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Low-cost and high-information content—the crux to achieving high penetrance of genomic technologies in the sheep sector

Donagh Berry, Quantitative genetics research officer, Teagasc

Axiom genotype panel was developed to provide high-quality genotype calls, at a low cost, to facilitate the generation of considerable information for use by sheep producers and the sheep sector as a whole.

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Customizing genomic profiles for dairy and beef cattle using targeted GBS

Aaron Larsen, Chief Science Officer, United Bio Research, Inc.

The targeted genotyping-by-sequencing (GBS) approach using the AgriSeq workflow streamlines the process of developing custom assays and provides the flexibility to quickly modify or combine existing assays.

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Salmon breeding transformed: Marine Harvest enters the genomic era with Axiom genotyping technology

Matt Baranski, Genetics Manager, Marine Harvest Norway

Marine Harvest’s selective breeding program transitioned to a full implementation of genomics using Axiom genotyping technology. Over 60,000 samples were genotyped.

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Advancing vegetable breeding with AgriSeq targeted genotyping by sequencing

Hans Peter Koelewijn, Scientist, Genetics, BAYER Vegetable Seeds

Bayer Vegetable Seeds identified a need for a platform that would result in greater throughput, higher marker density, and a fast turnaround time to advance their breeding program.

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Determination of purity and quantification of varietal components through AgriSeq targeted GBS

Dr. Carlos Azambuja, Director, GENIA

The barley industry requires strict control of varieties; Genia was asked to develop a method to enable the determination of varietal purity as well as to identify and quantify the components of varietal mixtures.

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Diverse applications of Applied Biosystems Axiom Genotyping Arrays in plant and animal breeding and research

Ali Pirani, Manager, Bioinformatics, Microarray, Thermo Fisher Scientific

The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. An apt high-throughput genotyping platform can enable marker-assisted breeding, association mapping, and genomic selection.

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Investigating the genetics of mixed breed dogs with the new Axiom array

Elinor K. Karlsson, PhD, Assistant Professor, Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Director of Vertebrate Genomics, Broad Institute of Harvard and MIT

Most dogs throughout the world are mixed-breed dogs, yet past genetic studies in dogs have focused on purebreds. In part, this reflected technological limitations, as the genotyping panels available were designed for purebred dog populations.

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Ovine genotyping by numbers

Donagh Berry, Principal Investigator in Quantitative Genetics, Teagasc

Sheep, because of their relatively low unit value and lack of widespread use of artificial insemination and single-sire mating, differ from many other farmed species in their requirements for low-cost genomic technologies.

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Implementation of an AgriSeq genotyping workflow in a service lab

Maarten de Groot, Chief Financial Officer, VHLGenetics

Recent advances in targeted next-generation sequencing technologies are creating new opportunities for service labs to expand the breadth of variants evaluated in a single, low-cost test.

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Yield testing in the lab

Tom Osborn, Director of Molecular Breeding Technology, Monsanto

Genotyping at Monsanto has been transformed through a series of technology innovations to the current state of automated workflows that deliver high-volume genetic data for key decisions in product advancement. Some recent innovations utilizing genome-wide selection and data from genotyping by sequencing have led to our ability to conduct yield testing in the lab. The success of this new workflow is dependent on collaborations with internal and external technology partners to deliver scalable, low-cost, and rapid lab processes.

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Thermo Fisher Scientific and Informa: agribusiness insights and outlook

Tom Scott, CEO, Informa Agribusiness Intelligence IEG

The world’s agriculture market is dynamic and subject to constant change. Investments in agricultural technologies and innovations are driven by the underlying economics of commodities and the markets they support. This session will provide both short- and long-term perspectives on the impact of mega-trends, trade, industry consolidation, and other market drivers on innovation and technology in agriculture. 

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Enabling more accurate animal parentage and genetic testing through targeted GBS and CE approaches

Wim van Haeringen, PhD, CEO, VHLGenetics

As a pioneer with a successful history of applying molecular technologies to animal genotyping, VHLGenetics is again leading the way with the application of genotyping by sequencing (GBS). VHL will present the output of a collaborative effort with Thermo Fisher Scientific on feline, canine, and bovine GBS panels for detecting genetic variants and conducting parentage testing.

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50K Axiom SNP microarray allows high-quality genotyping of coffee, cashew, cassava, Brazilian pine, and eucalyptus

Dr. Dario Grattapaglia, Senior Research Scientist and Project Leader, Brazilian Agricultural Research Corporation (Embrapa)

The identification of new sources of genetic variation is a key component of any long-term breeding strategy to increase the productivity, resilience, and sustainability of crop varieties. Over six million crop accessions are currently being conserved worldwide in still largely untapped gene banks. High-throughput, low-cost, and robust SNP genotyping technologies are necessary to unlock this wealth of diversity and release the data in an organized and user-friendly fashion to allow adoption by germplasm curators and breeders.

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Applications of Axiom microbiome arrays in food safety

Emily Rose, Sequencing Lab Supervisor, GeneSeek-Neogen

Bacterial classifications and phylogenetic studies have been largely improved by the targeted amplicon sequencing of the hypervariable regions within the 16S rRNA gene, which is represented in all bacteria. However, limiting the classification investigation to 16S sequencing can still lead to difficulty in discerning closely related organisms down to the species level. To aid in the pursuit of accurately identifying bacterial species and serotypes (strains), Thermo Fisher Scientific has recently created the Applied Biosystems Axiom Microbiome Array as an effective assay to distinguish thousands of microorganisms at the species and even serotype level.

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Parentage-based tagging for Pacific salmon

We have assembled a panel of primers for coho salmon that produces 360 amplicons containing approximately 440 single nucleotide polymorphisms (SNPs), with all sequences amplified via a single polymerase chain reaction. Application of the panel to coho salmon from hatchery populations in southern British Columbia (BC) has indicated substantial differentiation among populations, as well as differentiation among brood years and individuals within hatcheries.

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Novel workflow for SNP genotyping in sugar beet

Sugar beet is one of the world’s most important crops, currently supplying around 20% of the sugar consumed worldwide. The development of varieties that require less technical inputs for cultivation is one of the main research goals in sugar beet. To achieve this, sugar beet breeding is focusing on genetic improvement programs assisted by SNP (single nucleotide polymorphisms) molecular markers.

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Applied innovation for the agriculture and food system

A number of global dynamics are changing the agriculture and food ecosystem. The simplicity, accessibility, and ease of use of molecular technologies and next-generation sequencing are reshaping the animal and plant breeding sciences. Thermo Fisher Scientific products and services offer high quality, innovative life science solutions for every plant and animal research or breeding lab.

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Ion AmpliSeq technology: a tool for genetic trait selection

Through the use of Ion AmpliSeq™ custom panels, GeneSeek—a Neogen Corporation subsidiary—has designed a primer pool that is able to target ~4,000 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.

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Targeted resequencing in maize using Ion AmpliSeq technology

Genotyping by sequencing (GBS) is a cost-effective alternative for obtaining a large number of markers across a large sample size, but markers are randomly distributed throughout the genome. Alternately, enrichment coupled with next-generation sequencing is a cost-effective strategy for obtaining sequence information for loci of interest across a large sample.

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