Microsatellite standardization and genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.) (original) (raw)
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Genetica, 2011
Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.
The Use of Microsatellite DNA Loci for Genetic Monitoring of Atlantic Salmon Populations
North American Journal of Aquaculture, 2000
This work addresses the application of a new group of molecular markers, microsatellite loci, to monitor genetic diversity in stocks used in fish enhancement programs. To illustrate the potential use of these markers, we examined the genetic variation associated with the Connecticut River and Penobscot River populations of Atlantic salmon Salmo salar in the United States. Both rivers are stocked annually with fry from captive or cultured stocks that are one generation removed from sea-run adults. We analyzed microsatellite loci variation among sea-run adults and the derived cultured stock for the Connecticut River in a given year, along with two consecutive cohorts of cultured age-0 juveniles for the Penobscot River. Our results reveal subtle differences in allele frequencies between the two samples for each stock and some potential increases of homozygotes. These results demonstrate the potential value of microsatellite loci for routine genetic monitoring of cultured Atlantic salmon populations associated with restoration programs in the eastern United States.
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]
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.
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, 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.
Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon
Molecular Ecology, 2000
Spawning aggregations of Pacific herring (Clupea pallasi) often exhibit significant interannual variation in allele frequencies of neutral gene markers. We isolated 14 tetranucleotide microsatellites to examine hypothetical processes that may produce this unique genetic signal. We developed and tested primer pairs for each locus and then estimated locus variability in samples (n = 60) from two populations. The number of alleles per locus ranged from five to 49. The expected heterozygosity across loci and populations ranged from 0.20 to 0.96. These microsatellites will be useful for estimating genetic variation in herring on a fine geographical scale.
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.
Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites
Animal Genetics, 1998
Microsatellite genetic markers are becoming increasing important tools in the investigation of alternate reproductive strategies in wild plants and animals, and in the implementation of optimal breeding programs for endangered species, and managed cultured populations. Overall, little attention is paid to the frequency and impact of scoring errors and mutations on the resolution and accuracy of such analyses. Here, parentage of 792 Atlantic salmon (Salmo salar) reared communally were determined using di-and tetranucleotide microsatellites. Over 99 . 5% of the offspring could be unambiguously matched to one set of parents in the original 12 (1´1) experimental cross (each of 12 males uniquely crossed to one of 12 females) and in a simulated 36 (1´1) cross (involving additional parents), and over 80% in a 12´12 cross (all 12 males crossed to all 12 females). Mutations were rare (»3 . 4´10 ±4 ), though scoring errors were relatively common (2±3% per allele scored), with the rate of error varying among loci. Approximately 90% of scoring errors (or mutations) are expected to be detected in this analysis, and of those that are not, fewer than 0 . 5% should lead to a false or incorrect determinations of parentage. Based on several indices, we expect that greater than 99 . 7% of offspring assayed were matched to their true parents.