A Comparative Evaluation of SNP Genotyping Assay Chemistries in Atlantic Salmon

Single nucleotide polymorphisms (SNP) represent the most wide spread variation in organisms genome. With automated data analysis options SNP are a popular marker choice in a range of applications and are being widely used in MAS, GWAS and genetic profiling. IdentiSNP is a novel end-point assay chemistry that provides both a cost and time effective way of genotyping SNP variation. The IdentiSNP assay contains DNA polymerase, universal labelled probes, ROX reference dye, nucleotides and optimised buffer; allele specific oligos and template DNA are added to complete the genotyping reaction. Here we compare the performance of IdentiSNP with an establised universal SNP genotyping assay chemistry using the Douglas Scientific Array Tape^TM genotyping platform.

The dataset used in this evaluation comprises Atlantic salmon (Salmo salar) fin clips sampled for parentage analysis. DNA was extracted using a proteinase K buffer and magnetic bead based method. Dried DNA was set up for genotyping with both IdentiSNP and an alternative SNP genotyping assay chemistry according to the manufacturer’s protocol. IdentiSNP produced equivalent genotyping data with a concordance level of >99% between chemistries. Parentage assignments in both analyses were identical and consistent with the known pedigrees. IdentiSNP is amenable to a single end-point read, whereas in our experience, the alternative method requires successive rounds of re-cycling and re-reading to establish the optimal data collection cycle number.  IdentiSNP delivers dramatic savings in data scoring time (>60%) and also reduces handling time in the laboratory.