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

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.

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

“…SNP genotyping of historical specimens has previously been reported from animal samples, such as cattle (for example, Svensson et al, 2007) and salmon (for example, Johnston et al, 2013), and in small-scale studies of plants (for example, Lister et al, 2013). To our knowledge, this is the first report where historical plant samples have been analyzed by large-scale SNP genotyping, with more than one individual per accession and a high number of markers.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…While the degraded nature of historical DNA poses a particular set of challenges and requires stringent data quality control and validation, a number of different methods can be used to obtain reliable high-throughput sequence or genotype data from ancient and historical samples (see Rizzi et al, 2012). We now have the technology to fully sequence the entire genome of samples that are thousands of years old (e.g., Rasmussen et al, 2010;Prüfer et al, 2014), and recent studies with archived fish samples or other museum specimens have generated high-quality data through minor methodological modifications using standard genotyping assays of 100s or 1000s of SNPs (e.g., Johnston et al, 2013;Therkildsen et al, 2013a, b), sequence capture methodology (Bi et al, 2012;Carpenter et al, 2013), or whole-genome sequencing (Rowe et al, 2011;Staats et al, 2013).…”

Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees

“…Although a salmon farm was established near the mouth of the Teno in 1984, regional levels of salmon aquaculture were relatively low in the early 1980s, and the hybrid offspring of early escapes from this farm are not expected to return to the river before 1989 (Erkinaro et al., ). We chose not to use pre‐1982 samples due to the decrease in SNP genotyping quality with sample age when using similar SNP arrays (Johnston et al., ). Individuals were collected from the Teno mainstem ( n = 120, hereafter referred to as ‘Old Teno Mainstem’), the Teno headwaters (Inarijoki, n = 114) and four tributaries: Kevojoki ( n = 114), Pulmankijärvi ( n = 114), Tsarsjoki ( n = 114) and Utsjoki ( n = 120) (Fig.…”