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Genetic diversity and relationships among three Southern African Nguni cattle populations

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Abstract

The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.

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Acknowledgments

The authors would like to duly acknowledge the collaboration and contribution provided by the Agricultural Research Council, Animal Production, South Africa; Agrarian Research Institute of Mozambique, Directorate of Animal Science, Mozambique; and Ministry of Agriculture, Department of Livestock and Veterinary Services, Swaziland, for the execution of this study.

Funding

This project received financial support from the Technology Innovation Agency, National Research Foundation (Grant Number 103042), University of Venda: Research and Publication Committee grant (SARDF/16/ANS/03/1404) and Southern African Science Service Centre for Climate Change and Adaptive Land Management (SASSCAL) - Council for Scientific and Industrial Research (CSIR) of South Africa.

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Authors and Affiliations

  1. Department of Animal Science, University of Venda, Private Bag X5050, Thohoyandou, 0950, South Africa

    Matome A. Madilindi & Evison Bhebhe

  2. ARC-Animal Production, Private Bag X2, Irene, 0062, South Africa

    Matome A. Madilindi, Cuthbert B. Banga, Yandisiwe P. Sanarana & Khanyisani S. Nxumalo

  3. Directorate of Animal Science, Agrarian Research Institute of Mozambique, Av. Namaacha Km 11.5, P.O. Box 1410, Maputo, Mozambique

    Maria G. Taela

  4. Department of Veterinary and Livestock Services, Ministry of Agriculture, P.O. Box 162, Mbabane, Swaziland

    Bongani S. Magagula

  5. Department of Life and Consumer Sciences, University of South Africa, Private Bag X6, Florida, 1710, South Africa

    Ntanganedzeni O. Mapholi

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  1. Matome A. Madilindi
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  2. Cuthbert B. Banga
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  8. Ntanganedzeni O. Mapholi
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Correspondence to Matome A. Madilindi.

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All the international, regional, national and institutional guidelines for the care and use of animals were followed. Approval of the study was granted by the Animal Ethics Committee (AEC) of the University of Venda, South Africa (SARDF/16/ANS/03/1404).

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Madilindi, M.A., Banga, C.B., Bhebhe, E. et al. Genetic diversity and relationships among three Southern African Nguni cattle populations. Trop Anim Health Prod 52, 753–762 (2020). https://doi.org/10.1007/s11250-019-02066-y

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