Male Atlantic salmon display variation in life history strategies, where sexual maturation occurs during the freshwater phase as parr, after smoltification as jacks, as grilse after one, or after multiple winters at sea as anadromous adults, each strategy exhibiting evolutionary trade-offs. Spermatogenesis starts during puberty, salmon being a typical example for the unrestricted spermatogonia type of cystic spermatogenesis. If and how life history strategies affect the process of spermatogenesis is unknown. We characterized the germ cell stages appearing during spermatogenesis histologically and determined the increasing number of germ and Sertoli cells stereologically. We found 9 mitotic divisions and a loss of 64% of germ cells occurring during development, the highest ratio found in teleost fish yet. This may relate to the observation that salmon showed, with 207, the so far highest number of germ cells supported per Sertoli cell in vertebrates. We hypothesize that next to circulating hormones, such as follicle-stimulating hormone, local mechano-transduction pathways regulate changes in Sertoli cell number. Such changes accompany the development of spermatogenic cysts, apparently in response to the increasing and then again decreasing volume of individual germ cell clones. This coordinates Sertoli cell number with spermatogenic cyst maturation. No major differences in spermatogenesis were found between parr and two sea winter Atlantic salmon, consistent with a genetic fixation of the major traits of spermatogenesis, as found in most vertebrates.

When puberty starts before males reach harvest size, animal welfare and sustainability issues occur in Atlantic salmon (Salmo salar) aquaculture. Hallmarks of male puberty are an increased proliferation activity in the testis and elevated androgen production. Examining transcriptional changes in salmon testis during the transition from immature to maturing testes may help understanding the regulation of puberty, potentially leading to procedures to modulate its start. Since differences in body weight influence, via unknown mechanisms, the chances for entering puberty, we used two feed rations to create body weight differences. Maturing testes were characterized by an elevated proliferation activity of Sertoli cells and of single undifferentiated spermatogonia. Pituitary gene expression data suggest increased Gnrh receptor and gonadotropin gene expression, potentially responsible for the elevated circulating androgen levels in maturing fish. Transcriptional changes in maturing testes included a broad variety of signaling systems (e.g. Tgfβ, Wnt, insulin/Igf, nuclear receptors), but also, activation of metabolic pathways such as anaerobic metabolism and protection against ROS. Feed restriction lowered the incidence of puberty. In males maturing despite feed restriction, plasma androgen levels were higher than in maturing fish receiving the full ration. A group of 449 genes that were up-regulated in maturing fully fed fish, was up-regulated more prominently in testis from fish maturing under caloric restriction. Moreover, 421 genes were specifically up-regulated in testes from fish maturing under caloric restriction, including carbon metabolism genes, a pathway relevant for nucleotide biosynthesis and for placing epigenetic marks. Undifferentiated spermatogonia and Sertoli cell populations increased at the beginning of puberty, which was associated with the up-regulation of metabolic pathways (e.g. anaerobic and ROS pathways) known from other stem cell systems. The higher androgen levels in males maturing under caloric restriction may be responsible for the stronger up-regulation of a common set of (449) maturation-associated genes, and the specific up-regulation of another set of (421) genes. The latter opened regulatory and/or metabolic options for initiating puberty despite feed restriction. As a means to reduce the incidence of male puberty in salmon, however, caloric restriction seems unsuitable.

Following publication of the original article [1], the authors would like to apologize for an error in Fig. 5e, the correct graph is presented below and shows the significant increase in pituitary mRNA levels of fshb in recruited males in the SGA stage.

Vgll3 is linked to age at maturity in Atlantic salmon (Salmo salar). However, the molecular mechanisms involving Vgll3 in controlling timing of puberty as well as relevant tissue and cell types are currently unknown. Vgll3 and the associated Hippo pathway has been linked to reduced proliferation activity in different tissues. Analysis of gene expression reveals for the first time that vgll3 and several members of the Hippo pathway were down-regulated in salmon testis during onset of puberty and remained repressed in maturing testis. In the gonads, we found expression in Sertoli and granulosa cells in males and females, respectively. We hypothesize that vgll3 negatively regulates Sertoli cell proliferation in testis and therefore acts as an inhibitor of pubertal testis growth. Gonadal expression of vgll3 is located to somatic cells that are in direct contact with germ cells in both sexes, however our results indicate sex-biased regulation of vgll3 during puberty.

The timing of puberty can be strongly variable in fishes, and is modulated both by environmental conditions and by somatic growth patterns. There are also strong genetic components affecting both age and size at puberty. Combinations of genetics, growth patterns and environmental factors result in a considerable plasticity of the timing of puberty within a species. Comparing different species introduces the additional factor of species-specific, evolutionary adaptations. Irrespective of what specific set of conditions triggers puberty in a given individual or species, in fish the increased release of follicle-stimulating hormone from the pituitary gland seems to be the main switch recruiting the juvenile gonad into pubertal development. Knowledge about the physiological control of puberty, the ability to arrest/delay or induce/promote puberty, is important both in an aquaculture/food-production setting as well as for the conservation of species.

Triploid Atlantic salmon (Salmo salar L.) may play an important role in the sustainable expansion of the Norwegian aquaculture industry. Therefore, the susceptibility of triploid salmon to common infections such as salmonid alphavirus (SAV), the causative agent of pancreas disease (PD), requires investigation. In this study, shortly after seawater transfer, diploid and triploid post-smolts were exposed to SAV type 3 (SAV3) using a bath challenge model where the infectious dose was 48 TCID50 ml-1 of tank water. Copy number analysis of SAV3 RNA in heart tissue showed that there was no difference in viral loads between the diploids and triploids. Prevalence reached 100% by the end of the 35-day experimental period in both infected groups. However, prevalence accumulated more slowly in the triploid group reaching 19% and 56% at 14 and 21 days post exposure (dpe) respectively. Whereas prevalence in the diploid group was 82% and 100% at the same time points indicating some differences between diploid and triploid fish. Both heart and pancreas from infected groups at 14 dpe showed typical histopathological changes associated with pancreas disease. Observation of this slower accumulation of prevalence following a natural infection route was possible due to the early sampling points and the exposure to a relatively low dose of virus. The triploid salmon in this study were not more susceptible to SAV3 than diploid salmon indicating that they could be used commercially to reduce the environmental impact of escaped farmed fish interbreeding with wild salmon. This is important information regarding the future use of triploid fish in large scale aquaculture where SAV3 is a financial threat to increased production.

Mapping statistics of mRNA and miRNA mapping. (XLSX 7 kb)

In recent years rapidly growing research has led to identification of several fish leptin orthologs and numerous duplicated paralogs possibly arisen from the third and fourth round whole genome duplication (3R and 4R WGD) events. In this study we identify in Atlantic salmon a duplicated LepRA gene, named LepRA2, that further extend possible evolutionary scenarios of the leptin and leptin receptor system. The 1121 amino acid sequence of the novel LepRA2 shares 80% sequence identity with the LepRA1 paralog, and contains the protein motifs typical of the functional (long form) leptin receptor in vertebrates. In silico predictions showed similar electrostatic properties of LepRA1 and LepRA2 and high sequence conservation at the leptin interaction surfaces within the CHR/leptin-binding and FNIII domains, suggesting conserved functional specificity between the two duplicates. Analysis of temporal expression profiles during pre-hatching stages indicate that both transcripts are involved in modulating leptin developmental functions, although the LepRA1 paralog may play a major role as the embryo complexity increases. There is ubiquitous distribution of LepRs underlying pleiotropism of leptin in all tissues investigated. LepRA1 and LepRA2 are differentially expressed with LepRA1 more abundant than LepRA2 in most of the tissues investigated, with the only exception of liver. Analysis of constitutive LepRA1 and LepRA2 expression in brain and liver at parr, post-smolt and adult stages reveal striking spatial divergence between the duplicates at all stages investigated. This suggests that, beside increased metabolic requirements, leptin sensitivity in the salmon brain might be linked to important variables such as habitat, ecology and life cycle. Furthermore, leptins and LepRs mRNAs in the brain showed gene-specific variability in response to long term fasting, suggesting that leptin's roles as modulator of nutritional status in Atlantic salmon might be governed by distinct genetic evolutionary processes and distinct functions between the paralogs.

Maturing male and female Atlantic salmon (Salmo salar L.) were held under three temperature regimes for 10 weeks between September and December: warm (constant 14–16 °C), ambient (decreasing from 11 to 5 °C), and cold (decreasing from 7 to 3 °C). Blood samples were analyzed for plasma steroid levels, and the fish were inspected for the presence of expressible milt (total volume and spermatocrit) and ovulation weekly. Samples of eggs were dry-fertilized with milt stripped from three males held at the same temperatures and incubated until the eyed stage. In females, levels of plasma testosterone (T) and 17β-oestradiol (E2) dropped as ovulation approached, concurrent with a rapid increase in levels of plasma 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P). In males, levels of T and 11-ketotestosterone (11-KT) peaked 2–3 weeks after the first appearance of expressible milt, while levels of 17,20β-P increased steadily and did not exhibit a definite peak. Exposure of females to cold water amplified and advanced the profiles of all three steroids compared with the ambient group, and increased the survival rates to the eyed egg stage. Cold water had no immediate effect on the male steroid profiles, but later, higher levels of 17,20β-P were evident compared with both the ambient controls and the warm water group, while the effects on 11-KT and T were more variable. Exposure to warm water completely inhibited both milt production and ovulation. Moreover, warm water modulated the steroid profiles of the males with lower 11-KT levels compared with ambient controls and lower 17,20β-P level compared with cold-water-treated males. In females, warm water resulted in total inhibition of the peri-ovulatory peak in 17,20β-P and prevented the normal decline of T and E2 levels associated with ovulation. The findings of the present study are highly relevant for broodstock management in aquaculture, as well in understanding the impact of climate change/temperature variability on wild salmon spawning.

Salmonid alphavirus subtype 3 (SAV3) causes pancreas disease (PD) and adversely affects salmonid aquaculture in Europe. A better understanding of disease transmission is currently needed in order to manage PD outbreaks. Here, we demonstrate the relationship between viral dose and the outcome of SAV3 infection in Atlantic salmon post-smolts using a bath challenge model. Fish were challenged at 12 °C with 3 different SAV3 doses; 139, 27 and 7 TCID 50 L −1 of seawater. A dose of as little as 7 TCID 50 L −1 of seawater was able to induce SAV3 infection in the challenged population with a substantial level of variation between replicate tanks and, therefore, likely represents a dose close to the minimum dose required to establish an infection in a population. These data also confirm the highly infectious nature of SAV through horizontal transmission. The outcome of SAV3 infection, evaluated by the prevalence of viraemic fish, SAV3-positive hearts, and the virus shedding rate, was positively correlated to the original SAV3 dose. A maximal shedding rate of 2.4 × 10 4 TCID 50 L −1 of seawater h −1 kg −1 was recorded 10 days post-exposure (dpe) from the highest dose group. The method reported here, for the quantification of infectious SAV3 in seawater, could be useful to monitor PD status or obtain data from SAV3 outbreaks at field locations. This information could be incorporated into pathogen dispersal models to improve risk assessment and to better understand how SAV3 spreads between farms during outbreaks. This information may also provide new insights into the control and mitigation of PD.

Introgression of farmed salmon escapees into wild stocks is a major threat to the genetic integrity of wild populations. Using germ cell-free fish in aquaculture may mitigate this problem. Our study investigated whether it is possible to produce germ cell-free salmon in F0 by using CRISPR-Cas9 to knock out dnd, a factor required for germ cell survival in vertebrates. To avoid studying mosaic animals, sgRNA targeting alb was simultaneously used as a visual tracer since the phenotype of alb KO is complete loss of pigmentation. Induced mutations for the tracer (alb) and the target ( dnd) genes were highly correlated and produced germ cell-less fish lacking pigmentation, underlining the suitability of alb KO to serve as tracer for targeted double allelic mutations in F0 animals in species with prohibitively long generation times. This is also the first report describing dnd knockout in any fish species. Analyzing gene expression and histology of dnd KO fish revealed that sex differentiation of the somatic compartment does not depend on the presence of germ cells. However, the organization of the ovarian somatic compartment seems compromised in mutant fish.

The use of triploid fish can potentially reduce two of the major obstacles in Atlantic cod aquaculture; early sexual maturation that causes reduced profitability, and avoiding introgression between farmed cod and native populations, by preventing spawning in the netpens or that escapees reproduce. Cod eggs were pressure treated to produce triploid fish. However, we observed that the pressure treatment produced a mixture of triploid and diploid individuals. The diploid and triploid fish were reared together; in a seawater pond during their larval and juvenile period, and in a commercial cod farm from juveniles to slaughter. Two experiments were performed on two separate year-classes of cod: in the first experiment, fish were reared under artificial continuous light, while in the second experiment the fish were reared under ambient light conditions. Triploicl cod had lower gonadosomatic index at all measurements compared to the diploids. However, from a production point of view, triploidisation alone only slightly reduced the gonaclosomatic index and had to be combined with traditionally employed artificial light in order to be effective. Triploicl fish were generally lighter than the diploids, but this difference disappeared towards time-of-harvest in the year-class without artificial light, possibly because of the lower maturation rate among the triploicls. The triploid fish had a higher incidence of skeletal deformities compared to the diploids.Statement of Relevance: The use of sterile fish by means of triploiclisation is a promising methocl to reduce sexual maturation and the same time eliminate potential interbreeding of escaped cod with wild cod. In this paper we compare growth, maturation and deformities between triploid and diploid cod reared in common garden under commercial condition. (C) 2016 Elsevier B.V. All rights reserved.

Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a GWAS using a pool sequencing approach (20 individuals per river and trait) of salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNP in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild salmon and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33-36% phenotypic variation. This study demonstrates a single locus playing a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in human (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates. 3 . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/024927 doi: bioRxiv preprint first posted online Aug. 17, 2015;

Water homeostasis and the structural integrity of the vertebrate lens is partially mediated by AQP0 channels. Emerging evidence indicates that external pH may be involved in channel gating. Here we show that a tetraploid teleost, the Atlantic salmon, retains 4 aqp0 genes (aqp0a1, -0a2, -0b1, and -0b2), which are highly, but not exclusively, expressed in the lens. Functional characterization reveals that, although each paralog permeates water efficiently, the permeability is respectively shifted to the neutral, alkaline, or acidic pH in Aqp0a1, -0a2, and -0b1, whereas that of Aqp0b2 is not regulated by external pH. Mutagenesis studies demonstrate that Ser(38), His(39), and His(40) residues in the extracellular transmembrane domain of -helix 2 facing the water pore are critical for the pH modulation of water transport. To validate these findings, we show that both zebrafish Aqp0a and -0b are functional water channels with respective pH sensitivities toward alkaline or acid pH ranges and that an N-terminal allelic variant (Ser(19)) of Aqp0b exists that abolishes water transport in Xenopus laevis oocytes. The data suggest that the alkaline pH sensitivity is a conserved trait in teleost Aqp0 a-type channels, whereas mammalian AQP0 and some teleost Aqp0 b-type channels display an acidic pH permeation preference.

Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33-36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates.

Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if species specific "egg life history traits" can be hidden in the unfertilized egg. This was done by investigating egg transcriptome differences between Atlantic salmon and Atlantic cod. Salmon and cod eggs were selected due to their largely differencing phenotypes. An oligo microarray analysis was performed on ovulated eggs from cod (n = 8) and salmon (n = 7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated with SWISS-Prot and KEGG genes to retrieve an official gene symbol and an orthologous KEGG annotation, in salmon and cod arrays this represented 14,009 and 7,437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score >300, resulting in a total of 2,457 KEGG annotations (genes) being differently expressed between the species (FD > 2). This analysis revealed that immune, signal transduction and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.

The gonadotropic system and ovarian growth and development were studied during vitellogenesis in female Atlantic salmon subjected to either simulated natural photoperiod and ambient water temperature (NL-amb), or an accelerating photoperiod (short day of LD8:16 from May 10) combined with either warmed (ca 2°C above ambient; 8L-warm) or cooled water (ca 2°C below ambient; 8L-cold) from May to September. Monthly samples were collected from 10 females/group for determination of transcript levels of pituitary gonadotropin subunits (fshb and lhb) and ovarian gonadotropin receptors (fshr and lhr), plasma sex steroids (testosterone: T and estradiol-17β: E2), gonadosomatic index (GSI) and oocyte size. Short day in combination with either warmed or cooled water induced an earlier increase in pituitary fshb and lhb levels compared with NL-amb controls, and advanced ovarian growth and the seasonal profiles of T, E2. By contrast only minor effects were seen of the photothermal treatments on ovarian fshr and lhr. The 8L-cold had earlier increase in fshb, lhb and E2, but similar oocyte and gonadal growth as 8L-warm, suggesting that the 8L-cold group tried to compensate for the lower water temperature during the period of rapid gonadal growth by increasing fshb and E2 production. Both the 8L-warm and 8L-cold groups showed incomplete ovulation in a proportion of the females, possibly due to the photoperiod advancement resulting in earlier readiness of spawning occurring at a higher ambient temperature, or due to some reproductive dysfunction caused by photothermal interference with normal neuroendocrine regulation of oocyte development and maturation.