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Influence of population structure on the compilation of the Bonsmara genomic reference population

  • L. Bosman (a1), R. R. van der Westhuizen (a1), C. Visser (a1) and E. van Marle-Köster (a1)


The most popular beef breed in South Africa is the Bonsmara, a locally developed composite breed adapted to sub-tropical conditions. The establishment of a genomic reference population is currently ongoing for the application of genomic selection. To date, 583 Bonsmara cattle (388 bulls and 195 cows) have been genotyped with the GeneSeek® Genomic Profiler Bovine HD™ Chip (GGP-HD) 80 K chip, and the population structure of the reference population was studied. The average minor allele frequency for the Bonsmara was 0.280 across 56 248 autosomal single-nucleotide polymorphisms (SNPs), whereas the observed and expected heterozygosity values were 0.361 and 0.365, respectively. After pruning the data set for SNPs in linkage disequilibrium, 19 119 SNPs were retained, averaging 659 SNPs per autosomal chromosome. This generated an average SNP density of 1 SNP per 90 kb. Structure analysis revealed a non-homogenous population with a high level of genetic admixture, which may negatively influence genomic breeding value prediction accuracy. Genotyping of a further 990 Bonsmara cattle are pending, using the GeneSeek® GGP-HD 150 K chip. As more animals will be added to the reference population, the profile of the reference population are expected to change in such a way to ensure improved genomic estimated breeding value accuracies.


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Advances in Animal Biosciences
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