Comparison of Diploid and Triploid Atlantic Salmon (Salmo salar) Physiological Embryonic Development.

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.

DNA extraction from recently fertilised Atlantic salmon embryos for use in microsatellite validation of triploidy.

The current methods used for producing triploid Atlantic salmon are generally reliable but not infallible, and each batch of triploids must be validated to ensure consumer trust and licensing compliance. Microsatellites have recently been shown to offer a cheaper and more convenient alternative to traditional flow cytometry for triploidy validation in a commercial setting. However, incubating eggs to at least the eyed stage for microsatellite validation poses challenges, such as reduced quality and performance of triploids produced from later eggs in the stripping season. To address these issues, we propose another option: extracting DNA from recently fertilised eggs for use in conjunction with microsatellite validation. To achieve this, we have developed an optimized protocol for HotSHOT extraction that can rapidly and cheaply extract DNA from Atlantic salmon eggs, which can then be used for triploidy validation through microsatellites. Our approach offers a simpler and more cost-effective way to validate triploidy, without the need for skilled dissection or expensive kits.

Development of genomic markers associated to growth-related traits and sex determination in lumpfish (Cyclopterus lumpus).

Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 high Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal's phenotype by machine learning. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programmes in lumpfish.

Photoreception and transcriptomic response to light during early development of a teleost with a life cycle tightly controlled by seasonal changes in photoperiod.

Light cues vary along the axis of periodicity, intensity and spectrum and perception of light is dependent on the photoreceptive capacity encoded within the genome and the opsins expressed. A global approach was taken to analyze the photoreceptive capacity and the effect of differing light conditions on a developing teleost prior to first feeding. The transcriptomes of embryos and alevins of Atlantic salmon (Salmo salar) exposed to different light conditions were analyzed, including a developmental series and a circadian profile. The results showed that genes mediating nonvisual photoreception are present prior to hatching when the retina is poorly differentiated. The clock genes were expressed early, but the circadian profile showed that only two clock genes were significantly cycling before first feeding. Few genes were differentially expressed between day and night within a light condition; however, many genes were significantly different between light conditions, indicating that light environment has an impact on the transcriptome during early development. Comparing the transcriptome data from constant conditions to periodicity of white light or different colors revealed overrepresentation of genes related to photoreception, eye development, muscle contraction, degradation of metabolites and cell cycle among others, and in constant light, several clock genes were upregulated. In constant white light and periodicity of green light, genes associated with DNA replication, chromatin remodeling, cell division and DNA repair were downregulated. The study implies a direct influence of light conditions on the transcriptome profile at early developmental stages, by a complex photoreceptive system where few clock genes are cycling.

Efficacy testing of an immersion vaccine against Aeromonas salmonicida and immunocompetence in ballan wrasse (Labrus bergylta, Ascanius).

The development of effective vaccines is a critical step towards the domestication of emerging fish species for aquaculture. However, traditional vaccine delivery through intraperitoneal (i.p.) injection requires fish to reach a minimum size and age and therefore cannot provide protection at early developmental stages when infection may occur. This study investigated the effectiveness of immersion vaccination with respect to immunocompetence in a cleaner fish species (ballan wrasse, Labrus bergylta, Ascanius) used in Atlantic salmon farming as an alternative means to control sea lice. The species is susceptible to atypical strains of Aeromonas salmonicida (aAs) at early life stages (<15 g), when i.p. vaccination is not applicable. While immersion vaccination is currently used in commercial hatcheries, the optimal fish size for vaccination, and efficacy of the vaccine delivered by this route has not yet been established. Importantly, efficacy depends on the capability of the species immune system to recognise antigens and process antigens to trigger and produce an adaptive immune response, (process known as immunocompetence). In this study, the efficacy of a polyvalent autogenous vaccine administered by immersion in juvenile ballan wrasse and the subsequent immune response induced was investigated after prime and booster vaccination regimes. In addition, temporal expression (0-150 days post hatch) of adaptive immune genes including major histocompatibility complex (MHC II CD74 molecule) and immunoglobulin M (IgM) was assessed using quantitative PCR (qPCR). Prime and/or boost vaccination by immersion of juvenile ballan wrasse (0.5 g and 1.5 g corresponding to 80 and 170 days post hatch (dph), respectively) did not provide significant protection against aAs vapA V after bath challenge under experimental conditions. Despite no evident protection >80 dph, MHC II and IgM transcripts were first reported at 35 and 75 dph, respectively, suggesting a window of immunocompetence. The results provide important new information on the onset of adaptive immunity in ballan wrasse and highlight that immersion vaccination in the species for protection against aAs should be performed at later developmental stages (>1.5 g) in the hatchery.

Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain.

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum.

BACKGROUND: Tambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays a clear sex dimorphism in growth performance, with females reaching larger sizes at harvest. In aquaculture, the production of monosex populations in selective breeding programmes has been therefore identified as a key priority. RESULTS: In the present study, a genetic linkage map was generated by double digest restriction-site associated DNA (ddRAD) sequencing from 248 individuals sampled from two F1 families. The map was constructed using 14,805 informative SNPs and spanned 27 linkage groups. From this, the tambaqui draft genome was improved, by ordering the scaffolds into chromosomes, and sex-linked markers were identified. A total of 235 markers on linkage group 26 showed a significant association with the phenotypic sex, supporting an XX/XY sex determination system in the species. The four most informative sex-linked markers were validated on another 206 sexed individuals, demonstrating an accuracy in predicting sex ranging from 90.0 to 96.7%. CONCLUSIONS: The genetic mapping and novel sex-linked DNA markers identified and validated offer new tools for rapid progeny sexing, thus supporting the development of monosex female production in the industry while also supporting breeding programmes of the species.

Neural activation in photosensitive brain regions of Atlantic salmon (Salmo salar) after light stimulation.

Photoreceptive inputs to the teleost brain are perceived as image of the visual world and as photo-modulation of neuroendocrine and neuronal signals. The retina and pineal organ are major receptive organs with projections to various parts of the brain, but in the past decades deep brain photoreceptors have emerged as candidates for photoreceptive inputs, either independent or in combination with projections from light sensory organs. This study aimed to test the effects of narrow bandwidth light using light-emitting diodes technology on brain neural activity through putative opsin stimulation in Atlantic salmon. The expression of c-fos, a known marker of neural activity, was compared in situ between dark-adapted salmon parr and following light stimulation with different wavelengths. c-fos expression increased with duration of light stimulation and the strongest signal was obtained in fish exposed to light for 120 minutes. Distinct and specific brain regions were activated following dark to light stimulation, such as the habenula, suprachiasmatic nucleus, thalamus, and hypothalamus. The c-fos expression was overlapping with photoreceptors expressing melanopsin and/or vertebrate ancient opsin, suggesting a potential direct activation by light. Interestingly in the habenula, a distinct ring of vertebrate ancient opsin and melanopsin expressing cells is overlapping with c-fos expression after neural activation. Salmon exposed to different spectra had neural activation in similar brain regions. The most apparent difference was melanopsin expression in the lateral cells of the lateral tuberal nuclus in the hypothalamus, which appeared to be specifically activated by red light. Light-stimulated neuronal activity in the deep brain was limited to subpopulations of neurons, mainly in regions with neuronal modulation activity, retinal and pineal innervations and known presence of nonvisual photoreceptors. The overlapping expression patterns of c-fos and nonvisual opsins support direct light stimulation of deep brain photoreceptors and the importance of these systems in light induced brain activity.

Development of diagnostic assays for differentiation of atypical Aeromonas salmonicida vapA type V and type VI in ballan wrasse (Labrus bergylta, Ascanius).

Aeromonas salmonicida (As) is a highly heterogeneous bacterial species, and strains' host specificity has been reported. Ballan wrasse (Labrus bergylta Ascanius, 1767) is susceptible to atypical As (aAs) vapA type V and type VI in Scotland and Norway. Identification of the bacterium is achieved by culture and molecular techniques; however, the available methods used to distinguish the As types are costly and time-consuming. This paper describes the development of a PCR and a restriction enzyme assay for the detection of aAs vapA type V and type VI in ballan wrasse, respectively. Type V-specific primers were designed on conserved regions of the vapA gene, and the restriction enzyme assay was performed on the PCR products of the hypervariable region of vapA gene for the detection of type VI isolates. Amplification product was produced for type V (254 bp) and restriction bands (368 and 254 bp) for type VI isolates only. In addition, the assays detected type V and type VI isolates in spiked water samples and type V in diagnostic tissue samples. The assays are fast, specific and cost-effective and can be used as specific diagnostic tools for cleaner fish, to detect infectious divergence strains, and to manage and mitigate aAs disease outbreaks through vaccine development.

Novel atypical Aeromonas salmonicida bath challenge model for juvenile ballan wrasse (Labrus bergylta, Ascanius).

Atypical Aeromonas salmonicida (aAs) is currently one of the most routinely recovered bacterial pathogens isolated during disease outbreaks in farmed cleaner fish, ballan wrasse (Labrus bergylta, Ascanius). Vibrionaceae family bacteria have also been isolated from ballan wrasse in Scotland. This study determined the infectivity, pathogenicity and virulence of aAs and Vibrionaceae isolates in juvenile farmed ballan wrasse (n = 50; approx. 2 g) using a bath challenge, and fish were monitored for a period of 16 days. Atypical As caused significant mortalities in contrast to Vibrionaceae isolates. Notably, differential virulence was observed between two aAs vapA type V strains at similar challenge doses. Diseased fish exhibited a systemic infection where aAs was detected in all analysed tissues (liver, spleen and kidney) by PCR and qPCR. Macroscopically, moribund and survivor fish exhibited hepatomegaly and splenomegaly. In moribund and surviving fish, histopathology showed granulomatous hepatitis with eosinophilic granular cells surrounding bacterial colonies and endocarditis along with splenic histiocytosis. This is the first report of a successful aAs bath challenge model for juvenile ballan wrasse which provides an important tool for future studies on vaccine efficacy and immunocompetence.

GnRHa implants and size pairing effects on plasma and cephalic secretion sex steroids in Arapaima gigas.

Arapaima gigas, one of the world's largest freshwater fish, is considered an emerging species for aquaculture development in Brazil given its high growth rate and meat quality. However, the lack of reproductive control in captivity has limited the expansion of Arapaima farming. This study aimed to test the effects of hormonal induction using mGnRHa implants and size pairing on broodstock reproduction through the analyses of sex steroids. To do so, broodstock of different sizes (large, small or mixed) were paired and implanted. Plasma and cephalic secretion profiles of testosterone (T), 11-ketotestosterone (11-KT) and 17ß-oestradiol (E2) were analysed. Compared to control (non-implanted), implanted broodstock showed a significant increase in plasma 11-KT (large and small males) and T (large and mixed females) post GnRHa implantation. In females, a significant increase in plasma T levels was shown, however, E2 remained unchanged after implantation. Despite the lack of clear spawning induction, this study showed the potency of GnRHa on sex steroid production regardless of pairing groups. Interestingly, significant correlations between blood plasma and cephalic secretion levels of 11-KT in males and T in females were observed, indicating the possible release of pheromones through the cephalic canals of A. gigas.

Physiological impact and comparison of mutant screening methods in piwil2 KO founder Nile tilapia produced by CRISPR/Cas9 system.

The application of genome engineering techniques to understand the mechanisms that regulate germ cell development opens promising new avenues to develop methods to control sexual maturation and mitigate associated detrimental effects in fish. In this study, the functional role of piwil2 in primordial germ cells (PGCs) was investigated in Nile tilapia using CRISPR/Cas9 and the resultant genotypes were further explored. piwil2 is a gonad-specific and maternally deposited gene in Nile tilapia eggs which is known to play a role in repression of transposon elements and is therefore thought to be important for maintaining germline cell fate. A functional domain of piwil2, PIWI domain, was targeted by injecting Cas9 mRNA and sgRNAs into Nile tilapia embryos at 1 cell stage. Results showed 54% of injected mutant larvae had no or less putative PGCs compared to control fish, suggesting an essential role of piwil2 in survival of PGCs. The genotypic features of the different phenotypic groups were explored by next generation sequencing (NGS) and other mutant screening methods including T7 endonuclease 1 (T7E1), CRISPR/Cas-derived RNA-guided engineered nuclease (RGEN), high resolution melt curve analysis (HRMA) and fragment analysis. Linking phenotypes to genotypes in F0 was hindered by the complex mosacism and wide indel spectrum revealed by NGS and fragment analysis. This study strongly suggests the functional importance of piwil2 in PGCs survival. Further studies should focus on reducing mosaicism when using CRISPR/Cas9 system to facilitate direct functional analysis in F0.

The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus.

The hard-shelled mussel (Mytilus coruscus) is an economically important shellfish that has been cultivated for the last decade. Due to over-exploitation, most mussel stocks have dramatically declined. Efforts to study this species' natural distribution, genetics, breeding, and cultivation have been hindered by the lack of a high-quality reference genome. To address this, we produced a hybrid high-quality reference genome of M. coruscus using a long-read platform to assemble the genome and short-read, high-quality technology to accurately correct for sequence errors. The genome was assembled into 10,484 scaffolds, a total length of 1.90 Gb, and a scaffold N50 of 898 kb. Ab initio annotation of the M. coruscus genome assembly identified a total of 42,684 genes. This accurate reference genome of M. coruscus provides an essential resource with the advantage of enabling the genome-scale selective breeding of M. coruscus. More importantly, it will also help in deciphering the speciation and local adaptation of the Mytilus species.

Investigating the kisspeptin system in the hermaphrodite teleost gilthead seabream (Sparus aurata).

The kisspeptin system, a known regulator of reproduction in fish, was investigated during two key phases within the gilthead seabream (Sparus aurata) life cycle: protandrous sex change and larval ontogeny. Seabream specific partial cDNA sequences were identified for two key targets, kissr4 and kiss2, which were subsequently cloned and qPCR assays developed. Thereafter, to examine association in expression with sex change, a group of adult seabream (2+ years old) undergoing sex change were sampled for gene expression at two different periods of the annual cycle. To study the kisspeptin system ontogeny during early life stages, transcript levels were monitored in larvae (till 30 days-post-hatch, DPH) and post-larvae (from 30 till 140 DPH). During sex change, higher expression of kissr4 and kiss2 was observed in males when compared to females or individual undergoing sex change, this is suggestive of differential actions of the kisspeptin system during protandrous sex change. Equally, variable expression of the kisspeptin system during early ontogenic development was observed. The higher expression of kissr4 and kiss2 observed from 5 DPH, with elevations at 5-20 and 90 DPH for kissr4 and at 5, 10, 20, and 60 DPH for kiss2, is coincident with the early ontogeny of gnrh genes previously reported for seabream, and possibly related with early development of the reproductive axis in this species.

Response of triploid Atlantic salmon (Salmo salar) to commercial vaccines.

While triploid Atlantic salmon represent a practical and affordable solution to the issues associated with sexual maturation in the salmonid aquaculture industry, empirical evidence suggests triploids are more susceptible to disease and vaccine side-effects than diploids. With vaccination now part of routine husbandry, it is essential their response be studied to confirm their suitability for commercial production. This study tested the response of triploid and diploid Atlantic salmon to vaccination with commercially available vaccines. Triploid and diploid Atlantic salmon siblings were injected with one of three commercial vaccines (or sham-vaccinated) and monitored for performance throughout a commercial production cycle. Sampling at smolt and harvest was undertaken along with individual weight and length assessments through the cycle. Antibody response to Aeromonas salmonicida vaccination was similar in both ploidy, with a positive response in vaccine-injected fish. For both adhesions and melanin, analysis found that higher scores were more likely to occur as the anticipated severity of the vaccine increased. In addition, for adhesion scores at smolt and melanin scores at smolt and harvest, triploids were statistically more likely to exhibit high scores than diploids. Triploids maintained a significantly higher body weight during freshwater and until 11 months post-seawater transfer, with diploids weighing significantly more at harvest. Growth, represented by thermal growth coefficient (TGC), decreased in both ploidy as the severity of adhesions increased, and regression patterns did not differ significantly between ploidy. Vertebral deformity prevalence was consistently higher in triploids (smolt 12.3 ± 4.5%; harvest 34.9 ± 5.9%) than diploids (smolt 0.8 ± 0.5%; harvest 15.9 ± 1.9%), with no significant difference between vaccine groups in each ploidy. This study demonstrates that triploids respond as well to vaccination as diploids and provides further supporting evidence of triploid robustness for commercial aquaculture.

Enhanced micronutrient supplementation in low marine diets reduced vertebral malformation in diploid and triploid Atlantic salmon (Salmo salar) parr, and increased vertebral expression of bone biomarker genes in diploids.

Previously we showed that, for optimum growth, micronutrient levels should be supplemented above current National Research Council (2011) recommendations for Atlantic salmon when they are fed diets formulated with low levels of marine ingredients. In the present study, the impact of graded levels (100, 200, 400%) of a micronutrient package (NP) on vertebral deformities and bone gene expression were determined in diploid and triploid salmon parr fed low marine diets. The prevalence of radiologically detectable spinal deformities decreased with increasing micronutrient supplementation in both ploidy. On average, triploids had a higher incidence of spinal deformity than diploids within a given diet. Micronutrient supplementation particularly reduced prevalence of fusion deformities in diploids and compression and reduced spacing deformities in triploids. Prevalence of affected vertebrae within each spinal region (cranial, caudal, tail and tail fin) varied significantly between diet and ploidy, and there was interaction. Prevalence of deformities was greatest in the caudal region of triploids and the impact of graded micronutrient supplementation in reducing deformities also greatest in triploids. Diet affected vertebral morphology with length:height (L:H) ratio generally increasing with level of micronutrient supplementation in both ploidy with no difference between ploidy. Increased dietary micronutrients level in diploid salmon increased the vertebral expression of several bone biomarker genes including bone morphogenetic protein 2 (bmp2), osteocalcin (ostcn), alkaline phosphatase (alp), matrix metallopeptidase 13 (mmp13), osteopontin (opn) and insulin-like growth factor 1 receptor (igf1r). In contrast, although some genes showed similar trends in triploids, vertebral gene expression was not significantly affected by dietary micronutrients level. The study confirmed earlier indications that dietary micronutrient levels should be increased in salmon fed diets with low marine ingredients and that there are differences in nutritional requirements between ploidies.

Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes.

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

Temperature-induced testicular germ cell loss and recovery in Nile tilapia Oreochromis niloticus.

Water temperature is a critical external factor influencing gonadal development in fish. This research aimed to study the impact of elevated temperature on testicular germ cell survival and reproductive capacity of Nile tilapia. Male Nile tilapia were exposed to high temperatures of either 36 (HT1) or 37 °C (HT2) for 3000 degree-days (DD) and thereafter returned to the control temperature of 27 °C (CT) for 2200 DD. The deleterious effects on testicular germ and somatic cells were observed histologically, characterised by vacuolisation, atrophy and the loss of spermatogenic cells in testes with a more severe impact of HT2 compared to HT1. Interestingly, serum 11-ketotestosterone (11-KT) and testosterone (T) levels tended to be higher during the heat treatments than CT. Expression levels of germline-specific genes piwil1, piwil2 and nanos2 and Bcl-2 family genes, bcl-xLb and baxa were significantly reduced during the heat treatment compared to CT, more so in the HT2, while the levels of nanos3 and gfra1 transcripts were only significantly reduced in HT2, implying a significant loss of spermatogonial stem cell (SSC) and spermatogonia in HT2. The effect of HT2 is further evidenced by the significantly reduced sperm density and fertilisation rate compared to CT and HT1 at the end of the recovery period but complete sterility was not induced by HT2. Overall, the present study showed significant effects of HT2 on germ cell survival with histological changes in testes, reduced milt quality, increased 11-KT, and decreased expression of germline-specific genes, SSC marker genes and Bcl-2 family genes in testes which could therefore be potential target genes for sterilisation by genome editing.

Environmental Cycles, Melatonin, and Circadian Control of Stress Response in Fish.

Fish have evolved a biological clock to cope with environmental cycles, so they display circadian rhythms in most physiological functions including stress response. Photoperiodic information is transduced by the pineal organ into a rhythmic secretion of melatonin, which is released into the blood circulation with high concentrations at night and low during the day. The melatonin rhythmic profile is under the control of circadian clocks in most fish (except salmonids), and it is considered as an important output of the circadian system, thus modulating most daily behavioral and physiological rhythms. Lighting conditions (intensity and spectrum) change in the underwater environment and affect fish embryo and larvae development: constant light/darkness or red lights can lead to increased malformations and mortality, whereas blue light usually results in best hatching rates and growth performance in marine fish. Many factors display daily rhythms along the hypothalamus-pituitary-interrenal (HPI) axis that controls stress response in fish, including corticotropin-releasing hormone (Crh) and its binding protein (Crhbp), proopiomelanocortin A and B (Pomca and Pomcb), and plasma cortisol, glucose, and lactate. Many of these circadian rhythms are under the control of endogenous molecular clocks, which consist of self-sustained transcriptional-translational feedback loops involving the cyclic expression of circadian clock genes (clock, bmal, per, and cry) which persists under constant light or darkness. Exposing fish to a stressor can result in altered rhythms of most stress indicators, such as cortisol, glucose, and lactate among others, as well as daily rhythms of most behavioral and physiological functions. In addition, crh and pomca expression profiles can be affected by other factors such as light spectrum, which strongly influence the expression profile of growth-related (igf1a, igf2a) genes. Additionally, the daily cycle of water temperature (warmer at day and cooler at night) is another factor that has to be considered. The response to any acute stressor is not only species dependent, but also depends on the time of the day when the stress occurs: nocturnal species show higher responses when stressed during day time, whereas diurnal fish respond stronger at night. Melatonin administration in fish has sedative effects with a reduction in locomotor activity and cortisol levels, as well as reduced liver glycogen and dopaminergic and serotonergic activities within the hypothalamus. In this paper, we are reviewing the role of environmental cycles and biological clocks on the entrainment of daily rhythms in the HPI axis and stress responses in fish.

Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins.

BACKGROUND: Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requires the development of genetic tools to study polymorphism, differentiation, and stock structure. This study aimed to investigate genomic polymorphism through ddRAD sequencing, in order to identify a panel of single nucleotide polymorphisms (SNPs) and to simultaneously assess genetic diversity and structure in wild (from rivers Amazon, Solimões, Tocantins and Araguaia) and captive populations. RESULTS: Compared to many other teleosts, the degree of polymorphism in A. gigas was low with only 2.3% of identified RAD-tags (135 bases long) containing SNPs. A panel of 393 informative SNPs was identified and screened across the five populations. Higher genetic diversity indices (number of polymorphic loci and private alleles, Shannon's Index and HO) were found in populations from the Amazon and Solimões, intermediate levels in Tocantins and Captive, and very low levels in the Araguaia population. These results likely reflect larger population sizes from less urbanized environments in the Amazon basin compared to Araguaia. Populations were significantly differentiated with pairwise FST values ranging from 0.086 (Amazon × Solimões) to 0.556 (Amazon × Araguaia). Mean pairwise relatedness among individuals was significant in all populations (P < 0.01), reflecting a degree of inbreeding possibly due to severe depletion of natural stocks, the species sedentary behaviour and possible sampling biases. Although Mantel test was not significant (P = 0.104; R2 = 0.65), Bayesian analysis in STRUCTURE and discriminant analysis of principal components (DAPC) showed populations of Amazon and Solimões to be genetically differentiated from Araguaia, with Tocantins comprising individuals from both identified stocks. CONCLUSIONS: This relatively rapid genotyping by sequencing approach proved to be successful in delineating arapaima stocks. The approach and / or SNP panels identified should prove valuable for more detailed genetic studies of arapaima populations, including the elucidation of the genetic status of described discrete morphotypes and aid in delivery of conservation programs to maintain genetic diversity in reservoirs across the Amazon region.