Fig 4 - uploaded by Gianluca Amoroso
Content may be subject to copyright.
Relative expression (2 -ΔΔCT , mean ± SEM) of col2a1 in Normal and lower jaw deformity (LJD) affected triploid Atlantic salmon Salmo salar (n = 6 per jaw trait) from the experimental sample set at standard (14˚C) and elevated (18˚C) temperature. Means significantly different from one another are indicated by different letters (P < 0.05). doi:10.1371/journal.pone.0168454.g004
Source publication
Lower jaw deformity (LJD) is a skeletal anomaly affecting farmed triploid Atlantic salmon (Salmo salar L.) which leads to considerable economic losses for industry and has animal welfare implications. The present study employed transcriptome analysis in parallel with real-time qPCR techniques to characterise for the first time the LJD condition in...
Similar publications
While research into the growth, survival, nutrition and, more recently, disease susceptibility of triploid Atlantic salmon has expanded, there remains an overall lack of studies assessing the response of triploids to chemical treatments. It is essential that the response of triploids to disease treatments be characterised to validate their suitabil...
The present study investigated nutritional programming in Atlantic salmon to improve utilisation of a vegetable-based diet. At first exogenous feeding, fry were fed either a marine-based diet (Diet M stimulus , 80% fishmeal (FM)/4% fish oil (FO)) or a vegetable-based diet (Diet V stimulus , 10% FM/0% FO) for 3 weeks. Subsequently, all fish were the...
ABSTRACT: In salmon farming, the use of sterile triploids (3N) can mitigate the problem of escapees interbreeding with wild salmon. However, triploid salmon appear less tolerant to high water temperatures and low oxygen levels compared to diploids (2N). To investigate how the thermal performance and physiology of large (2.5 kg) triploid Atlantic sa...
Few studies have focussed on the health and immunity of triploid Atlantic salmon and therefore much is still unknown about their response to commercially significant pathogens. This is important if triploid stocks are to be considered for full-scale commercial production. This study aimed to investigate and compare the response of triploid and dipl...
Citations
... These differences include various aspects such as gill filament density [4,5], as well as gut [6], brain [7,8], and heart morphology [9,10]. Triploids tend to display a higher susceptibility to a variety of deformities, including those affecting the vertebrae [11], lower jaw [12], eyes [13], and heart [10]. They require lower incubation temperatures [10,14,15] and ploidyspecific diets with increased histidine [13,16,17], phosphorus [11,18,19], and protein [18]. ...
Diploid and triploid Atlantic salmon show distinct physiological differences including heart, brain, and digestive system morphology, propensity for certain deformities, temperature tolerance as eggs and once hatched, and different nutritional requirements. Whilst several studies have looked in detail at the rate of embryogenesis in diploid salmon, no study has compared the rate of embryogenesis between ploidies from fertilisation to hatch. This study based its assessment on a seminal paper by Gorodilov (1996) and used the same techniques to compare the rate at which triploid and diploid embryos developed morphological characteristics. Whilst no significant difference was found, this study provides well-needed justification for the assumption that both ploidies develop at the same rate and gives scientific weight to studies which involve manipulation at these stages of development. Two factors that did differ, however, were the timing of hatch, and mortality. Triploids hatched more quickly than diploids and reached 50% hatch at a significantly earlier point. Triploids also suffered from a significantly higher rate of mortality.
... Also, Atlantic salmon (Salmo salar) triploids were reported to be prone to show curved lower jaw, being linked to a vitamin and/or mineral (mainly phosphorus) deficiency, as well as environmental factors such as low dissolved oxygen, elevated temperature and husbandry practices Lijalad & Powell, 2009Amoroso et al., 2016aFjelldal et al., 2016). Indeed, a higher incidence of curved lower jaw has been observed when Atlantic salmon was reared at high temperatures (14 versus 18 ºC), and this was associated to an J o u r n a l P r e -p r o o f Journal Pre-proof altered hormonal regulation of the cartilage development (Amoroso et al., 2016b). In our case, rearing temperature during early development seemed to not be the causative factor of such jaw deformity (comparing reared larvae at 13 and 16 ºC; see below). ...
Wreckfish (Polyprion americanus) is a promising new species for aquaculture diversification due to its fast growth, late reproductive maturation, and high market price. Nowadays, low larval survival is considered the biggest limitation in wreckfish farming. Here, the fertilization, hatching and survival rates of 20 spawning events from an established wreckfish broodstock have been analyzed in order to characterize the main bottlenecks in wreckfish early and larval development. The ontogenesis of the skeletal system and the incidence of skeletal deformities have been assessed in 632 samples from larval rearing trials using currently available protocols. Furthermore, the effect of different rearing temperatures (13 vs 16 °C) and light intensities at water surface (600, 900 and 1200 lx) on the skeletal development have been also explored. Results showed as while a variable egg fertilization rate (61.75 ± 34.62%) were achieved, a very poor hatching (4.52 ± 9.27%) and survival rate (0.01 ± 0.00%) until 71 days post hatching (dph) were observed. Swim bladder inflation was first seen at 7 dph, and at 11 and 25 dph a 61–63% of fish functional swim bladder. The first skeletal structures to be formed were those related with breathing and feeding activities (e.g., cleithrum, Meckel's cartilage and ceratobranchials) and were visible in larvae of 4–5 mm of standard length (SL). Ossification of the vertebral column progressed in an anterior-to-posterior direction, being fully ossified at 7–14 mm of SL. Regarding the skeletal deformities, a high incidence (63%) of jaw deformity (particularly lower jaw deformity) was observed in larvae of 4–5 mm of SL, progressively decreasing (up to 5%) in larvae of >6 mm of SL. Deformed vertebrae (compressed, fused, and/or displaced) were mainly located at 13 to 15th vertebra, and were associated to lordosis, most probably due to the no swim bladder inflation. No clear relationship between temperature and the incidence of lower jaw deformity was observed during endotrophic larval development. Light intensity had a clear effect on survival but not in skeletal development. Larvae reared under 600 lx had lower survival (0.15 ± 0.21%) at 21 dph than when reared with 900 and 1200 lx (0.6 ± 0.28 and 0.7 ± 0.28%, respectively). The present research work represents an important step forward to solve wreckfish larval rearing bottlenecks, suggesting that while temperature and light intensity might have an effect on wreckfish larval survival and development, egg quality and incubation seemed to be the most limiting factors for successful wreckfish aquaculture.
... Over a decade ago, next-generation sequencing (NGS) has been applied in transcriptomic analysis [22,23] and has since evolved into a universally-applied tool in molecular biology. Using NGS technologies, RNAsequencing (RNA-Seq), can be aligned to the reference genome or de novo assembled, making it a widely used tool also for non-model organisms [24,25]. Not only does it enable characterization of the transcriptome's complexity, but RNA-Seq also enables quantification of gene expression level, calling alternative splicing variations and single nucleotide polymorphisms (SNPs) [24,26]. ...
Background
The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3’ mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3’ mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes.
Results
In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR.
Conclusions
Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1 .
... Therefore, findings of genomic regions under selection harboring genes related to growth might be expected. As described in Supplementary [80][81][82][83][84][85][86][87]. In addition, we also detected nine genes which have been related to growth in studies performed in livestock species, including chicken (Dhcr24 [88]; Slain2 and Sgcb [89]), sheep (C1qtnf7 [90]), pigs (Arl15 [91]) and cattle (Gdf10 [92] and Zn3h3 [93]). ...
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
... Over a decade ago, next-generation sequencing (NGS) has been applied in transcriptomic analysis (20,21) and has since evolved into a universally-applied tool in molecular biology. Using NGS technologies, RNA-sequencing (RNA-Seq), can be aligned to the reference genome or de novo assembled, making it a widely used tool also for non-model organisms (22,23). Not only does it enable characterization of the transcriptome's complexity, but RNA-Seq also enables quanti cation of gene expression level, calling alternative splicing variations and single nucleotide polymorphisms (SNPs) (22,24). ...
Background: The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3’ mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3’ mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes.
Results: In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR.
Conclusion: Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for Duox2 and DuoxA1.
... It has been proposed to act as a negative but indirect regulator of osteoblastic bone formation during skeletal development (Bassett et al., 2015). In support of this notion, it was reported in the Atlantic salmon Salmo salar (Linnaeus, 1758) that increased GPB5 at the base of the lower jaw was correlated with jaw deformity (Amoroso et al., 2016). Transgenic overexpression of GPB5 in mice elevated serum T4 levels and caused reductions in body weight and proptosis, opposite to GPA2 overexpression where no effect was observed (Okada et al., 2006). ...
Over many decades there were numerous attempts to isolate gonad-stimulating factors (GSF) in crustaceans. Before omic technologies, the main neuroendocrine factors identified as ovarian development regulators in crustaceans were inhibitory in nature, belonging to the CHH family of neuropeptides produced in the eyestalk. Eyestalk ablation thus leads to ovarian development and this technique is still used in shrimp farms to induce maturation although some biological issues arise. In this manuscript, we review the current knowledge on potential GSF with emphasis on several key candidates and discuss how novel sequencing technologies might aid in better understanding the nature of the ovarian development in crustaceans. However, the gap between the rapid pace at which sequence databases are produced and mined and the experimental work that lags behind do not yet allow us to know the nature of the GSF in crustaceans. Three possible reasons are suggested: (1) crustaceans represent a very large and diverse group, then different species could have GSF of different compounds; (2) it is possible that crustaceans employ multiple hormonal factors to control vitellogenesis; (3) crustaceans might not need a GSF. Reproduction is only negatively regulated by CHH family peptides.
... In this respect, dietary P deficiency during freshwater grow-out may further exacerbate already pre-existing jaw malformation in triploids. Furthermore, Amoroso et al. (2016b) also demonstrated cartilage impairment and associated gene (col2a1) downregulation in LJD affected triploids, and that prevalence of LJD was greater in triploids experiencing higher water temperatures during ongrowing (Amoroso et al., 2016a). Thus, given bone that mineral content of the jaw was not different between diets in this study, this supports the hypothesis that dietary minerals may be sufficient for jaw formation, but that cartilage impairment of the lower jaw formation, particularly in response to rearing temperature, is the primary cause of jaw malformation through incorrect architectural arrangement. ...
... Conversely, in our study, no differences in fgf23 expression were observed between ploidy or dietary P at smolt, however, levels of expression were significantly higher than at parr stages. Similarly, Amoroso et al. (2016b) also found no change in fgf23 between normal jaw and LJD affected triploid smolts. Collectively, this may suggest that early life stages (i.e. ...
In order to assess the effect of dietary phosphorus (P) in reducing vertebral malformations and improving freshwater (FW) performance in triploid Atlantic salmon (Salmo salar), both triploid and diploid Atlantic salmon were fed three different dietary P inclusion levels (low: 4.9, medium: 7.7, and high: 9.7 g available P kg⁻¹) from first feeding until smolt. Somatic and skeletal response was assessed at fry (~0.5 g), parr (~5 g) and smolt (~45 g) stages. Triploid parr initially grew faster on the high P diet, while groups fed low P resulted in a significantly higher weight at smolt. Image analysis of double stained Alcian blue and Alizarin red S fry revealed that low P fed triploid fish presented less well mineralised vertebrae, and significantly more malformed vertebrae in both parr and smolt stages following x-ray radiographic assessment. Triploid parr fed high and medium P had similar numbers of malformed vertebrae relative to their diploid counterparts but greater numbers than at smolt. Low P fed triploids had the highest prevalence of jaw and vertebral malformations as well as the highest number of deformed vertebrae in the central caudal vertebral region, which was more pronounced at parr than at smolt. Shorter vertebrae dorso-ventral lengths were observed throughout the spinal column (R1–R4) in parr fed low P and only in the caudal region (R3) at smolt. In parr, both ploidies showed reduced phosphate homeostasis protein fgf23 gene expression in vertebrae when fed low P diets, while triploids showed greater down-regulation of osteogenic factors (alp, opn and igf1r) between diets relative to diploids, suggesting possible greater active suppression of mineralisation and reduced osteogenic potential in triploids. No effects of diet or ploidy on gene expression were evident at smolt. Comparisons between development stages suggest early P supplementation in triploids is crucial for skeletal development. Ultimately, reducing vertebral deformities observed at smolt with higher P supplementation in triploids could contribute towards improving skeletal performance and welfare of the stocks in the marine phase.
Suitable feeds and feeding regimes are crucial to hatchery success and are often complex and species-specific. This review considers the role of formulated feeds in aquaculture hatcheries and early production. It will focus mainly on fish (finfish) and crustacean aquaculture. Important aquaculture fish include species with either freshwater or marine hatcheries. In freshwater, commercial manufactured feeds are successfully fed at first-feeding to many important aquaculture species. Freshwater fish typically have large larvae with well-developed digestive tracts and include salmonids, tilapia, carp, and catfish. Almost all marine larvae require a period of feeding on live feeds and can only use manufactured feeds several days after first-feeding when the larvae have grown larger and have a more advanced digestive tract. The hatchery phase for important crustacean species is carried out in brackish or marine waters, and for all the important cultured crustaceans, prawns, crayfish, and crabs, hatcheries rely on live feeds at first-feeding and then co-feeding with manufactured feeds until the completion of the larval cycle. Different live feeds and manufactured feeds are introduced in relation to the changing nutritional physiology of larvae and postlarvae. Current hatchery feeding regimes are outlined for several key species selected to represent different taxa and aquaculture systems. Future developments and trends are suggested to include increased development and use of manufactured larval feeds, ultimately from first-feeding; tailored hatchery regimes to meet a wider range of grow-out options; increased focus on broodstock nutrition and increased use of formulated feeds; and nutritional programming.
The study investigated the effects of a temperature shift during embryogenesis on diploid and triploid Atlantic salmon (Salmo salar L.) embryo development and juvenile skeletal deformities. From fertilization, sibling populations were incubated under one of three temperatures (6, 8 or 11°C) until 400 °days when all fish were then reared under a common temperature until smolt. Survival was negatively impacted by increasing temperatures irrespective of ploidy. There was no effect of incubation temperatures on growth in diploids, but triploids incubated at 6°C had improved growth rates (thermal growth coefficient, TGC: 6°C: 1.05, 8°C: 0.94, 11°C: 0.48). Fish from 11°C in both ploidies showed increased jaw and vertebral deformity prevalence. In response to the temperature change at 400 °days post fertilization, upregulation of bmp2, bmp4, col2a1, mmp13, opn and sparc, and downregulation of ocn further suggest that bone and cartilage formation is compromised after experiencing a thermal shift. The data show that temperature profile during embryogenesis strongly influences future growth and deformity prevalence. Triploids appear to require a lower incubation temperature than the current industry standard of 8°C to promote better overall performance; however, a thermal shift during embryogenesis was shown to impact expression of important developmental genes.
