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

BMC Genomics

Methodology Article

Sigbjørn Lien¹  Matthew P Kent¹  Meri Lindqvist²  Craig R Primmer²  Juha-Pekka Vähä²  Anti Vasemägi³  Susan E Johnston⁴  Panu Orell⁵  Eero Niemelä⁵  Jaakko Erkinaro⁵ 

[1] Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, N - 1432, Aas, Norway;Department of Biology, University of Turku, FIN-20014, Turku, Finland;Department of Biology, University of Turku, FIN-20014, Turku, Finland;Department of Aquaculture, Estonian University of Life Sciences, Kreutzwaldi 48, 51014, Tartu, Estonia;Department of Biology, University of Turku, FIN-20014, Turku, Finland;Institute of Evolutionary Biology, University of Edinburgh, EH9 3JT, Edinburgh, United Kingdom;Finnish Game and Fisheries Research Institute, FIN-99980, Utsjoki, Finland;

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

DOI  :  10.1186/1471-2164-14-439

 received in 2013-02-27, accepted in 2013-06-18,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundDNA 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.ResultsIn 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.ConclusionsSNP 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.

【 授权许可】

CC BY   
© Johnston et al.; licensee BioMed Central Ltd. 2013