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Open Access Methodology article

Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)

Mikhail Ozerov1, Anti Vasemägi27, Vidar Wennevik3, Eero Niemelä4, Sergey Prusov5, Matthew Kent6 and Juha-Pekka Vähä2*

Author affiliations

1 Kevo Subarctic Research Institute, University of Turku, Turku, 20014, Finland

2 Department of Biology, Division of Genetics and Physiology, University of Turku, Turku, 20014, Finland

3 Institute of Marine Research, PO Box 1870, Nordnes, N-5817, Bergen, Norway

4 Finnish Game and Fisheries Research Institute, Rakentajantie 3,PL 413, 90014, Oulun yliopisto, Finland

5 Freshwater Resources Laboratory, Knipovitch Polar Research Institute of Marine Fisheries and Oceanography, 6. Knipovitch Street, 183767, Murmansk, Russia

6 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences (IHA), Norwegian University of Life Sciences, PO Box 5003, Ås, Norway

7 Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014, Tartu, Estonia

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Citation and License

BMC Genomics 2013, 14:12  doi:10.1186/1471-2164-14-12

Published: 16 January 2013

Abstract

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.

Keywords:
DNA pooling; Atlantic salmon; SNP; Allele frequency estimation; Allelotyping; Population genomics