Mitochondrial DNA variation in Atlantic salmon, Salmo, salar L., populations

Mitochondrial DNA (mtDNA) variation was examined in 209 Atlantic salmon from two river systems, the R. Itchen in Hampshire (Southern England) and the R. Conwy (North Wales). Within each system, five spawning sites were sampled. Four enzymes (AVA II, HAE III, HINF I and MBO I) revealed restriction fragment polymorphisms that were informative. Ten clonal lines were observed. These clones were differentially distributed between the two river systems and single clonal types were found to predominate at several spawning sites. MBO I variants were found in salmon from the R. Itchen but not the R. Conwy. A significant heterogeneity in frequency distribution of clonal lines between parr and smolt assemblages of the same year class within the R. Itchen was detected. This heterogeneity suggests that differences in survival or migratory behaviour may be identified by changes in mtDNA clonal frequencies.     

Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites

Seven novel and highly variable tetranucleotide microsatellite markers, and conditions for multiplexing and simultaneous genotyping six of these in a single run, are described for Atlantic salmon. These provide a highly informative and cost‐effective set of molecular markers for genetic studies on cultured and wild populations of the species. The primers sets showed cross‐species amplification of appropriately sized amplified products in a number of other salmonid species and suggests the primer sets may have wider application.     

Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags

The detection of simple sequence repeats (SSRs) within expressed sequence tags (ESTs) connects potential microsatellite markers with specific genes, generating Type I markers. Using an in silico approach, we identified 1975 SSRs from the Genome Research on Atlantic Salmon Project EST database. We designed primers to amplify 158 SSRs, of which 65 amplified 76 loci (including 11 duplicated loci). Sixty‐one of the 76 loci were variable in 24 Atlantic salmon from seven populations, and 96% of these markers also amplify DNA from other salmonids. Functions for 16 of the SSR associated ESTs have been determined, confirming them as Type I markers.     

Cloning and characterization of alpha-amylase from Atlantic salmon (Salmo salar L.)

Amylase has a lower activity in carnivorous fish species, particularly in Atlantic salmon. We report the first cloning of a salmonid alpha-amylase cDNA from Atlantic salmon, a major species in aquaculture. By amino acid alignment of several species, we identified a seven amino acid deletion in one of the large loops of the enzyme in relatively close proximity to the active site, that could impair substrate binding. We also found the signal peptide to be less hydrophobic compared to other species. This may affect import into ER during protein synthesis. Active site residues were shown to be conserved. Amylase mRNA expression was shown in pancreatic tissue, liver, and in the heart. Using blocked p-nitrophenyl-maltoheptaoside as a substrate, we measured a low amylase activity in Atlantic salmon intestinal content, which was about half of the activity measured in Atlantic cod, whereas activity measured in rainbow trout was fourteen times higher. Amylase activities in all three species showed similar degree of reduction in hydrolytic activity in a dose-response trial with a wheat amylase inhibitor preparation. This indicates similar specific activity per amylase molecule.     

Genetic variation in haemolytic activity in Atlantic salmon (Salmo salar L.)

Spontaneous and antibody-dependent haemolytic activity against sheep red blood cells (SRBC) has been studied in serum from Atlantic salmon, Salmo salar L. Considerable increase in haemolytic activity was detected when SRBC were sensitized with haemolysin produced in Atlantic salmon. Haemolytic activity was sensitive both to divalent cations and to heat treatment. Significant reduction in haemolytic activity was detected after absorption with SRBC, indicating the presence of natural antibody against SRBC in Atlantic salmon serum. Persistent haemolytic activity of unsensitized SRBC in serum absorbed to remove natural antibodies was found, which suggests the activation of the alternative complement pathway, while the observed increased haemolytic activity in the presence of specific antibody against SRBC suggests activation of the classical complement pathway. Spontaneous and antibody-dependent haemolytic activity were both analysed in absorbed and non-absorbed sera in a family material of Atlantic salmon. The material consisted of 574 fish belonging to 57 fullsib groups within 20 paternal halfsib groups. Fish with signs of sexual maturity generally showed reduced haemolytic activity. Statistically significant effect of sire on the spontaneous haemolytic activity of both absorbed and nonabsorbed serum, and on antibody-dependent activity, provides evidence of significant additive genetic variation in both the alternative and the classical complement activation in Atlantic salmon. Neither on a phenotypical nor on a family basis were the two traits statistically correlated. The estimated heritabilities were 0.2–0.3 with a standard error of approximately 0.1.     

Genetic differentiation among natural European populations of Atlantic salmon, Salmo salar L., from drainages of the Atlantic Ocean

Previously published allelic frequencies at four polymorphic protein coding loci were used as a basis for examining genetic relationships among 19 European populations of Atlantic salmon, Salmo salar L.--exclusive of Baltic drainages--from the Barents Sea to Spain. The data did not support a model of distinct ancestral (e.g. Boreal and Celtic) origins, but were consistent with all populations descending from a single ancestral group within this region with genetically diverged populations drawn together through limited local migrations.     

A microsatellite linkage map for Atlantic salmon (Salmo salar)

A linkage map of the Atlantic salmon is described here consisting of 15 linkage groups containing 50 microsatellite loci with a 14 additional unlinked markers (including three allozymes). The map shows the largest sex-specific recombination rate differences so far found in any vertebrate species (3.92:1 female:male). Homologies with previous linkage mapping studies of Atlantic salmon and rainbow trout are described. An in silico search of the Genbank database carried out using the microsatellites used in the mapping process identified significant matches between the flanking regions of the microsatellite SS11 and the calcium-binding mitochondrial carrier protein, 'Aralar1'.     

Genetic variation in Atlantic salmon, Salmo salar L., within the Tamar catchment in south-west England

Electrophoretic analysis of enzymes in 383 juvenile Atlantic salmon, Salmo salar L., within the Tamar catchment (south-west England) revealed significant genetic differences at the IDHP-3* locus between the three tributaries studied. Aspects of temporal and spatial variation, and management policy within catchments, are discussed.     

Amount and distribution of biochemical-genetic variation among wild populations and a hatchery stock of Atlantic salmon, Salmo salar L., from north-east Ireland

The effects of tributyltin (TBT) compounds on gill morphology were examined in the mummichog, Fundulus heteroclitus , in 96-h LC50 and 6-week sublethal exposures. Morphometry was used for the identification and quantification of effects with the light microscope. A 96-h LC50 of 17.2 μg 1 ¹ was determined. Morphometric analysis of gill tissues revealed hypertrophy of the lamellar epithelium in fish exposed to 17.2 μg 1–1. Relative diffusing capacity was significantly decreased (−41 %); ( P <0.05, ANOVA, Bonferroni t -test). At 35.6 μg 1⁻¹, TBT exposure resulted in a significant reduction (− 40%) in the volume of the lamellar blood channels. Both of these observations occurred in fish that showed signs of acute poisoning including loss of equilibrium. In fish exposed to sublethal concentrations of 0.105–2.000 μg TBT 1⁻¹ for 6 weeks, there were no pathological changes in the gill. There were no treatment-related changes in the surface morphology of the gills of fish from both experiments upon scanning electron microscopic examination. Although gill pathology was observed in acutely toxic exposures, it does not appear to be a major mechanism of TBT toxicity.     

Astaxanthin binding to solubilized muscle proteins of Atlantic salmon (Salmo salar L.), haddock (Melanogrammus aeglefinus L.) and Atlantic halibut (Hippoglossus hippoglossus L.)

A study was conducted to compare astaxanthin binding ability of solubilized muscle proteins of Atlantic salmon (Salmo salar L.), haddock (Melanogrammus aeglefinus L.) and Atlantic halibut (Hippoglossus hippoglossus L.). Muscle proteins of juvenile Atlantic salmon, haddock and halibut were solubilized by sequential extraction of muscle tissue using low ionic strength solutions. Electrophoretic protein profiles of the six solubilized fractions from these species were similar. Each solubilized fraction from the three species was examined for its relative astaxanthin binding capacity. The amount of bound astaxanthin was significantly different (P < 0.05) among the six fractions of each species. Significant differences in astaxanthin binding were only found for fractions A and E among the species. The amount of bound astaxanthin in various fractions of each species showed a good correlation (R² = 0.80–0.92) with the ANS (8-anilino-1-naphthalenesulfonate) fluorescence intensity of those fractions. The pattern and extent of astaxanthin binding to the muscle proteins of juvenile salmon, haddock and halibut is comparable to that reported previously for adult Atlantic salmon [Saha, M.R., Ross, N.W., Gill, T.A., Olsen, R.E., Lall, S.P., 2005. Development of a method to assess binding of astaxanthin to Atlantic salmon S. salar L. muscle proteins. Aquacult. Res. 36, 336–343.]. These combined observations suggest that the carotenoid binding capacity of the muscle proteins of salmon is not the limiting factor in the deposition of carotenoid in their flesh.     

Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.)

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salar L.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within-river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member-vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life-history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.     

Quantitative genetics of disease resistance in vaccinated and unvaccinated Atlantic salmon (Salmo salar L.)

Furunculosis (Aeromonoas salmonicida) is an important disease in Atlantic salmon (Salmo salar) farming. Vaccination and selective breeding for increased resistance to the disease on the basis of challenge tests of unvaccinated fish are used as complementary prophylactic methods. An important issue is whether genetic predisposition to infection is consistent across vaccinated and unvaccinated fish. Hence, the main objective of this study was to determine the magnitude of the genetic associations (correlations) between resistance to furunculosis in vaccinated and unvaccinated fish, and to estimate the magnitude of the correlation of resistance to furunculosis with resistance to the viral diseases infectious pancreatic necrosis (IPN) and infectious salmon anaemia (ISA). Sub-samples of unvaccinated and vaccinated salmon from 150 full-sib families were subjected to separate cohabitation challenge tests. Substantial genetic variation was found in resistance to furunculosis in both the unvaccinated (heritabilities of 0.51 ± 0.05) and vaccinated (0.39 ± 0.06) fish. However, the genetic correlation between resistance to furunculosis in the two groups was low (0.32 ± 0.13), indicating a weak genetic association between resistance in the two groups. Hence, the current selection strategy on the basis of challenge tests of unvaccinated fish is likely to produce low genetic improvement in resistance to furunculosis under field conditions, where fish are vaccinated with an effective vaccine. Evidence was found of significantly favourable genetic associations of resistance to furunculosis in unvaccinated (but less so for vaccinated) fish with resistance to both IPN and ISA (unvaccinated fish), indicating that vaccination 'mask' genetic associations between resistance to different diseases.     

An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin-biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half-sibs in nature most probably reduce the opportunity and advantage of kin-biased behaviour, in contrast to laboratory studies conducted in artificial, high-density conditions.     

An evaluation of the quality of fall-fingerling Atlantic salmon (Salmo salar L.) released to natural lacustrine nursery areas in Newfoundland,Canada

Results of experiments on controlled releases of fall-fingerling Atlantic salmon to lacustrine habitats in Newfoundland are reviewed in terms of survival during freshwater residence and smolt yield per unit of standing water habitat. Average survival from parr to smolt in three consecutive annual releases was 12.9% and we conclude that the quality of fall-fingerling salmon, produced from our semi-natural rearing techniques, was satisfactory. Year-class survival decreased progressively with consecutive releases. Rate of increase in juvenile salmon biomass remained stable over the duration of the study, suggesting that the average annual biomass of 1.6 kg ha^–1 of juvenile salmon released did not exceed habitat carrying capacity. Precocity did not appear to represent a significant deterrent to fall-fingerling survival. Annual smolt yield (by year-class) from stocking ranged from 53 to 130 ha^–1 (mean = 77 smolts ha^–1).     

Prior residence, territory quality and life-history strategies in juvenile Atlantic salmon (Salmo salar L.)

Three groups of juvenile salmon were introduced sequentially into an artificial stream to investigate the effects of prior residence on behaviour and territory choice. Almost half of the first group obtained and defended distinct territories, the other half being constrained to an area approximately the size of one large territory. All of the fish in the subsequent groups, bar one, were also constrained to the same site. Since the fish were of similar size, prior residence alone seemed to influence which individuals obtained territories. However, within the first group, the fish that obtained territories were larger and more aggressive. The territorial fish did not appear to choose the most profitable territories, although they had the greatest opportunity to do so. Since juvenile salmon emerge from their gravel nests fairly synchronously, a time constraint on site sampling is hypothesised: there may be a risk in taking time to sample sites, since these same sites may become occupied with conspecifics. However, fish with territories fed at faster rates than non-territorial fish, possibly because of reduced competition for prey items. Consequently, fish from the first group (containing most of the territorial fish) grew faster than the other two groups. Moreover, most of the territory holders, but only one of the non-territorial fish, reached the threshold size that increases their probability of smolting the following year. This suggests that ability to obtain a defensible territory, primarily through prior residence, influences the age at which juvenile salmon can migrate to sea.     

Variation in the timing of river entry of Atlantic salmon (Salmo salar L.) in the Baltic

The timing of river entry in the Atlantic salmon is known to depend on genetic,demographic and environmental factors,but little is known about the relative magnitude of among population and among year variation and covariation in this respect in natural state Atlantic salmon rives.To investigate this,variability in the timing of river entry in three historical Finnish Atlantic salmon populations were analyzed using salmon trap data collected during 1870-1902.The analyses reveled that 1)the timing of river e...     

Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.)

It may often be necessary to perform genetic analyses of temporal replicates to estimate the significance of spatial variation independently from that of temporal variation in order to ensure the reliability of estimates of a defined population structure. Nevertheless, temporal studies of genetic diversity remain scarce in the literature relative to the plethora of empirical studies of population structure. In vertebrates, a limited number of studies have specifically assessed the temporal stability of population structure for more than one generation. In this study, we performed a microsatellite analysis of DNA obtained from archived scales to compare the population structure among four sympatric landlocked populations of Atlantic salmon ( Salmo salar ) over a time frame of three to five generations. The same patterns of allele frequency distribution, θ, R _ST and genetic distance estimates were observed among populations for two time periods, confirming the temporal stability of the population structure. Despite population declines and stocking during this period, no statistically significant changes in intrapopulation genetic diversity were apparent. This study illustrates the feasibility and usefulness of microsatellite analysis of temporal samples, not only to infer changes of intrapopulation genetic diversity, but also to assess the stability of population structure over a time frame of several generations.     

Cortisol stimulates hypo-osmoregulatory ability in Atlantic salmon, Salmo salar L.

Hypo-osmoregulatory ability in juvenile Atlantic salmon, Sulrno salur L., was improved by cortisol treatment. Implantation of a vegetable shortening pellet containing cortisol (50 mg kg⁻¹) resulted in elevated plasma cortisol titres. Maximum cortisol levels (160–170ngml⁻¹) were observed at days 6 and 12 after the implantation and dropped significantly by day 55. Cortisol-implanted fish in fresh water developed a twofold increase in gill Na⁺/K⁺-ATPase activity at days 6 and 12, and a threefold increase by day 55. Intestinal mucosa Na⁺/K⁺-ATPase activity was not affected by cortisol. Cortisol-implanted fish exposed to 28 ppt sea water for 48 h tended to show an improved ability to regulate their plasma osmolarity and reduce their ionic load. The osmo-regulatory ability attained at days 12 and 55 was further evaluated by exposing fish to 37 ppt sea water for 96 h. While all the control fish died relatively early in these tests, cortisol-implanted fish showed a clear reduction in their mortality rate. These results indicate that cortisol can induce biochemical and organismal changes during winter months that typify preadaptive events normally occurring in the spring.     

Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar)

Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.