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'.     

Characterization of transferrin‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar)

The transferrin (TF) gene has recently received increased interest in fish given its fitness relevance as a resistance gene against pathogenic bacteria. In this study, we characterized five TF‐linked microsatellites in brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). Interestingly, each marker amplified duplicated loci and linkage analysis revealed that the TF gene has most likely experienced a tandem duplication during salmonid evolution. In addition, the amplification of all five markers across a wide range of salmonid species suggests that they may be of general interest for the genetic analysis of the TF gene(s) in this teleost family.     

Territory size and distribution of newly-emerged Atlantic salmon (Salmo salar)

Newly emerged Atlantic salmon (Salmo salar) were observed from May to August 1981 at six isolated redds in Washington County, Maine, USA. Territorial size and distribution were measured. At the end of the emergence period (12 to 28 May), fish maintained positions (stations) at redds where water velocity did not exceed 52 cm s^–1 By 12 June, most salmon (80–96%) had moved off the redds of origin and had established territories 1 to 5 m from the redd. The area defended increased substantially after mid-June, but territorial aggression diminished by 15 July, and the fry dispersed downstream. All fish observed were territorial, and the percentage of time during which stations were held decreased from 89 in mid-May to as low as 40% in mid-June.Cooperators are the Maine Department of Inland Fisheries and Wildlife, University of Maine, U.S. Fish and Wildlife Service, and the Wildlife Management Institute     

Spawning behaviour of a farmed escaped female Atlantic salmon (Salmo salar)

Excavation of stranded redds revealed differences in spawning behaviour between farmed and wild Atlantic salmon. The redd of a farmed fish contained more egg pockets (nine v . average of two) and fewer eggs per pocket (averages: 459 v . 707). No other pocket measures differed.     

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.     

Beyond MHC: signals of elevated selection pressure on Atlantic salmon (Salmo salar) immune‐relevant loci

Using Atlantic salmon (Salmo salar) as a model system, we investigated whether 18 microsatellites tightly linked to immune‐relevant genes have experienced different selection pressures than 76 loci with no obvious association with immune function. Immune‐relevant loci were identified as outliers by two outlier tests significantly more often than nonimmune linked loci (22% vs. 1.6%). In addition, the allele frequencies of immune relevant markers were more often correlated with latitude and temperature. Combined, these results support the hypothesis that immune‐relevant loci more frequently exhibit footprints of selection than other loci. They also indicate that the correlation between immune‐relevant loci and latitude may be due to temperature‐induced differences in pathogen‐driven selection or some other environmental factor correlated with latitude.     

Diel activity pattern of juvenile Atlantic salmon (Salmo salar) in early and late winter

Radiotelemetry was used to investigate the diel activity pattern of juvenile Atlantic salmon (Salmo salar) in early and late winter. Fish were active throughout the diel cycle. However, there was significantly less daytime than nighttime movement and movement declined significantly with increasing fork length. Maximizing winter growth rate, through an overall increase in foraging activity, may reduce the risk of starvation in smaller fish. The results of the present study provide evidence that the activity patterns of juvenile salmonids are quite complex and support the suggestion that individual variation in activity patterns are, at least, partially driven by body size.     

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.     

Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar)

Major histocompatibility complex (MHC)-dependent mating preferences have been observed across vertebrate taxa and these preferences are expected to promote offspring disease resistance and ultimately, viability. However, little empirical evidence linking MHC-dependent mate choice and fitness is available, particularly in wild populations. Here, we explore the adaptive potential of previously observed patterns of MHC-dependent mate choice in a wild population of Atlantic salmon (Salmo salar) in Québec, Canada, by examining the relationship between MHC genetic variation and adult reproductive success and offspring survival over 3 years of study. While Atlantic salmon choose their mates in order to increase MHC diversity in offspring, adult reproductive success was in fact maximized between pairs exhibiting an intermediate level of MHC dissimilarity. Moreover, patterns of offspring survival between years 0+ and 1+, and 1+ and 2+ and population genetic structure at the MHC locus relative to microsatellite loci indicate that strong temporal variation in selection is likely to be operating on the MHC. We interpret MHC-dependent mate choice for diversity as a likely bet-hedging strategy that maximizes parental fitness in the face of temporally variable and unpredictable natural selection pressures.     

Vertical distribution of Atlantic salmon (Salmo salar) as a function of illumination

The vertical distribution of cultured Atlantic salmon larger than 1 kg was monitored by hydroacoustics in both a shallow (6 m) and a deep (20 m) cage. Surface light levels and fish distribution were registered for three periods throughout the year. The two fish groups were fed calculated rations twice a day. During the winter and spring (including vernal equinox), the fish were distributed at around 5 m depth in both cages when not feeding. Around summer solstice, the fish preferred deeper waters when not feeding. The light dependency of the vertical migration was pronounced, and indicates clearly that even a 20 m deep cage is not deep enough to meet the depth requirements of large Atlantic salmon during summer.     

Novel set of multiplex assays (SalPrint15) for efficient analysis of 15 microsatellite loci of contemporary samples of the Atlantic salmon (Salmo salar)

We report the development of new PCR assays and loading panels for the Atlantic salmon using 15 microsatellite loci. A total of 8, 3 and 4 loci were coamplified in three separate PCRs using labelled primers and loaded on the ABI DNA analyzer in two separate panels. Amplified alleles were clearly typed, and easily interpretable results were obtained. The method was successfully applied in different laboratories, even when different types of DNA polymerase were employed. The method is useful for analysing paternity, population genetics and conservation as well as for selective breeding programmes.     

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.     

Microsatellite loci reveal highly significant genetic differentiation among Atlantic salmon (Salmo salar L.) stocks from the east coast of Canada

Allele frequency data from eight microsatellite loci provide evidence of highly significant genetic differentiation among stocks of Atlantic salmon Salmo salar L. from the Bay of Fundy, eastern and north-western Nova Scotia and Newfoundland. Estimates of genetic structure ( R _ST and θ) were significant both among all samples taken from the different geographical locations and among samples from geographical regions for which more than one stock was sampled. Samples from the Bay of Fundy taken from stocks which are phenotypically and behaviourally diverse showed particularly high levels of genetic structure. Rogers', allele sharing and (δμ)² distances also revealed significant differences among stock samples and were significantly correlated [Rogers' and (δμ)²] with sea distance between rivers. Results suggest that stocks of Atlantic salmon in eastern Canada are highly diverse genetically and that this should be an important consideration in any management programme for stocks in the area.     

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.