311 Genomic Selection: Historical perspective and development of methods in use today.

Abstract

Genomic selection (GS) is a reality for the majority of livestock species and has continued to evolve for close to a decade. Methods used to implement GS have changed substantially such that the majority of breeding companies/associations have migrated from ‘two-step’ to ‘single-step’ methods of incorporating genomic data into routine genetic evaluations. As implemented, one such approach utilizes variable selection to only fit more informative SNP while the other does not. Regardless, the elimination of ‘two-step’ methods based on ‘blending’ or a ‘correlated trait’ approach represents one of the largest evolutions in genetic evaluation systems. This change was necessitated by several factors, including: 1) inflation of genotyped animals EBV, and 2) the need to continually re-estimate marker effects and corresponding genetic parameters to properly blend. Given the increasing trend in the number of animals genotyped within some breeds/companies, various strategies have been proposed and employed such as the algorithm for proven and young animals and data (pedigree, phenotype, and genotype) truncation; both seeking to reduce the complexity of a growing genomic relationship matrix. On the other end of the spectrum, in some species/breeds, more genotyped females are required and in many cases additional phenotypes (e.g., carcass, health, fertility, etc.) are needed to fully exploit GS. Although progress is being made in terms of describing additive genetic merit for routinely collected phenotypes, additional information can be garnered from the growing wealth of genotypes. Potential additional uses of the large numbers of genotyped animals include, but are not limited to: Identification of lethal and sub-lethal haplotypes, tracking inbreeding more precisely, estimating retained heterozygosity, and creating planned matings at the commercial level. Strategic data collection (genotyping, sequencing, and phenotyping) at all levels of the breeding pyramid will be required to fully capture the benefits of GS in an economical framework.