The objectives of this study were to evaluate the genetic diversity between and within the indigenous Tswana goat populations in five agro-ecological regions of Botswana and to assess the gene flow and population structure among them using microsatellite markers. DNA was analyzed from 500 Tswana goats sampled from communal farms in Botswana. There were 481 alleles detected, ranging from 3 to 14 per locus. The Southern region population had the lowest mean number of alleles (5.857±0.404), whereas the Central population had the highest (9.071±0.675). AMOVA analysis revealed that differences across populations accounted for 5.95% of total genetic diversity, while variations between individuals within populations accounted for 94.05%. Gaborone and Ngamiland populations had the greatest genetic distance (0.660), indicating the least gene flow between the two. The Factorial Correspondence Analysis results showed an overlap of some individuals between Central and Kgalagadi, suggesting a close genetic relationship. In the multivariate space defined by Principal Coordinates Analysis, the Southern and Ngamiland populations were relatively genetically distant. Despite some admixture in the Central population, each population was independently assigned to its inferred cluster in structure analysis. It can be concluded that the five goat populations are sufficiently diverse to be considered distinct ecotypes.

Keywords: Botswana, Tswana goat, genetic diversity, microsatellite markers, heterozygosity