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

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....

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Mikhail Ozerov, Anti Vasemägi, Vidar Wennevik, Rogelio Diaz-Fernandez, Matthew Kent, John Gilbey, Sergey Prusov, Eero Niemelä, Juha-Pekka Vähä
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e7cf3db1bb424cd1a03c00320c4697e9
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:e7cf3db1bb424cd1a03c00320c4697e9
record_format	dspace
spelling	oai:doaj.org-article:e7cf3db1bb424cd1a03c00320c4697e92021-11-18T08:41:49ZFinding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.1932-620310.1371/journal.pone.0082434https://doaj.org/article/e7cf3db1bb424cd1a03c00320c4697e92013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24358184/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Genetic 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.Mikhail OzerovAnti VasemägiVidar WennevikRogelio Diaz-FernandezMatthew KentJohn GilbeySergey PrusovEero NiemeläJuha-Pekka VähäPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e82434 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mikhail Ozerov Anti Vasemägi Vidar Wennevik Rogelio Diaz-Fernandez Matthew Kent John Gilbey Sergey Prusov Eero Niemelä Juha-Pekka Vähä Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
description	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.
format	article
author	Mikhail Ozerov Anti Vasemägi Vidar Wennevik Rogelio Diaz-Fernandez Matthew Kent John Gilbey Sergey Prusov Eero Niemelä Juha-Pekka Vähä
author_facet	Mikhail Ozerov Anti Vasemägi Vidar Wennevik Rogelio Diaz-Fernandez Matthew Kent John Gilbey Sergey Prusov Eero Niemelä Juha-Pekka Vähä
author_sort	Mikhail Ozerov
title	Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
title_short	Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
title_full	Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
title_fullStr	Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
title_full_unstemmed	Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.
title_sort	finding markers that make a difference: dna pooling and snp-arrays identify population informative markers for genetic stock identification.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/e7cf3db1bb424cd1a03c00320c4697e9
work_keys_str_mv	AT mikhailozerov findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT antivasemagi findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT vidarwennevik findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT rogeliodiazfernandez findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT matthewkent findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT johngilbey findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT sergeyprusov findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT eeroniemela findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification AT juhapekkavaha findingmarkersthatmakeadifferencednapoolingandsnparraysidentifypopulationinformativemarkersforgeneticstockidentification
_version_	1718421476229513216

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

Ejemplares similares