Abstract:
The dairy goatindustry is a small, butimportant role player in the South African agricultural
sector. The limited number of animals representing the three main breeds (Saanen, British
Alpine and Toggenburg) has raised concerns over the genetic diversity of these animals and
the impact on their genetic management. In this study, 240 dairy goats representing three
breeds were genotyped with 25 microsatellite markers. Sufficientlevels of genetic diversity
were observed in all the breeds, with observed heterozygosity values exceeding 60%. A
slight population differentiation was indicated by the low FST values across and within
the populations. This was confirmed by the AMOVA analyses with most of the variation
shown within populations (91.7%). Negative FIS values in the three breeds indicated limited
inbreeding. Population structure analyses revealed six distinct groups, with the Saanen
population clustering into three sub-groups. The Toggenburg and British Alpine breeds
formed their own separate cluster, with a last cluster formed by animals from all three
pure-bred populations, indicating high levels of admixture. These results caution farmers
against uncontrolled crossbreeding practices and recommend routine evaluation of genetic
diversity.
