ArticlePloS one2013
Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Contrasting population genomic structuring of northern pike (Esox lucius L.) in fresh- and brackish water environments: Implications for management and conservation.Journal of fish biology · 2026Article
- A web tool for the global identification of pig breeds.Genetics, selection, evolution : GSE · 2023Article
- Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations.Animals : an open access journal from MDPI · 2023Review
- Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs.Frontiers in genetics · 2023Article
- A new GTSeq resource to facilitate multijurisdictional research and management of walleyeEcology and evolution · 2022Article
- In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment.Molecular ecology resources · 2022Article
- Selection of Genome-Wide SNPs for Pooled Allelotyping Assays Useful for Population Monitoring.Genome biology and evolution · 2022Article
- Lack of genetic differentiation in yellowfin tuna has conservation implications in the Eastern Pacific Ocean.PloS one · 2022Article
- Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids.PloS one · 2020Article
- Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array.Frontiers in plant science · 2020Article
- DNA Methylation Changes in the Sperm of Captive-Reared Fish: A Route to Epigenetic Introgression in Wild Populations.Molecular biology and evolution · 2019Article
- Determination of Varying Group Sizes for Pooling Procedure.Computational and mathematical methods in medicine · 2019Article
- Applications of random forest feature selection for fine-scale genetic population assignment.Evolutionary applications · 2018Article
- Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri.BMC genomics · 2017Article
- Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing.PloS one · 2017Article
- Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees.Evolutionary applications · 2016Article
- Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection.BMC genomics · 2016Article
- Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera).PloS one · 2015Article
- Challenges in analysis and interpretation of microsatellite data for population genetic studies.Ecology and evolution · 2014Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global F ST, pairwise F ST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise F ST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species.
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