A species-specific microsatellite marker to discriminate European Atlantic salmon, brown trout, and their hybrids (original) (raw)
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Canadian Journal of Fisheries and Aquatic Sciences, 1995
Atlantic salmon populations show Bow levels of genetic differentiation relative to other salmonid species, when surveyed by allozymes, and with mitochondrial DNA and nuclear ribosomal DNA markers. Here we report the application of three novel microsatellite VNTR loci to population differentiation in Atlantic salmon. A total of 232 microsatellites, cloned from Atlantic salmon, were classified as perfect. imperfect, and compound repeats. Microsatellite length, as in other teleosts, was significantly larger than published mammalian microsatellites. Primers for PCW amplification of three salmon microsatellites were designed. Allele frequencies, degree of polymorphism, and heterozygosity were estimated for five populations from Nova Scotia, Canada, and from Europe. Nei's genetic distances of 0.02-0.9 were observed among populations. There was a clear discrimination between Canadian and European fish based on unique alleles present at two loci. These Atlantic salmon primers also amplify presumably homologous loci in nine other salmonid species. The polymorphic microsatellites loci reported here demonstrate great potential as genetic markers in population, breeding, and evolutionary studies.
Canadian Journal of Fisheries and Aquatic Sciences, 1996
Twenty-two variable number of tandem repeat microsatellite dinucleotide repeat ([GA] n and [CA] n) loci were cloned from sockeye salmon (Oncorhynchus nerka) partial genomic libraries. Characteristics and optimal polymerase chain reaction (PCR) conditions were defined for each locus. The degree of conservation of sequences flanking microsatellite repeat motifs and the utility of heterologous PCR primers for analyses in closely related taxa was tested using 10 salmonid species from four genera. Nearly all microsatellite primers produce amplification products in multiple species, suggesting broad application in salmonid research. The utility of these loci for population genetic studies was tested using individuals (N = 83) from three spawning populations of chinook salmon (Oncorhynchus tshawytscha) from the Yukon River, Yukon Territories. Twelve of 16 loci screened were polymorphic (mean heterozygosity = 0.254). Genetic distance estimates between populations were concordant with results from a previous allozyme survey of these same populations. Discussions of the utility of microsatellite markers in salmonid population genetic research are presented in light of recently described statistical methodologies based on mutational properties and interallelic differences in repeat score. Résumé : À partir de banques génomiques partielles de saumons sockeye (Oncorhychus nerka), on a cloné 22 loci de microsatellite séquences répétées en tandem dinucléotidiques ([GA] n et [CA] n). Les caractéristiques et les conditions optimales pour la PCR ont été définies pour chaque locus. Le degré de conversion des séquences qui flanquent les motifs répétés des microsatellites et l'utilité des amorces hétérologues de la PCR pour des analyses dans des taxons étroitement apparentés ont été évalués avec 10 espèces de salmonidés appartenant à quatre genres. Presque toutes les amorces de microsatellites ont donné des produits d'amplification chez plusieurs espèces, ce qui laisse supposer qu'elles sont applicables à grande échelle dans les recherches sur les salmonidés. On a évalué l'utilité de ces loci dans les études génétiques des populations, en utilisant des individus (N = 83) provenant de trois populations de saumons quinnat (Oncorhychus tshawytscha) en cours de reproduction, vivant dans le fleuve Yukon (Territoires du Nord-ouest). Douze des 16 loci examinés étaient polymorphes (hétérozygotie moyenne = 0,254). Les estimations de distance génétique entre les populations concordaient avec les résultats obtenus au cours d'une étude allozymatique précédente des mêmes populations. On examine l'utilité de marqueurs à microsatellites dans les recherches génétiques de populations de salmonidés, à la lumière de méthodes statistiques récemment décrites, basées sur les propriétés mutationnelles et les différences inter-alléliques des résultats obtenus avec les séquences répétées. [Traduit par la Rédaction]
Microsatellite Variation in Populations of Atlantic Salmon from North Europe
Environmental Biology of Fishes, 2000
Our aim was to investigate the level of genetic differentiation in northern European populations of Atlantic salmon, to establish the genetic relationship among major salmon populations in Russia and North Norway, and to compare these to populations from the western Atlantic lineage. Samples were collected along an east-west axis, from Pechora River in Russia to Restigouche River in Quebec, Canada. A total of 439 individual salmon were collected from seven rivers (sample sizes from 50 to 84 individuals). The samples were analysed for variation at four microsatellite loci; Ssa13.37, Ssa14, Ssa171 and Ssa171. Significant differences were found between most of the European populations, and the populations from the Tana and Pechora Rivers were most distinct. The samples from the Rivers Mezenskaya Pizhma and Emtsa in Arkhangelsk oblast in Russia were not significantly different from each other in an exact test of population differences. All other river pairs were significantly different. These results confirmed the deep genetic divergence between American and European salmon populations demonstrated in earlier studies, with alleles specific to continent found in three of the microsatellites.
Transactions of the American Fisheries Society, 2000
Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( ϭ 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic , which ␦ estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because is more likely to be large, presumably as a result ␦ of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations.
Molecular Ecology, 2001
Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5 -37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.
Freshwater Biology, 2009
1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its conservation in Normandy (France).2. Samples collected from 10 natural sites revealed that 13 of 14 microsatellite loci were polymorphic. Significant differentiation among populations was detected (FST = 0.054, P < 0.001), and all FST pairwise comparisons except one were significant. A genetic split was observed between populations inhabiting streams with limestone geology compared to those inhabiting streams with siliceous geology, which could reflect adaptative differences.3. Hatchery stocks used for the restocking of two rivers were genetically distinct from native stocks.4. Analysis of three stream habitats restored in 1995 showed that all were recolonized naturally by wild salmon from geographically close populations and no founder effects were detected. Allelic richness was similar between recolonized and wild populations.5. From a management perspective, our study revealed that restoration of habitat is very effective to recreate new populations in rivers from which salmon have disappeared and that natural recolonization can be fast and effective in terms of genetic diversity.
ICES Journal of Marine Science, 2017
Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectiv...
Molecular Ecology Notes, 2005
Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise F ST , 0.12, was highly significant. These findings are consistent with patterns of continental-level differentiation observed previously using an alternate suite of microsatellite loci. Locus-by-locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.
Microsatellite allele ladders in two species of Pacific salmon: preparation and field-test results
Molecular Ecology Notes, 2002
To support microsatellite data communication, we have developed a convenient method for creating locus-specific microsatellite allele ladders used to align data from different laboratories. The ladders were constructed by pooling polymerase chain reaction (PCR) products to create a template for amplification. Four ladders were field-tested in six different laboratories using different genotyping platforms. Despite substantial differences in absolute size estimates of DNA fragments, each laboratory correctly scored unknown sample genotypes according to the ladder designations. The results indicate that our simple preparation method provides reliable allele ladders in a time-efficient manner for verifying microsatellite genotypes across platforms.