title: Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
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.
authors.affiliation: Kevo Subarctic Research Institute, University of Turku, Turku, Finland.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Ozerov
authors.affiliation: Department of Biology, Division of Genetics and Physiology, University of Turku, Turku, Finland ; Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, Tartu, Estonia.
authors.forename: Anti
authors.initials: A
authors.lastname: Vasemägi
authors.affiliation: Research group Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.
authors.forename: Vidar
authors.initials: V
authors.lastname: Wennevik
authors.affiliation: Kevo Subarctic Research Institute, University of Turku, Turku, Finland.
authors.forename: Rogelio
authors.initials: R
authors.lastname: Diaz-Fernandez
authors.affiliation: Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway.
authors.forename: Matthew
authors.initials: M
authors.lastname: Kent
authors.affiliation: Freshwater Laboratory, Marine Scotland, Faskally, Pitlochry, United Kingdom.
authors.forename: John
authors.initials: J
authors.lastname: Gilbey
authors.affiliation: Freshwater Resources Laboratory, Knipovitch Polar Research Institute of Marine Fisheries and Oceanography, Murmansk, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Prusov
authors.affiliation: Finnish Game and Fisheries Research Institute, Oulu, Finland.
authors.forename: Eero
authors.initials: E
authors.lastname: Niemelä
authors.affiliation: Kevo Subarctic Research Institute, University of Turku, Turku, Finland.
authors.forename: Juha-Pekka
authors.initials: JP
authors.lastname: Vähä
mesh_terms: D000483:Alleles; D000818:Animals; D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D012474:Salmon / Q000235:genetics*
chemical_list: D005819:Genetic Markers