title: Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers.
abstract: The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.|Agricultural Research Council, Private Bag X2, Irene, 0062, South Africa.
authors.forename: Yandisiwe
authors.initials: Y
authors.lastname: Sanarana
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
authors.forename: Carina
authors.initials: C
authors.lastname: Visser
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
authors.forename: Lydia
authors.initials: L
authors.lastname: Bosman
authors.affiliation: Department of Animal Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa.
authors.forename: Khathutshelo
authors.initials: K
authors.lastname: Nephawe
authors.affiliation: Agricultural Research Council, Private Bag X2, Irene, 0062, South Africa.
authors.forename: Azwihangwisi
authors.initials: A
authors.lastname: Maiwashe
authors.affiliation: Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa. evm.koster@up.ac.za.
authors.forename: Este
authors.initials: E
authors.lastname: van Marle-Köster
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000502:physiology*; D060146:Ecotype; D005260:Female; D059647:Gene-Environment Interaction; D014644:Genetic Variation; D008297:Male; D018895:Microsatellite Repeats; D010375:Pedigree; D010641:Phenotype; D013019:South Africa
keywords: Conservation; Ecotypes; Microsatellites; Population structure