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Development and characterization of a high-throughput targeted genotyping-by-sequencing solution for agricultural genetic applications

Genotyping by sequencing (GBS) is emerging as a powerful and cost-effective method for discovery and genotyping SNPs in agricultural species. Targeted GBS provides a lower-cost alternative to microarrays when analyzing 5000 variants or less, and can dramatically increase sample throughput up to thousands of samples per day.

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Using 500+-plex Eureka Genotyping to understand migration and harvest of subpopulations of residual tetrasomic chum salmon

Using a low density genotyping panel for surveillance is critical to the management of coastal fishery populations. The amount of genetic information required depends on the application and can range from a few hundred markers to full genome sequence for more complicated questions.

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Development of targeted GBS panels for breeding and parentage applications in cattle and swine

Parentage testing and genomics-assisted breeding are critical aspects of successful herd management. Due to its highly accurate and reproducible results, targeted GBS is becoming an increasingly favored technology for SNP genotyping.

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Evolving next-generation sequencing for production agriculture: increasing throughput, decreasing effort, and delivering more

The utility of restriction-enzyme genotyping by sequencing (GBS) in production agriculture is challenged because of the technology’s limitations in SNP targeting and high rates of allele dropout between samples. In contrast, targeted genotyping by sequencing (GBS) can deliver consistent, high marker call rates for specified SNPs in a high-throughput, cost-effective manner

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Targeted Next-Generation Sequencing Approaches in Corn, Cucumber, and Soy for High-Throughput Genotyping

With advances in plant phenotyping approaches for quantitative genetic analysis and increasing complexity of gene pyramiding schemes, the number of markers required for successful molecular breeding programs in agriculture is increasing. Historically, technology has been polarized between high-marker, high-cost microarrays or low-cost singleplex approaches that are not easily scalable.

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Same day, low marker density, high-throughput genotyping

Genetic gain effectively relates four core factors that influence breeding progress: the degree of phenotypic variation present in a population, the probability that a trait will be transmitted from parent to offspring, the proportion of the population selected as parents for the next generation, and the length of time necessary to complete a cycle of selection. The length of time is not only how many generations are required to complete a selection cycle, but also how quickly the generations can be completed.

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Implementation of a high-throughput AgriSeq workflow for GBS

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.

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Ion AmpliSeq targeted sequencing panel for determination of bovine parentage

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.

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Accurate genotypes on the Eureka Genotyping Solution with Bayesian clustering

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.

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Ion AmpliSeq targeted sequencing panel for determination of canine and feline parentage

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.

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Accelerating genetic improvement in sheep by increased pedigree accuracy

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.

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