ArticleGenetica2011
Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).
Article in Genetica, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Effects of a hydropower project on a high-value Asian elephant population.Ecology and evolution · 2023Article
- Optimization of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout (Ecology and evolution · 2023Article
- A new GTSeq resource to facilitate multijurisdictional research and management of walleyeEcology and evolution · 2022Article
- Country-wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter,Evolutionary applications · 2022Article
- Forensic Genetic Analyses of Melanistic Iguanas Highlight the Need to Monitor the Iguanid Trade.Animals : an open access journal from MDPI · 2022Article
- First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach.BMC genomics · 2021Article
- Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm.Plants (Basel, Switzerland) · 2021Article
- mtDNAcombine: tools to combine sequences from multiple studies.BMC bioinformatics · 2021Article
- Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa.Molecular biology and evolution · 2021Article
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- Genomic approach for conservation and the sustainable management of endangered species of the Amazon.PloS one · 2021Article
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- Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.Evolutionary applications · 2019Article
- Sea lice loads correlate with the diversity at the Major Histocompatibility Complex -related loci in farmed Atlantic salmon, Salmo salar.Journal of fish diseases · 2019Article
Corrections and comments
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Authors and funding
30 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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