Genetic diversity of cattle in three regions of Gauteng province in South Africa using microsatellite markers.

Livestock production in South Africa remains an important contributor to ensuring food security and provides many social and economic attributes to the country. Locally adapted and indigenous breeds are able to survive in extreme weather conditions and produce and reproduce for long periods of time. Cattle (non-descript) in these areas constitute a valuable genetic resource. The study was conducted to assess the genetic diversity and population structure of cattle populations in three regions of Gauteng. Hair samples were collected from Western Gauteng (n = 266), Lesedi (n = 132) and Tshwane (n = 69) regions. Direct polymerase chain reaction (PCR) was conducted using eleven International Society for Animal Genetics (ISAG) recommended bovine microsatellite markers. Fragment analysis was performed. Five local cattle breeds (n = 473) were included as reference populations (Afrikaner, Nguni, Brahman, Bonsmara and Drakensberger breeds). The Angus breed was included as an outgroup. Statistical analysis was performed using MS Toolkit, STRUCTURE and GenAlEx programs. High level of genetic diversity was found across the populations, with an average expected heterozygosity of 75%. Levels of inbreeding varied from - 0.031 to 0.042 with a mean of 0.015, illustrating low levels of inbreeding within the populations. The results from this study indicated that more genetic differentiation found within populations rather than between populations. These findings may serve as a baseline for the management of genetic resources and contribute in developing future breeding programmes in these municipalities.