PCR-Based SNP Genotyping Assay Development for Plant and Animal Genomic Research

The importance and usefulness of Single Nucleotide Polymorphisms (SNPs) are increasingly apparent.  SNPs are valuable tools for many aspects of plant and animal genetic research, ranging from marker assisted selection to trait associations and disease prediction.  With this increase in knowledge and use of SNPs comes the need for economical and reliable methods of SNP genotyping for a wide variety of laboratory settings.

Endpoint PCR-based SNP genotyping assays fill this need because of their simplicity, accuracy, and ease of use.  Additionally, these assays are compatible with standard laboratory equipment such as real-time PCR instruments.  For laboratories with high throughput needs PCR-based SNP assays can be automated and miniaturized using the Array Tape Platform from Douglas Scientific.  Regardless of a laboratory’s throughput, SNP genotyping assays can be used as effective tools in genetic research.

Here we will discuss methods for developing, optimizing, and miniaturizing PCR-based SNP genotyping assays for plant and animal genomic DNA samples for low and high throughput laboratories.  We will examine the impact of reaction volume, sample preparation method, master mix choice, and primer/probe design on the accuracy and scorability of SNP genotyping results.