Ion AmpliSeq Targeted Sequencing Panel for Determination of Canine and Feline Parentage

DNA based tests are commonly used to determine animal pedigrees. Ensuring an accurate pedigree is particularly important for purebreds, having both economic and animal health implications. Historically, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent years, single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. Genotyping-by-Sequencing (GBS) using the Applied Biosystems AgriSeq™ target enrichment technology in combination with the Ion S5™ sequencing system allows one to simultaneously and accurately interrogate a large number of genetic loci (SNPs/Idels) to identify the heritage of an animal, as well as screen for known genetic defects. In addition to the ability to screen for both animal heritage and disease-related genetic defects, advantages of this GBS approach include increased accuracy and improved assay flexibility (i.e. the ability to easily add or remove genetic loci being interrogated) which is desirable to both animal owners and breeders.

Here we describe the development of AmpliSeq™ panels targeting canine and feline SNP markers for the purpose of determining parentage and genetic health. We tested these panels on samples derived from buccal swabs by sequencing them as a multiplexed (barcoded) pool on an Ion S5 540 chip. Variant calling was performed using the Torrent Variant Caller (TVC) plugin as part of the Ion Torrent Suite™ software package. The mean call rate for this dataset indicated that the majority of SNPs were of sufficient quality to make a genotype call.