Abstract
Indigenous goats in Southern Africa represent a valuable genetic resource adapted to local environments, yet their genetic diversity remains poorly characterized. This study assessed the genetic diversity and population structure of five indigenous goat populations (Boer, Savannah, Kalahari Red, Tswana, and Landim) from Botswana, South Africa, and Mozambique using 20 microsatellite markers. Blood samples were collected from 250 unrelated individuals (50 per population). All markers were polymorphic, with a total of 198 alleles detected. Mean observed heterozygosity (Ho) ranged from 0.58 (Tswana) to 0.69 (Boer), while expected heterozygosity (He) ranged from 0.65 (Tswana) to 0.74 (Boer). The overall inbreeding coefficient (Fis) was low (0.04), indicating minimal inbreeding. Genetic differentiation among populations was moderate (Fst = 0.10), with the highest pairwise Fst between Boer and Landim (0.16) and the lowest between Savannah and Kalahari Red (0.05). STRUCTURE analysis revealed two main clusters: one comprising Boer, Savannah, and Kalahari Red, and another comprising Tswana and Landim. These results indicate substantial genetic diversity within Southern African indigenous goats and moderate differentiation among populations, supporting their conservation and sustainable utilization. The findings provide baseline data for genetic improvement programs and highlight the need for conservation strategies to preserve this unique genetic heritage.