Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.

• Published in: PLoS ONE
• Main Authors: Mikhail Ozerov, Anti Vasemägi, Vidar Wennevik, Rogelio Diaz-Fernandez, Matthew Kent, John Gilbey, Sergey Prusov, Eero Niemelä, Juha-Pekka Vähä
• Format: Article in Journal/Newspaper
• Language: English
• Published: Public Library of Science (PLoS) 2013
• Subjects: Medicine; R; Science; Q; Atlantic salmon
• Online Access: https://doi.org/10.1371/journal.pone.0082434; https://doaj.org/article/e7cf3db1bb424cd1a03c00320c4697e9

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.