A comprehensive coding and microRNA transcriptome of vertebral bone in postlarvae and juveniles of Senegalese sole (Solea senegalensis)

Understanding vertebral bone development is essential to prevent skeletal malformations in farmed fish related to genetic and environmental factors. This is an important issue in Solea senegalensis, with special impact of spinal anomalies in postlarval and juvenile stages. Vertebral bone transcriptomics in farmed fish mainly comes from coding genes, and barely on miRNA expression. Here, we used RNA-seq of spinal samples to obtain the first comprehensive coding and miRNA transcriptomic repertoire for postlarval and juvenile vertebral bone, covering different vertebral phenotypes and egg-incubation temperatures related to skeleton health in S. senegalensis. Coding genes, miRNA and pathways regulating bone development and growth were identified. Differential transcriptomic profiles and suggestive mRNA-miRNA interactions were found between postlarvae and juveniles. Bone-related genes and functions were associated with the extracellular matrix, development and regulatory processes, calcium binding, retinol and lipid metabolism or response to stimulus, including those revealed by the miRNA targets related to signaling, cellular and metabolic processes, growth, cell proliferation and biological adhesion. Pathway enrichment associated with fish skeleton were identified when comparing postlarvae and juveniles: growth and bone development functions in postlarvae, while actin cytoskeleton, focal adhesion and proteasome related to bone remodeling in juveniles. The transcriptome data disclosed candidate coding and miRNA gene markers related to bone cell processes, references for functional studies of the anosteocytic bone of S. senegalensis. This study establishes a broad transcriptomic foundation to study healthy and anomalous spines under early thermal conditions across life-stages in S. senegalensis, and for comparative analysis of skeleton homeostasis and pathology in fish and vertebrates.

Exploring Omega-3's Impact on the Expression of Bone-Related Genes in Meagre (Argyrosomus regius)

Dietary supplementation with Omega-3 fatty acids seems to promote skeletal health. Therefore, their consumption at imbalanced or excessive levels has offered less beneficial or even prejudicial effects. Fish produced in aquaculture regimes are prone to develop abnormal skeletons. Although larval cultures are usually fed with diets supplemented with Omega-3 Long Chain Polyunsaturated fatty acids (LC-PUFAs), the lack of knowledge about the optimal requirements for fatty acids or about their impact on mechanisms that regulate skeletal development has impeded the design of diets that could improve bone formation during larval stages when the majority of skeletal anomalies appear. In this study, Argyrosomus regius larvae were fed different levels of Omega-3s (2.6% and 3.6% DW on diet) compared to a commercial diet. At 28 days after hatching (DAH), their transcriptomes were analyzed to study the modulation exerted in gene expression dynamics during larval development and identify impacted genes that can contribute to skeletal formation. Mainly, both levels of supplementation modulated bone-cell proliferation, the synthesis of bone components such as the extracellular matrix, and molecules involved in the interaction and signaling between bone components or in important cellular processes. The 2.6% level impacted several genes related to cartilage development, denoting a special impact on endochondral ossification, delaying this process. However, the 3.6% level seemed to accelerate this process by enhancing skeletal development. These results offered important insights into the impact of dietary Omega-3 LC-PUFAs on genes involved in the main molecular mechanism and cellular processes involved in skeletal development.

Skeletal Morphogenesis and Anomalies in Gilthead Seabream: A Comprehensive Review

The gilthead seabream, one of the most important species in Mediterranean aquaculture, with an increasing status of exploitation in terms of production volume and aquafarming technologies, has become an important research topic over the years. The accumulation of knowledge from several studies conducted during recent decades on their functional and biological characteristics has significantly improved their aquacultural aspects, namely their reproductive success, survival, and growth. Despite the remarkable progress in the aquaculture industry, hatchery conditions are still far from ideal, resulting in frequent abnormalities at the beginning of intensive culture, entailing significant economic losses. Those deformities are induced during the embryonic and post-embryonic periods of life, and their development is still poorly understood. In the present review, we created a comprehensive synthesis that covers the various aspects of skeletal morphogenesis and anomalies in the gilthead seabream, highlighting the genetic, environmental, and nutritional factors contributing to bone deformities and emphasized the potential of the gilthead seabream as a model organism for understanding bone morphogenesis in both aquaculture and translational biological research. This review article addresses the existing lack in the literature regarding gilthead seabream bone deformities, as there are currently no comprehensive reviews on this subject.

Variability of key-performance-indicators in commercial gilthead seabream hatcheries

Skeletal abnormalities are one of the most important key-performance-indicators (KPIs) in finfish hatcheries. Coping with the problem of skeletal abnormalities relies on the understanding of the link between the variability in the rearing conditions, and the variability in abnormalities incidence. Here, 74 seabream larval populations, from four commercial hatcheries, were examined for the presence of abnormalities and monitored with respect to the applied conditions. The inward folding of gill-cover and pugheadedness were the most frequent abnormalities present, with a mean (± SD) frequency of 11.3 ± 17.9 and 6.0 ± 7.2%, respectively. Other abnormalities were observed at very low mean rates (≤ 1%). A new abnormality type, ray-resorption syndrome, was also found. The recorded rate of normally inflated swimbladder was 92.3 ± 7.4% and mean survival rate was 25.9 ± 21.0%. Classification tree analysis indicated six rearing variables as potentially important predictors for pugheadedness, six variables for caudal-fin abnormalities and 10 variables for survival rate. Complementary genetic analysis, revealed differentiating genetic diversity and significant genetic distances among participating hatcheries, suggestive of the role of company-specific management of genetic resources in KPIs' variability. The results are discussed with respect to their potential use in the control of skeletal abnormalities by commercial hatcheries, as well as for benchmarking among different hatcheries.

A comparative whole genome sequencing analysis identified a candidate locus for lack of operculum in cultivated gilthead seabream (Sparus aurata)

The gilthead seabream (Sparus aurata, Sparidae family) is commonly used for aquaculture. Despite its great economic value, several problems in its cultivation remain. One of the major concerns is the high frequency of morphological abnormalities occurring during the early developmental stages. Partial and/or total lack of operculum is the most frequent anomaly affecting the fish cranial region. The existence of genetic factors that can at least partially determine this defect has been hypothesized. In this work, two DNA pools of highly related fry, one composed of normal-looking (control) fish and the other lacking an operculum (case), were constructed and whole-genome resequencing data produced from the two were compared. The analysis revealed a 1 Mb region on chromosome 2 with higher heterozygosity in the lack of operculum DNA pool than in the control DNA pool, consistent with the enrichment, in the first DNA pool, of one or more haplotypes causing or predisposing to the defect together with other normal haplotypes. A window-based F_ST analysis between the two DNA pools indicated that the same region had the highest divergence score. This region contained 2921 SNVs, 10 of which, with predicted high impacts (three splice donor and seven stop-gained variants), were detected in novel genes that are homologous to calcium-sensing receptor-like genes, probably involved in bone development. Other studies are needed to clarify the genetic mechanisms involved in predisposing fry to this deformity and then to identify associated markers that could be used in breeding programs to reduce the frequency of this defect in the broodstock.

Influence of Genetic Selection for Growth and Broodstock Diet n-3 LC-PUFA Levels on Reproductive Performance of Gilthead Seabream, Sparus aurata

Simple Summary

Gilthead seabream (GSB) broodstock were genetically selected based on their growth trait either high growth (HG) or low growth (LG) to evaluate the reproductive performance of these both traits under either fish oil (FO) or vegetable oil (VO) based diets feeding regime. The egg and larval quality were significantly improved by the broodstock selected for HG trait fed under FO based diet. This indicates that broodstock selected with HG trait has positive influence on the improving sperm, egg and larval quality in gilthead seabream.

Abstract

Genetic selection in gilthead seabream (GSB), Sparus aurata, has been undertaken to improve the growth, feed efficiency, fillet quality, skeletal deformities and disease resistance, but no study is available to delineate the effect of genetic selection for growth trait on GSB reproductive performance under mass spawning condition. In this study, high growth (HG) or low growth (LG) GSB broodstock were selected to evaluate the sex steroid hormones, sperm, egg quality and reproductive performance under different feeding regime of commercial diet or experimental broodstock diet containing either fish oil (FO) or vegetable oil (VO) based diet. Under commercial diet feeding phase, broodstock selected for either high growth or low growth did not show any significant changes in the egg production per kg female whereas egg viability percentage was positively (p = 0.014) improved by the high growth trait broodstock group. The experimental diet feeding results revealed that both growth trait and dietary fatty acid composition influenced the reproductive performance of GSB broodstock. In the experimental diet feeding phase, we observed high growth trait GSB males produced a higher number of sperm cells (p < 0.001) and also showed a higher sperm motility (p = 0.048) percentage. The viable egg and larval production per spawn per kg female were significantly improved by the broodstock selected for high growth trait and fed with fish oil-based diet. This present study results signifies that gilthead seabream broodstock selected on growth trait could have positive role in improvement of sperm and egg quality to produce viable progeny.

The Effect of Orally Supplemented Melatonin on Larval Performance and Skeletal Deformities in Farmed Gilthead Seabream (Sparus aurata)

The gilthead seabream larval rearing in continuous light is common in most Mediterranean hatcheries to stimulate larval length growth and increase food consumption. Several studies have shown that continuous light affects larval development and increases the prevalence of skeletal deformities. Melatonin is a crucial pineal neurohormone that displays daily secretion patterns, stimulates cell proliferation and embryonic development in Atlantic salmon and zebrafish, and improves osseointegration in mice and humans. However, no studies have examined the effects of orally supplemented melatonin on skeletal deformities in Sparus aurata larvae. We administered exogenous melatonin to gilthead seabream larvae via enriched rotifers and nauplii of Artemia. Exogenous melatonin induced bone deformities and stimulated parathyroid hormone-related protein-coding gene (PTHrP) mRNA expression. In addition to the melatonin-induced PTHrP high expression level, the recorded non coordinated function of skeletal muscle and bone during growth can be the fountainhead of bone deformities. Both myosin light chain 2 (mlc2) and bone gamma-carboxyglutamate protein-coding gene (bglap) expression levels were significantly affected by melatonin administration in an inverse dose–response manner during the exogenous melatonin administration. This is the first study to report the effect of inducing melatonin bone deformities on Sparus aurata larvae reared under ordinary hatchery conditions.

Radiographic characterisation of spinal curvature development in farmed New Zealand Chinook salmon Oncorhynchus tshawytscha throughout seawater production

Spinal anomalies are a recognised source of downgrading in finfish aquaculture, but identifying their cause(s) is difficult and often requires extensive knowledge of the underlying pathology. Late-onset spinal curvatures (lordosis, kyphosis, scoliosis) can affect up to 40% of farmed New Zealand Chinook (king) salmon (Oncorhynchus tshawytscha) at harvest, but little is known about their pathogenesis. Curvature development was radiographically documented in two related cohorts of commercially-farmed Chinook salmon throughout seawater production to determine (1) the timing of radiographic onset and relationships between (2) the curvature types, (3) the spinal regions in which they develop and (4) their associations with co-existing vertebral body anomalies (vertebral compression, fusion and vertical shift). Onset of curvature varied between individuals, but initially occurred eight months post-seawater transfer. There were strong associations between the three curvature types and the four recognised spinal regions: lordosis was predominantly observed in regions (R)1 and R3, kyphosis in R2 and R4, manifesting as a distinct pattern of alternating lordosis and kyphosis from head to tail. This was subsequently accompanied by scoliosis, which primarily manifested in spinal regions R2 and R3, where most of the anaerobic musculature is concentrated. Co-existing vertebral body anomalies, of which vertebral compression and vertical shift were most common, appeared to arise either independent of curvature development or as secondary effects. Our results suggest that spinal curvature in farmed New Zealand Chinook salmon constitutes a late-onset, rapidly-developing lordosis-kyphosis-scoliosis (LKS) curvature complex with a possible neuromuscular origin.

Skeletal anomalies in cultured golden pompano Trachinotus ovatus at early stages of development

Golden pompano Trachinotus ovatus (Linnaeus, 1758) is an important mariculture fish species with high commercial value in China. The present study thoroughly assessed the types and frequencies of skeletal deformities at the early developmental stages of golden pompano in an intensive aquaculture production system. Golden pompano (n = 500) were sampled 30 d posthatch (dph). The specimens were stained with Alcian blue and Alizarin red for the detection of deformities. The results of the study revealed that 77.2% of the specimens showed at least 1 spinal anomaly; most anomalies occurred in the prehemal region, and the most common deformity observed was vertebral fusion (37.4% incidence of deformities). The results of this study provide useful information for the early detection of skeletal deformities and for the optimization of fish fry breeding technologies.

Identification of a major locus determining a pigmentation defect in cultivated gilthead seabream (Sparus aurata)

The gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole-genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S. aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non-pigmented fish collected among the offspring of the same broodstock nucleus. Whole-genome resequencing reads from the two DNA pools were aligned to the S. aurata draft genome and variant calling was performed. A whole-genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5 Mbp on chromosome 6 in the non-pigmented pool that was not present in the normally coloured pool. The comparison of the non-pigmented with the normally coloured fish using a whole-genome F_ST analysis detected three main regions within the coordinates previously detected with the heterozygosity analysis. The results support the presence of a major locus affecting this discoloration defect in this fish population. The results of this study have practical applications, including the possibility of eliminating this defect from the breeding stock, with direct economic advantages derived from the reduction of discarded fry. Other studies are needed to identify the candidate gene and the causative mutation, which could add information to understand the complex biology of fish pigmentation.

Morphological and histological characterization of an ectopically mineralized structure in a gilthead sea bream Sparus aurata with opercular deformation

In this study, we describe an abnormal ectopically mineralized structure (EMS) that was found inside the skull of a juvenile Sparus aurata that also showed a bilateral opercular deformation. The overall phenotype and tissue composition were studied using micro-CT scanning and histological analyses. The ectopic structure occupies a large volume of the brain cavity, partially extruding into the gill cavity. It shows a dense mineralization and an extracellular matrix-rich phenotype, with variation in both the morphology and size of the cell lacunae, combined with an irregular fibre organization inside the matrix. This study is the first to report such an EMS in a juvenile teleost fish, where the tissue does not resemble any other connective tissue type described in bony fish so far. The tissue phenotype seems to rule out that the EMS corresponds to a tumorous cartilage. Yet, it is rather reminiscent of a highly mineralized structure found in cartilaginous fish, where it is suggested to be associated with damage repair.

Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing

Gilthead sea bream (Sparus aurata) is a teleost of considerable economic importance in Southern European aquaculture. The aquaculture industry shows a growing interest in the application of genetic methods that can locate phenotype–genotype associations with high economic impact. Through selective breeding, the aquaculture industry can exploit this information to maximize the financial yield. Here, we present a Genome Wide Association Study (GWAS) of 112 samples belonging to seven different sea bream families collected from a Greek commercial aquaculture company. Through double digest Random Amplified DNA (ddRAD) Sequencing, we generated a per-sample genetic profile consisting of 2,258 high-quality Single Nucleotide Polymorphisms (SNPs). These profiles were tested for association with four phenotypes of major financial importance: Fat, Weight, Tag Weight, and the Length to Width ratio. We applied two methods of association analysis. The first is the typical single-SNP to phenotype test, and the second is a feature selection (FS) method through two novel algorithms that are employed for the first time in aquaculture genomics and produce groups with multiple SNPs associated to a phenotype. In total, we identified 9 single SNPs and 6 groups of SNPs associated with weight-related phenotypes (Weight and Tag Weight), 2 groups associated with Fat, and 16 groups associated with the Length to Width ratio. Six identified loci (Chr4:23265532, Chr6:12617755, Chr:8:11613979, Chr13:1098152, Chr15:3260819, and Chr22:14483563) were present in genes associated with growth in other teleosts or even mammals, such as semaphorin-3A and neurotrophin-3. These loci are strong candidates for future studies that will help us unveil the genetic mechanisms underlying growth and improve the sea bream aquaculture productivity by providing genomic anchors for selection programs.

Gene expression analyses in malformed skeletal structures of gilthead sea bream (Sparus aurata)

The incidence of skeletal anomalies in reared fish has been translated for years in important economic losses for the aquaculture industry. In the present study, we have analysed the gene expression of extracellular matrix components and transcription factors involved in bone development in gilthead sea bream presenting different skeletal anomalies: lordosis (LD), lordosis-scoliosis-kyphosis (LSK) or opercular, dental or jaw malformations in comparison with control (CT) specimens. Results showed a possible link between the presence of LD and LSK and the significant downregulation of genes involved in osteoblasts' maturation and matrix mineralization (collagen type 1-alpha, osteopontin, osteocalcin, matrix Gla protein and tissue non-specific alkaline phosphatase), as well as in bone resorption (cathepsin K and matrix metalloproteinase 9) compared to CT animals. Contrarily, the key osteogenic transcription factor runx2 was upregulated in the malformed vertebra suggesting impaired determination of mesenchymal stem cells towards the osteoblastic lineage. Despite the gene expression patterns of the other malformed structures were not affected in comparison with CT fish, the results of the present study may contribute in the long term to identify potential candidate gene profiles associated with column deformities that may help reducing the incidence of appearance of skeletal anomalies in this important aquaculture species.

Saddleback syndrome in European sea bass Dicentrarchus labrax (Linnaeus, 1758): anatomy, ontogeny and correlation with lateral-line, anal and pelvic fin abnormalities

This study focused on the anatomy and ontogeny of saddleback syndrome (SBS) in reared European sea bass. The abnormality was detected at an unusually high frequency (12-94%) during a routine quality control in a commercial hatchery. Anatomically the abnormality was mainly characterized by the loss of 1-5 hard spines and severe abnormalities of the proximal pterygiophores (anterior dorsal fin), size reduction of a few lepidotrichia, missing lepidotrichia and/or lepidotrichia of poor ossification (posterior dorsal fin). SBS was significantly correlated with abnormalities of the anal and pelvic fins in all the examined populations. Moreover, in juvenile fish, SBS was significantly correlated with an abnormal lack of sectors of the lateral line. The examination of early larval samples revealed that SBS was ontogenetically associated with severe abnormalities of the primordial marginal finfold, which developed at the flexion stage (ca 8.5-11.0 mm SL). Histologically, these abnormalities were associated with extensive epidermal erosion. The results are discussed in respect of the critical ontogenetic period and the possible causative factors of SBS in European sea bass. It is suggested that causative factors acted during a wide ontogenetic period including flexion and metamorphosis phases.

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.