World Congress on Genetics Applied to Livestock Production

Whatever the technology and whatever the business, a good return on investment is fundamental to market adoption. Return on investment is a function of profit accruing from the investment as well as the cost of investment; in agri-genomics, the latter is dictated by the cost of procuring the genotypes while the former is dictated by the information content and usefulness of the genotypes. Carefully selected genotype panels, as well as providing sufficient information for use in genomic evaluations, can also provide information for accurate parentage assignment, estimation of inter-animal coancestry (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 is 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. This newly developed panel consists of 51,575 unique SNPs, which are strongly segregated in a range of different breeds; for example, the within-breed minor allele frequency varies from 0.24 to 0.26 for Texel, Suffolk, Vendeen, Belclare, and Charollais , based on 1111 genotyped individuals. As well as including information on segregating SNPs for accurate imputation to higher density, the genotype panel also includes causal mutations within the PrP (i.e., high-quality genotypes from the five informative scrapie single nucleotide polymorphisms) gene as well as those affecting fecundity and other performance traits. The panel also includes parentage SNPs used globally and can be used for the detection of aneuploidy.

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 resulting in an accelerated 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 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 been able to use 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.

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.