Ion Ampliseq Targeted Sequencing Panel for Determination of Bovine Parentage

Historically, microsatellites have been the most popular genetic feature for distinguishing cattle breeds for the purpose of determining parentage. More recently, SNP genotyping has emerged as a desirable alternative to microsatellite typing. SNPs offer several advantages over microsatellites. Perhaps the most important advantage is that there is less ambiguity in distinguishing SNP alleles in order to confidently provide a genotype call.

Ion AmpliSeq™ is a sequencing technology that can be used for targeted amplification and re-sequencing of thousands of SNP targets in a single reaction. The Ion 540™ chip allows hundreds of samples to be genotyped at thousands of loci simultaneously. Ligating a unique barcode to each sample allows samples to be sequenced together in a single run on the Ion S5™ sequencing system.

We have developed a targeted sequencing panel based on 200 bovine SNP markers selected by the International Society of Animal Genetics (ISAG) for the purpose of determining parentage. We tested this panel on 96 bovine samples obtained from the USDA representing 19 different breeds. Each sample was tested in duplicate such that 192 libraries were pooled onto a single Ion 540 chip for sequencing. Variant calling was performed using the Torrent Variant Caller (TVC) plugin as part of the Torrent Suite™ software package. Mean call rate for this dataset was 98.5%, indicating that the vast majority of SNPs yielded data of sufficient quality to make a genotype call.