Welcome and Introduction

Ravi Ramadhar

Agrigenomics Product Management Leader

Thermo Fisher Scientific 

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

Carefully selected genotype panels, as well as providing sufficient information for use in genomic evaluations, can provide information for accurate parentage assignment, estimation of inter-animal co-ancestry (and its use in subsequent mating advice), monitoring of variants conferring major effects or congenital effects, and karyotyping. Consistency in genotype calls and file formats across panel vendors and genotyping service providers are vital in achieving low cost genotyping through intense competition.

Analysis of single nucleotide polymorphism (SNP) data from 84 animals genotyped on both Axiom and Illumina platforms revealed excellent concordance, especially if limited to high quality SNPs; the genotype concordance between vendors for the high quality SNPs was 99.5%. These results therefore imply that the platform is irrelevant when it comes to merging of genotypes; genotype results from Axiom can be outputted in several different formats, including that used by Illumina. Subsequently an 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.

Customizing Genomic Profiles for Dairy and Beef Cattle Using Targeted GBS

Aaron Larsen, PhD

Chief Science Officer

United Bio Research, Inc.

Utilizing genomic information to increase profitability and improve production in livestock has become an essential component of modern breeding strategies. With rapidly changing genomic technology accelerating the rate of discovery of new genetic markers, it is important that genetic laboratories adapt quickly and provide cost-effective solutions for producers to take advantage of this information. The targeted genotyping-by-sequencing (GBS) approach using the Applied Biosystems AgriSeq workflow streamlines the process of developing custom assays and provides the flexibility to quickly modify or combine existing assays.

Here, we present an example of using the AgriSeq workflow to develop genetic assays for both beef and dairy cattle. We’ve combined hundreds of genetic markers associated with production traits, genetic mutations associated with disease, and a parentage panel based on the 200 ISAG Bovine SNPs into a single test. In addition, we’ve used this technology to simultaneously detect larger genomic variations, including Y-chromosome detection used for gender identification and the presence of large duplications that cannot be detected by a single variant.

Salmon Breeding Transformed: Marine Harvest Enters the Genomic Era with Axiom Genotyping Technology

Matt Baranski, PhD

Genetics Manager

Marine Harvest Norway

Marine Harvest ASA is one of the largest seafood companies in the world and the world’s largest producer of Atlantic salmon. In 2017, Marine Harvest’s selective breeding program transitioned to a full implementation of genomics using Axiom genotyping technology. Over 60,000 samples were genotyped, and through a combination of genome-wide association studies and genomic selection, the breeding program has dramatically increased the accuracy of selection for traits including growth rate, disease resistance and product quality. Efficient pipelines have been established for logistics, data handling and analysis, and the breeding program now represents one of the most advanced for any aquaculture species.