A review of genomic selection - Implications for the South African beef and dairy cattle industries

Abstract

The major advancements in molecular technology over the past decades led to the discovery of DNA-markers, sequencing and genome mapping of farm animal species. New avenues were created for identifying major genes, genetic defects, quantitative trait loci (QTL) and ultimately applying genomic selection (GS) in livestock. The identification of specific regions of interest that affect quantitative traits aimed to incorporate markers linked to QTL into breeding programs by using marker assisted selection (MAS). Most QTL explained only a small proportion of the genetic variation for a trait with limited impact on genetic improvement. Single nucleotide polymorphism (SNP) markers created the possibility to genotype cattle in a single assay with hundreds of thousands of SNPs, providing sufficient genomic information to incorporate into breeding value estimation. Genomic selection is based on the principle of associating many genetic markers with phenotypic performance. A large database of genotyped animals with relevant phenotypes pertinent to a production system is therefore required. South Africa has a long history of animal recording for dairy and beef cattle. The challenge for implementation of GS would be the establishment of breed-specific training populations. Training populations should be genotyped using a high density SNP panel, and the most appropriate genomic prediction algorithm determined. The suitability of commercially available genotyping platforms to South African populations should be established. The aim of this review is to provide an overview of the developments that occurred over the past two decades to lay the foundation for genomic selection with special reference to application in the South African beef and dairy cattle industry.

Keywords: Molecular genetics, DNA-markers, QTL, GWAS, genomic selection