Genotyping Nguni Cattle Across South Africa

Blood samples were collected in 10 ml EDTA VACUETTE® tubes by means of venal puncture of the caudal vein from 492 Nguni animals distibuted across South Africa (Fig. 7). Genomic DNA was extracted by means of the Qiagen DNeasy Blood and Tissue Kit from the blood samples. The quantity and quality of extracted DNA was assessed by means of the Qubit and those samples exhibiting a minimum concentration of 50 μl were subsequently genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) containing 54,001 highly informative markers that uniformly span the bovine genome. Illumina BovineSNP50 BeadChip SNP markers were designed based on the Btau 4.0 reference genome. Markers were clustered and genotyped by means of Illumina GenomeStudio v2.0 software. Fifty four of the genotyped samples were derived from a previous study [7 (link)] and were approved for this research by the University of Pretoria Ethical Committee (E087-12).Fig. 7

Geographic origin of the 492 Nguni cattle sampled in the current study

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Wang M.D., Dzama K., Hefer C.A, & Muchadeyi F.C. (2015). Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics, 16, 894.

Publication 2015

DNeasy Blood and Tissue Kit Illumina BovineSNP50 BeadChip GenomeStudio v2.0 software

Animals Blood Cattle Edta Genome Tissue Vein puncture Venal

Corresponding Organization :

Other organizations : Stellenbosch University, Onderstepoort Veterinary Institute

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Variable analysis

independent variables

Geographic origin of the 492 Nguni cattle

dependent variables

Genomic DNA extracted from the blood samples
Quantity and quality of extracted DNA assessed by Qubit
Genotyping of samples exhibiting a minimum concentration of 50 μl using the Illumina BovineSNP50 BeadChip

control variables

Blood samples collected in 10 ml EDTA VACUETTE® tubes
Blood samples collected by means of venal puncture of the caudal vein
Genomic DNA extracted using the Qiagen DNeasy Blood and Tissue Kit
Illumina BovineSNP50 BeadChip SNP markers designed based on the Btau 4.0 reference genome
Markers clustered and genotyped using Illumina GenomeStudio v2.0 software
Fifty four of the genotyped samples derived from a previous study and approved by the University of Pretoria Ethical Committee (E087-12)

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