Genetic characterization of South African Nguni cattle ecotypes using microsatellite markers

Abstract

Genetic characterization is an important step to assess the genetic status of indigenous breeds for informed decision making with regard to genetic improvement and conservation. The Nguni cattle breed is an important indigenous animal genetic resource that is well-adapted to different ecological regions in South Africa. Nguni cattle differ phenotypically in terms of body frame, size of ears, coat colour, horn and head shape and these differences have resulted in the recognition of five major ecotypes within the breed. The aim of this study was to perform a molecular characterization of Makhathini, Pedi, Shangaan and Venda Nguni cattle ecotypes using 22 microsatellite markers. The data was generated from 189 unrelated Nguni cattle individuals sampled from stud herds and research stations. Genetic diversity among Nguni cattle ecotypes was high with heterozygosity values varying from 68% University of Fort Hare (UFH), 69% Shangaan (SHA), 70% Makhathini (MAK), 70% Venda (VEN), 71% Loskop (LOS) to 72% Pedi (PED) with a mean number of alleles that ranged from 6.0 and 6.9. The overall inbreeding value indicated limited inbreeding between the populations (FIS=0.01). The population differentiation (FST) and AMOVA analyses indicated that 4.8 % of the total variation was due to differences between populations and 95.2% accounted for differences within individuals in the population. The genetic distances revealed shortest relationship between MAK, PEDI and SHA ecotypes. The VEN ecotype differentiated from MAK and PED and was closer to SHA ecotype. In addition, structure analysis depicted the predominance of MAK ecotype into other ecotypes. The results of this study can be applied for the genetic conservation of Nguni bovine ecotypes.