Abstract
BACKGROUND/OBJECTIVES: The Tswana goat, an indigenous Botswana breed, remains genetically understudied despite its adaptation to local conditions. This study characterized its genetic diversity across regions, using Boer goats as a reference, to assess population structure, heterozygosity, and breeding patterns. METHODS: Genomic DNA from Tswana goats (Southern, Central, Northwest, and research ranch populations) and Boer goats was genotyped using the Illumina Goat_IGGC_65K_v2 BeadChip. Data were analyzed in PLINK v1.9 and R v4.3.2 to compute genetic diversity indices. RESULTS: Tswana goats showed higher genetic diversity than Boer goats, with greater minor allele frequency (MAF: 0.313 ± 0.127 vs. 0.287 ± 0.136) and expected and observed heterozygosity (Ho: 0.395 ± 0.019 vs. 0.367 ± 0.022, and He: 0.400 vs. 0.375). Regional variation emerged across the Central (Ho = 0.394, He = 0.401, and MAF = 0.320), Southern (Ho = 0.397, He = 0.399, and MAF = 0.318), Northwest (Ho = 0.364, He = 0.358, and MAF = 0.289), and research ranch populations (Ho = 0.394, He = 0.380, and MAF = 0.300). Inbreeding coefficients (F(IS)) ranged from mild inbreeding (Central: 0.019) to heterozygote excess (research ranch: -0.038), reflecting managed breeding. CONCLUSION: Tswana goats have high genetic diversity, with regional variation linked to breeding practices. Although regional structure suggests genetic differentiation, no distinct ecotypes were identified. These findings emphasize the need for controlled breeding to preserve genetic diversity for the Tswana goat.