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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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Complete Workflow Solutions for High-and Low-Density Canine Genotyping from Thermo Fisher Scientific

Genotyping applications can be varied based on customer needs and requirements. High to low density genomic testing can be useful, whether it is for a veterinary disease research company or a canine breeding program. Applied Biosystems Axiom Canine HD Array, a high-density genotyping platform, is useful for genome wide association studies and marker assisted selection for traits and diseases. Applied Biosystems AgriSeq targeted GBS platform, a low density targeted GBS method which allows for marker assisted selection for traits and diseases, identification of novel mutations, parentage verification and identification of individuals based on genotypes. Having one complete workflow solution from sample prep to genotyping for both platforms allows for more convenience and versatility.

Balancing Mitochondrial and Genomics Sequencing Coverage in Targeted GBS Applications

Mitochondrial SNPs are frequently used in targeted genotyping-by-sequencing (GBS) for the identification of individuals in forensic applications. However, having hundreds of copies of mitochondrial DNA (mtDNA) per cell as compared to only two copies of genomic DNA (gDNA) poses a challenge in next generation sequencing. The relatively high abundance of mtDNA can lead to over-representation during sequencing and poor coverage of gDNA targets. We have developed a strategy for combining mtDNA and gDNA targets in the same SNP panel while maintaining good coverage balance across all amplicons.

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.

Development of AgriSeqT targeted GBS panels for breeding and parentage applications in cats

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

Development of AgriSeq targeted GBS panels for breeding and parentage applications in dogs

Parentage testing and genomics-assisted breeding are critical aspects of successful veterinary management. Due to its highly accurate and reproducible results, targeted GBS is becoming an increasingly favored technology for SNP genotyping. With the utilization of next generation sequencing, labs can test hundreds of samples across thousands of SNPs simultaneously in a simple high throughput workflow starting from either extracted nucleic acid or crude lysis samples.

End-To-End AgriSeq Targeted GBS Long Indel Solution

AgriSeq targeted genotyping-by-sequencing (GBS) is successfully being used as a high throughput, customizable and cost effective genotyping solution in animal and plant breeding studies, parentage testing and genetic purity. One of the powers of this technology is its capability to support different types of markers including single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs), insertions and deletions (InDels), and other structural variants (e.g. inversions, duplications).

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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Versatile, Robust, Low Cost Genomic DNA Extraction Solution for Use Across Multiple Sample Types and Downstream Genomic Platforms

Here, we examine DNA isolated from bovine blood, blood cards, raw and extended semen, ear notch, and hair follicles isolated using the MagMAX CORE AgGenomic DNA Extraction Kit compared to a more expensive on market magnetic bead-based isolation kit. For down stream applications we tested capillary electrophoresis on an ABI 3500 Genetic Analyzer, Applied Biosystems Axiom Genotyping Arrays, and targeted GBS with AgriSeq HTS Library kits on an Ion GeneStudio 5S. The data shows the MagMAX CORE AgGenomic DNA Extraction Kit was able to extract DNA from all samples types tested and is compatible with all the genetic platforms tested.

Ultra High Throughput, High Quality Genotypes using the Applied Biosystems™ Eureka Genotyping Platform

The Applied Biosystems Eureka Genotyping Solution is a low cost, ultra-high throughput (20k samples/week) targeted genotyping by sequencing platform that supports the detection of tens to thousands of genetic markers (SNPs and insertions/deletions). It has been successfully used for a variety of applications (parentage, sex validation, genomic and trait evaluations) both in crops and animals.

Detection of genome-wide copy number variation using the Applied Biosystems™ Axiom™ Genotyping Solution

Copy number variations (CNVs) have been implicated in both disease phenotypes and phenotypic variation associated with quantitative traits in plant and animal species. Software tools available from Thermo Fisher Scientific offer a valuable resource for evaluation of the impact of CNVs with respect to variation in plant and animal health and production traits. Applied Biosystems Axiom Analysis Suite Software now has enhanced CNV capabilities that utilize intensity and genotypes to calculate log2 ratios and B-allele frequencies (BAFs) from genotyping data for detailed analysis and visualization.

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.

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.

Next-generation 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.

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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High Throughput Agrigenomic SNP Genotyping using the Applied Biosystems™ Axiom™ Genotyping Solution

High density DNA microarrays play an important role in agrigenomic research as climate change, population growth, and urbanization threaten the ability of farmers to meet the world’s food demands. Microarrays enable accurate, cost-effective genotyping of variants that include single nucleotide, insertion/deletion and multiallelic polymorphisms. Applications include genomic selection, marker-assisted selection (MAS) and marker-assisted breeding (MAB), parentage and characterization of genetically modified organisms (GMOs).

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A flexible automation solution for genotyping by sequencing in plant breeding to maximize sample throughput

Marker assisted breeding using targeted genotyping by sequencing (GBS) is gaining traction as an effective tool for advanced breeding. We have developed and validated a 1,536-barcode set for multiplexed sequencing using AgriSeq targeted GBS technology. While 1,536 barcodes provide a tremendous potential sample throughput, the logistics of handling four 384-well plates of barcoded samples can be arduous and time consuming to perform manually. The use of a traditional liquid handler can reduce hands-on-time, however, the number of tips required for processing large numbers of samples can be negatively impactful, both economically and environmentally. To mitigate this impact, we have incorporated a MANTIS liquid handler from Formulatrix into the AgriSeq workflow.

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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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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.

For Veterinary Use Only. For In Vitro Use Only. Regulatory requirements vary by country; products may not be available in your geographic area.