The Genetic Assessment of South African Nguni Sheep Breeds Using the Ovine 50K Chip

Khanyisani S. Nxumalo, Paul Grobler, Karen Ehlers, Lucky T. Nesengani and Ntanganedzeni O. Mapholi
Additional contact information
Khanyisani S. Nxumalo: Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
Paul Grobler: Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
Karen Ehlers: Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
Lucky T. Nesengani: Department of Agriculture and Animal Health, University of South Africa, Private Bag X6, Florida 1710, South Africa
Ntanganedzeni O. Mapholi: Department of Agriculture and Animal Health, University of South Africa, Private Bag X6, Florida 1710, South Africa

Agriculture, 2022, vol. 12, issue 5, 1-11

Abstract: The indigenous sheep breeds of South Africa, such as the Nguni, are well adapted to different ecological regions throughout the country. This has resulted into different ecotypes. However, it is not clear if the differences among Nguni sheep are genetically distinct. The present study aimed to use the latest technology to assess the genetic relationship between Nguni sheep ecotypes and the relationship to other selected South African breeds using SNP markers. In the current study, 144 South African sheep samples (75 Nguni sheep and 69 mixed-breed sheep as a reference) were genotyped using the OvineSNP50 Bead Chip assay from Illumina. The Nguni consisted of 25 Pedi, 25 Swazi, and 25 Zulu sheep, with the reference group comprising 25 Namaqua, 23 Dorper, and 21 Damara sheep. After quality control of 54,241 SNPs, 48,429 SNPs remained for analysis (MAF > 0.05). There were genetic differences in the Nguni sheep population; notably, the Zulu and Swazi populations clustered together, but with a clear distinction from the Pedi ecotype. Genetic admixtures were detected in the Damara and Dorper sheep. This is most likely a consequence of recent intermixing between indigenous and commercial breeds. The levels of genetic diversity within individual types were generally lower compared to commercial breeds. This study revealed an understanding regarding genetic variation within and among indigenous sheep breeds, which can be used as baseline information for establishing conservation and breeding programmes.

Keywords: genetic diversity; ecotypes; conservation (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2022
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