Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Methodology article

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 Johnston15*, Meri Lindqvist1, Eero Niemelä2, Panu Orell2, Jaakko Erkinaro2, Matthew P Kent3, Sigbjørn Lien3, Juha-Pekka Vähä1, Anti Vasemägi14 and Craig R Primmer1

Author Affiliations

1 Department of Biology, University of Turku, Turku FIN-20014, Finland

2 Finnish Game and Fisheries Research Institute, Utsjoki FIN-99980, Finland

3 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas N - 1432, Norway

4 Department of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 48, 51014, Tartu, Estonia

5 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom

For all author emails, please log on.

BMC Genomics 2013, 14:439  doi:10.1186/1471-2164-14-439

Published: 3 July 2013

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 R2 = 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.

Keywords:
Atlantic salmon; SNP genotyping; Illumina® iSelect SNP-array; Degraded DNA; Archived samples; Fish scales; DNA pooling; Allelotyping; Allele frequency; Fragment size