Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)
Background: New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wid...
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ftimr:oai:imr.brage.unit.no:11250/109053 2023-05-15T15:30:25+02:00 Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) Ozerov, Mikhail Vasemägi, Anti Wennevik, Vidar Niemelä, Eero Prusov, Sergey Kent, Matthew Vähä, Juha-Pekka 2013-01-16 application/pdf http://hdl.handle.net/11250/109053 https://doi.org/10.1186/1471-2164-14-12 eng eng Springer Ozerov et al.: Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.). BMC Genomics 2013 14:12 urn:issn:1471-2164 http://hdl.handle.net/11250/109053 https://doi.org/10.1186/1471-2164-14-12 9 p. 14 BMC Genomics 1 VDP::Agriculture and fishery disciplines: 900::Fisheries science: 920::Fish health: 923 Journal article Peer reviewed 2013 ftimr https://doi.org/10.1186/1471-2164-14-12 2021-09-23T20:15:17Z Background: New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results: In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions: Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits European Union, Kolarctic ENPI CBC project, Academy of Finland, Norwegian Directorate of Nature Management, Norwegian Research Council, Estonian Science Foundation Article in Journal/Newspaper Atlantic salmon Salmo salar Institute for Marine Research: Brage IMR BMC Genomics 14 1 12 |
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Open Polar |
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Institute for Marine Research: Brage IMR |
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ftimr |
language |
English |
topic |
VDP::Agriculture and fishery disciplines: 900::Fisheries science: 920::Fish health: 923 |
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VDP::Agriculture and fishery disciplines: 900::Fisheries science: 920::Fish health: 923 Ozerov, Mikhail Vasemägi, Anti Wennevik, Vidar Niemelä, Eero Prusov, Sergey Kent, Matthew Vähä, Juha-Pekka Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
topic_facet |
VDP::Agriculture and fishery disciplines: 900::Fisheries science: 920::Fish health: 923 |
description |
Background: New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results: In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions: Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits European Union, Kolarctic ENPI CBC project, Academy of Finland, Norwegian Directorate of Nature Management, Norwegian Research Council, Estonian Science Foundation |
format |
Article in Journal/Newspaper |
author |
Ozerov, Mikhail Vasemägi, Anti Wennevik, Vidar Niemelä, Eero Prusov, Sergey Kent, Matthew Vähä, Juha-Pekka |
author_facet |
Ozerov, Mikhail Vasemägi, Anti Wennevik, Vidar Niemelä, Eero Prusov, Sergey Kent, Matthew Vähä, Juha-Pekka |
author_sort |
Ozerov, Mikhail |
title |
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
title_short |
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
title_full |
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
title_fullStr |
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
title_full_unstemmed |
Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.) |
title_sort |
cost-effective genome-wide estimation of allele frequencies from pooled dna in atlantic salmon (salmo salar l.) |
publisher |
Springer |
publishDate |
2013 |
url |
http://hdl.handle.net/11250/109053 https://doi.org/10.1186/1471-2164-14-12 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
9 p. 14 BMC Genomics 1 |
op_relation |
Ozerov et al.: Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.). BMC Genomics 2013 14:12 urn:issn:1471-2164 http://hdl.handle.net/11250/109053 https://doi.org/10.1186/1471-2164-14-12 |
op_doi |
https://doi.org/10.1186/1471-2164-14-12 |
container_title |
BMC Genomics |
container_volume |
14 |
container_issue |
1 |
container_start_page |
12 |
_version_ |
1766360867573596160 |