Agrigenomics - Ion AmpliSeq technology: a tool for genetic trait selection

Alex Chubick, GeneSeek - Ion AmpliSeq™ technology is a next-generation sequencing protocol that is capable of processing low concentrations of DNA (≥10 ng) to yield results that have a high coverage uniformity, reproducibility, and specificity. Through the use of Ion AmpliSeq custom panels, GeneSeek—a Neogen Corporation subsidiary—has designed a primer pool that is able to target ~4000 SNP loci which allows certain traits such as tenderness and parentage to be identified in cattle. Within this process, GeneSeek has modified the Ion AmpliSeq protocol in order to sequence at least 192 samples in one run. In order to process such a high volume of samples, GeneSeek has begun to utilize the Tecan Fluent™ in conjunction with the Ion Chef™ and Ion Proton™. In the initial data calculated by the Ion Torrent™ browser, GeneSeek observed that on average there were 80 million reads being generated per run, with each sample generating 400,000 reads. The Ion Torrent browser also provided the mean depth and on-target percentage value for each sample in a run; and GeneSeek calculated that on average, these values are equal to 80% and 94%, respectively. The preliminary data that has been collected by GeneSeek suggests that Ion AmpliSeq technology can be utilized as a vital tool for genetic trait selection in cattle.