Abstract
The BovineSNP50 genotyping array is a product with a wide range of applications in cattle such as genome-wide association studies, identification of copy number variation and investigation of genetic relationships among cattle breeds. It also holds potential for genomic selection, especially for traits that are expensive and difficult to measure. The successfulness of this chip for any of these applications depends on the degree of polymorphisms in the cattle breeds. The SNP50 array has not been validated in any South African cattle population and this could lead to overestimating the number of polymorphic SNPs available for application in it. This study is a first attempt to evaluate the Bovine64SNP50 genotyping array in the South African cattle population. Ninety six bovine samples, consisting of 45 Holstein, 29 Nguni, 12 Angus and 10 Nguni x Angus crossbred animals, were genotyped with the BovineSNP50 infinium assay. The results of this study demonstrated that 40 555 SNPs were polymorphic (MAF >0.05) in these breeds and indicate potential for application in South African cattle populations. Genomic information generated from the BovineSNP50 can now be applied in genetic prediction, genetic characterization and genome-wide association studies.Keywords: Call rate, minor allele frequency
Highlights
No local or indigenous South African cattle breeds have been included in either the production or the validation of the BovineSNP50 array
Genotyping was conducted at the ARC-Biotechnology Platform with the Illumina BovineSNP50 BeadChip v2 which features 54 609 SNP probes distributed across the whole bovine genome with an average spacing of 49.9 kb (Matukumalli et al, 2009)
Five Holstein samples were removed because they had more than 10% missing genotype; these samples were part of the eleven samples with less than 1.8 260 : 280 ratio. Their 260 : 280 ratio ranged from 1.62 to 1.69, it was concluded that these failed to genotype owing to sample contamination; 77, 256 and 139 SNPs were removed in the Nguni, Angus and Holstein breeds, respectively, for violating HardyWeinberg Equilibrium (HWE) (P
Summary
No local or indigenous South African cattle breeds have been included in either the production or the validation of the BovineSNP50 array. The aim of the study was to determine the level of polymorphism and allele frequency distribution of the BovineSNP50 in South African populations of Nguni, Angus and Holstein cattle.
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