The use of single nucleotide polymorphism (SNP) genotyping with non-model organisms—those whose genomes are yet to be sequenced—has increased in importance as it provides robust, comparative data sets that can be easily shared across organism communities for a variety of purposes. Non-model organisms have the added burden of low available genomic sequence information requiring custom SNP assay development. Until recently, SNP genotyping technologies have been prohibitive to these communities due to the high cost of developing and running quality SNP genotyping panels. Standard BioTools SNPtype Assays and the X9 Real-Time PCR System have addressed these barriers with a custom assay design service, cost-effective and high quality SNP assays, and a high-throughput workflow minimizing hands-on time. The salmon research community has been specifically hampered by the cost barriers, and would benefit from the technology for conservation and management purposes. Using chum salmon (Oncorhynchus keta) as an example, we describe a simple workflow using Standard BioTools SNPtype Assays, the X9 System, and 96.96 Dynamic Array™ Integrated Fluidic Circuits (IFCs) for Genotyping to achieve cost-effective and rapid development of a SNP genotyping panel. Moreover, SNPtype Assays provide significant cost savings for high-throughput, routine testing post panel development.
SNPtype Assays and the X9 System provided a rapid and cost-effective way to develop and implement a SNP genotyping panel. For the chum salmon panel development, a candidate list of 143 SNPs was selected based on their ability to provide population structure and harvest composition information within the chum species of salmon. The sequences around these SNPs were submitted to the Standard BioTools Assay Design Group for design and manufacture of allele-specific PCR primers. TaqMan® assays were also ordered for the same SNPs for comparison. Assays were run with 95 samples from three different locations in Washington State (Hamma Hamma River – 24, Kalama River – 24, Skookum River – 23), and one from British Columbia (Squakum Creek – 24). The Standard BioTools SNP Genotyping User Guide (PN 68000098) was followed, including specific target amplification (STA), or preamplification.
SNPtype Assays greatly reduced routine running costs of SNP genotyping panels for non-model organisms that previously were inhibited by the high cost of TaqMan assays.
Recent developments in DNA sequencing technology greatly increased the numbers of SNPs available for non-model organisms. More SNPs can be tested using SNPtype Assays due to significant cost savings over TaqMan assays and researchers now have the option to develop multiple sets of high-quality 96 SNP panels for increased discrimination power. Additionally, Standard BioTools X9 System provided a rapid, high-throughput, low hands-on workflow that accelerated the panel development process and routine run time.