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Genomics for the SA beef industry

Genomics for the South African beef industry

Establishing genomic selection for the South African beef industry

Industry Sector: Cattle and Small Stock

Research focus area: Livestock production with global competitiveness

Research Institute: Department of Animal and Wildlife Science, University of Pretoria and SA Studbook Association

Researcher: Prof E. van Marle-Koster PhD

Research Dr J. van der Westhuizen PhD, Dr C. Visser PhD, Dr R.R. van der Westhuizen PhD, Dr H. Theron PhD

Final report approved: 16 February 2016

Aims of the project

  • To establish a reference population for SA beef cattle industry
  • To apply genomic data for genetic diversity, Linkage Disequilibrium, inbreeding and population structure
  • To apply genomic data in estimation of GEBV

Executive Summary

The project titled “Establishing genomic selection for the South African beef industry” was conducted at the University of Pretoria, Department of Animal & Wildlife Sciences in collaboration with South African Stud Book and Animal Improvement Association. 

The overall aim was to use high throughput SNP technology to establish reference populations for the SA beef industry. To attain this goal, a process for the identification of high impact animals was established, guidelines for sample collection were compiled and genotyping were performed with the available funding using both 80K SNP and 150K SNP GeneSeek (GeneSeek GGP HD) bead chips at GeneSeek (USA. Population structure analyses were performed and parameters for genetic diversity and inbreeding were calculated. 

Results has shown that breeds such as the Bonsmara and SA Hereford formed separate clusters while the other indigenous breeds such as the Tuli, Afrikaner and Drakensberger showed a closer relationship. These results are important for future across-breed analyses. The commercial chips also tended to be less informative for the indigenous breeds with regard to the number of SNPs available for analyses, but still had sufficient numbers for application in genomic selection. A substantial number of genotypes have been generated for Bonsmara cattle that have also been phenotypically recorded for the traits of interest. 

In this project, the Bonsmara genotypes are currently being applied as a training set for estimation of Genomic Breeding Values (GEBV’s). After GEBVs have been estimated for these animals, validation will commence followed by the roll-out of routine GEBV estimation. This genomic information will provide breeders with an additional, accurate tool for selection of superior stock.

Additional comments: The RMRDSA funds provided the opportunity for genomic analyses in SA beef cattle. Funds contributed to generation of genotypes for population analyses, structuring reference populations and specific genomic selection in the Bonsmara cattle breed.

Please contact the Primary Researcher if you need a copy of the comprehensive report of this project –
Este van Marle-Köster on