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

Published online by Cambridge University Press:  03 October 2017

L. Bosman ,
R. R. van der Westhuizen ,
C. Visser  and
E. van Marle-Köster
L. Bosman
Affiliation:
Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
R. R. van der Westhuizen
Affiliation:
Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
C. Visser
Affiliation:
Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
E. van Marle-Köster*
Affiliation:
Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
*
†E-mail: evm.koster@up.ac.za
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Abstract

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.

Keywords

admixturecattleselectionSNP
Type
Full Paper
Information
Advances in Animal Biosciences , Volume 8 , Supplement s1: Improving the quality and sustainability of beef production , October 2017 , pp. s45 - s47
Copyright
© The Animal Consortium 2017 

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