Genotypying by Sequencing through Ion AmpliSeq Technology: A Tool For Genetic Trait Selection

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 has designed a primer pool that is able to target ~4000 SNP loci which allow 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 Proton™. In the initial data calculated by the Torrent™ Browser GeneSeek observed that on average there were 80 million reads being generated per run with each sample generating 400,000 reads. The 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 suggest that Ion AmpliSeq™ technology can be utilized as a vital tool for genetic trait selection in cattle.