title: Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.).
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.
authors: Kevo Subarctic Research Institute, University of Turku, Turku 20014, Finland.
authors: Mikhail
authors: M
authors: Ozerov
authors: Anti
authors: A
authors: Vasemägi
authors: Vidar
authors: V
authors: Wennevik
authors: Eero
authors: E
authors: Niemelä
authors: Sergey
authors: S
authors: Prusov
authors: Matthew
authors: M
authors: Kent
authors: Juha-Pekka
authors: JP
authors: Vähä
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D003362:Cost-Benefit Analysis; D004247:DNA / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D023281:Genomics / Q000191:economics*; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011786:Quality Control; D020317:Salmo salar / Q000235:genetics*
chemical_list: D004247:DNA