Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

Susan E. Johnston*, Meri Lindqvist, Eero Niemela, Panu Orell, Jaakko Erkinaro, Matthew P. Kent, Sigbjorn Lien, Juha-Pekka Vaha, Anti Vasemagi, Craig R. Primmer

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA of a lower amount and quality, and the extent to which DNA degradation affects SNP genotyping success and allele frequency estimation is not well understood. We conducted high density SNP genotyping and allele frequency estimation in both individual DNA samples and pooled DNA samples extracted from dried Atlantic salmon (Salmo salar) scales stored at room temperature for up to 35 years, and assessed genotyping success, repeatability and accuracy of allele frequency estimation using a high density SNP genotyping array.

Results: In individual DNA samples, genotyping success and repeatability was very high (> 0.973 and > 0.998, respectively) in samples stored for up to 35 years; both increased with the proportion of DNA of fragment size > 1000 bp. In pooled DNA samples, allele frequency estimation was highly repeatable (Repeatability = 0.986) and highly correlated with empirical allele frequency measures (Mean Adjusted R-2 = 0.991); allele frequency could be accurately estimated in > 95% of pooled DNA samples with a reference group of at least 30 individuals. SNPs located in polyploid regions of the genome were more sensitive to DNA degradation: older samples had lower genotyping success at these loci, and a larger reference panel of individuals was required to accurately estimate allele frequencies.

Conclusions: SNP genotyping was highly successful in degraded DNA samples, paving the way for the use of degraded samples in SNP genotyping projects. DNA pooling provides the potential for large scale population genetic studies with fewer assays, provided enough reference individuals are also genotyped and DNA quality is properly assessed beforehand. We provide recommendations for future studies intending to conduct high-throughput SNP genotyping and allele frequency estimation in historical samples.

Original languageEnglish
Article number439
Number of pages13
JournalBMC Genomics
Volume14
DOIs
Publication statusPublished - 3 Jul 2013

Keywords

  • Atlantic salmon
  • SNP genotyping
  • Illumina (R) iSelect SNP-array
  • Degraded DNA
  • Archived samples
  • Fish scales
  • DNA pooling
  • Allelotyping
  • Allele frequency
  • Fragment size
  • SINGLE NUCLEOTIDE POLYMORPHISMS
  • GENETIC-STRUCTURE
  • GENOME
  • POPULATION
  • CONSERVATION
  • RIVER
  • COST
  • MANAGEMENT
  • DISCOVERY
  • PATTERNS

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