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 characterization 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 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 2 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.

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Context. Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims. The study was conducted to assess the genetic diversity and population structure of South African nondescript communal beef cattle populations by using 25 microsatellite markers. Methods. Unrelated and nondescript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu-Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results. High level of genetic diversity was found across the five nondescript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 K 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu-Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions. Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications. The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.