The performance of the high-throughput AgriSeq library prep workflow was validated with multiple Ion AmpliSeq panels. 384 barcoded samples were processed with the high-throughput AgriSeq library prep workflow and a standard volume 96-well workflow, and sequenced on the Ion S5 XL System. Equivalent performance was achieved between the two workflows, including genotyping call rate, mean coverage depth, and coverage uniformity. The high-throughput AgriSeq library prep workflow provides a fast and economical alternative to larger-volume, lower-throughput library prep methods, without sacrificing performance.
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. The 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.
The Eureka Genotyping Solution is an affordable, low- to mid-plex, high-throughput genotyping assay that uses common next-generation sequencing (NGS) platforms for signal readout. It enables the detection of tens to thousands of genetic markers which are increasingly in demand for routine crop and animal agrigenomics testing. Eureka NGS read count ratios, similar to microarray intensities, have been shown to be consistent across batches, resulting in repeatable spatial properties of genotype clusters.
Here we describe the development of Ion 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 540 chip. Variant calling was performed using the Torrent Variant Caller (TVC) plugin as part of the 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.
The Eureka Genotyping Solution is a novel technology that has utility in plant breeding and regulatory aspects. It allows for a 2-day turnaround time from sample to genotype calls, for catalog or fully customizable panels of a few hundred and up to 3,000 variants (substitutions or indels). The Eureka genotyping assay is a ligation-dependent polymerase chain reaction made ready for high-throughput sequencing. It consists of probe triplets in solution, where for each variant there are two left-side probes (one for each allele) immediately followed by a third, right-side probe. The probes are hybridized to target the input DNA, and a ligation step locks the correctly hybridized left and right probes.
The Eureka Ovine Parentage Panel is a comprehensive parentage panel for sheep with superior power to accurately verify parentage. It provides an affordable next-generation sequencing (NGS)–based panel for both parentage testing and traceability in diverse sheep breeds. The availability of over 3,000 barcodes enables processing of over 3,000 samples in a single sequencing run for fast turnaround time. As a result, this genotyping panel may be used as a tool in an ovine breeding and production system that has the potential to increase overall revenue.