Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle

Abstract

The South African beef cattle population is heterogeneous and consists of a variety of breeds, production systems and breeding goals. Indigenous cattle breeds are uniquely adapted to their native surroundings, necessitating conservation of these breeds as usable genetic resources to sustain efficient production of beef. Current projections indicate positive growth in human population size, with parallel growth in nutritional demand, in the midst of intensifying environmental conditions. Sanga cattle, therefore, are invaluable assets to the South African beef industry. Modern genomic methodologies allow for an extensive insight into the genome architecture of local breeds. The evolution of these methodologies has also provided opportunities to incorporate deoxyribonucleic acid (DNA) information into breed improvement programs in the form of genomic selection (GS). Certain challenges, such as the high cost of generating adequate numbers of dense genotypic profiles and the introduction of ascertainment bias when non-commercial breeds are genotyped with commercial single nucleotide polymorphism (SNP) panels, have caused a lag in progress on the genomics front in South Africa. Genotype imputation is a statistical method that infers unavailable or missing genotypic data based on shared haplotypes within a population using a population or breed representative reference sample. Genotypes are generated in silico, providing an animal with genotypic information for SNP markers that were not genotyped, based on predictive model-based algorithms. The validation of this method for indigenous breeds will enable the development of cost-effective low-density bead chips, allowing more animals to be genotyped, and imputation to high-density information. The improvement in SNP densities, at lower cost, will allow enhanced power in genome-wide association studies (GWAS) and genomic estimated breeding value (GEBV)-based selection for these breeds. To fully reap the benefits of this methodology, however, will require the setting up of accurate and reliable frameworks that are optimized for its application in Sanga breeds. This review paper aims, first, to identify the challenges that have been impeding genomic applications for Sanga cattle and second, to outline the advantages that a method such as genotype imputation might provide.