivity pattern of expanding gilthead seabream populations and its interactions with aquaculture sites: a combined population genetic and physical modelling approach

In gilthead seabream the number of domesticated individuals increased annually, and escape events occur regularly in the Adriatic Sea. Still there is a lack of population genetic characteristics and evidence of the extent and geographic scale of interbreeding resulting from fish-farm escapees. We screened 1586 individuals using a panel of 21 neutral microsatellite loci in several consecutive years and here report on the medium-scale detection of hybrid and farmed seabream in the natural environment. Wild adults showed a lack of genetic structure within basin and sampling years and reduced connectivity with wild offspring collection, suggesting their temporal residency within the Adriatic. On the contrary, by linking the results of multiannual genetic analyses with the results of coupled hydrodynamic and individual based models (IBM-Ichthyop), we observed a strong connection of wild seabream associated with tuna-aquaculture sites and offspring from the nursery grounds, indicating that the surroundings of tuna sea-cage farms can function as a spawning grounds. The study results present the genetic baseline of wild and farmed strains from the eastern Adriatic Sea, as a first step toward development of a mitigation strategy for fish escapees aimed at controlling further erosion of genetic integrity.

Co-expression Analysis of Sirtuins and Related Metabolic Biomarkers in Juveniles of Gilthead Sea Bream (Sparus aurata) With Differences in Growth Performance

Sirtuins (SIRTs) represent a conserved protein family of deacetylases that act as master regulators of metabolism, but little is known about their roles in fish and livestock animals in general. The present study aimed to assess the value of SIRTs for the metabolic phenotyping of fish by assessing their co-expression with a wide-representation of markers of energy and lipid metabolism and intestinal function and health in two genetically different gilthead sea bream strains with differences in growth performance. Fish from the fast-growing strain exhibited higher feed intake, feed efficiency and plasma IGF-I levels, along with higher hepatosomatic index and lower mesenteric fat (lean phenotype). These observations suggest differences in tissue energy partitioning with an increased flux of fatty acids from adipose tissue toward the liver. The resulting increased risk of hepatic steatosis may be counteracted in the liver by reduced lipogenesis and enhanced triglyceride catabolism, in combination with a higher and more efficient oxidative metabolism in white skeletal muscle. These effects were supported by co-regulated changes in the expression profile of SIRTs (liver, sirt1; skeletal muscle, sirt2; adipose tissue, sirt5-6) and markers of oxidative metabolism (pgc1α, cpt1a, cs, nd2, cox1), mitochondrial respiration uncoupling (ucp3) and fatty acid and triglyceride metabolism (pparα, pparγ, elovl5, scd1a, lpl, atgl) that were specific to each strain and tissue. The anterior intestine of the fast-growing strain was better suited to cope with improved growth by increased expression of markers of nutrient absorption (fabp2), epithelial barrier integrity (cdh1, cdh17) and immunity (il1β, cd8b, lgals1, lgals8, sIgT, mIgT), which were correlated with low expression levels of sirt4 and markers of fatty acid oxidation (cpt1a). In the posterior intestine, the fast-growing strain showed a consistent up-regulation of sirt2, sirt3, sirt5 and sirt7 concurrently with increased expression levels of markers of cell proliferation (pcna), oxidative metabolism (nd2) and immunity (sIgT, mIgT). Together, these findings indicate that SIRTs may play different roles in the regulation of metabolism, inflammatory tone and growth in farmed fish, arising as powerful biomarkers for a reliable metabolic phenotyping of fish at the tissue-specific level.

Identification of Quantitative Trait Loci Associated with the Skeletal Deformity LSK complex in Gilthead Seabream (Sparus aurata L.)

Morphological abnormalities, especially skeletal deformities, are some of the most important problems affecting gilthead seabream (Sparus aurata L.) aquaculture industry. In this study, a QTL analysis for LSK complex deformity in gilthead seabream is reported. LSK complex is a severe deformity consisting of a consecutive repetition of three vertebral deformities: lordosis, scoliosis, and kyphosis. Seventy-eight offspring from six breeders from a mass-spawning were analyzed: five full-sibling families, three maternal, and two paternal half-sibling families. They had shown a significant association with the LSK complex prevalence in a previous segregation analysis. Fish were genotyped using a set of multiplex PCRs (ReMsa1-13), which includes 106 microsatellite markers. Two methods were used to perform the QTL analysis: a linear regression with the GridQTL software and a linear mixed model with the Qxpak software. A total of 18 QTL were identified. Four of them (QTLSK3, 6, 12, and 14), located in LG5, 8, 17, and 20, respectively, were the most solid ones. These QTL were significant at genome level and showed an extremely large effect (>35%) with both methods. Markers close to the identified QTL showed a strong association with phenotype. Two of these molecular markers (DId-03-T and Bt-14-F) were considered as potential linked-to-this-deformity markers. The detection of these QTL supposes a critical step in the implementation of marker-assisted selection in this species, which could decrease the incidence of this deformity and other related deformities. The identification of these QTL also represents a major step towards the study of the etiology of skeletal deformities in this species.

Genetic parameters and genotype-environment interactions for skeleton deformities and growth traits at different ages on gilthead seabream (Sparus aurata L.) in four Spanish regions

One of the most important problems of fish aquaculture is the high incidence of fish deformities, which are mainly skeletal. In this study, genetic parameters on gilthead seabream (Sparus aurata L.) for skeleton deformities at different ages (179, 269, 389, 539 and 689 days) and their correlations with growth traits were estimated, as were as their genotype × environment interactions (G × E) at harvesting age. A total of 4093 offspring from the mass spawning of three industrial broodstocks belonging to the PROGENSA(®) breeding programme were mixed and on-grown by different production systems in four Spanish regions: Canary Islands (tanks and cage), Andalusia (estuary), Catalonia (cage) and Murcia (cage). Parental assignment was inferred using the standardized SMsa1 microsatellite multiplex PCR. From three broodstocks, 139 breeders contributed to the spawn and a total of 297 full-sibling families (52 paternal and 53 maternal half-sibling families) were represented. Heritabilities at different ages were medium for growth traits (0.16-0.48) and vertebral deformities (0.16-0.41), and low for any type of deformity (0.07-0.26), head deformities (0.00-0.05) and lack of operculum (0.06-0.11). The genetic correlations between growth and deformity traits were medium and positive, suggesting that to avoid increasing deformities they should be taken into account in breeding programmes when growth is selected. The G × E interactions among the different facilities were weak for length and deformity and strong for growth rate during this period. These results highlight the potential for the gilthead seabream industry to reduce the prevalence of deformities by genetic improvement tools.