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The majority of goats in Tanzania belong to the Small East African (SEA) breed, which exhibits large
phenotypic variation. This study aimed to determine the genetic structure of, and relationships among four
populations (Sukuma, Gogo, Sonjo, and Pare) of the SEA breed that have not been studied adequately. A
total of 120 individuals (24 from each population) were analysed at eight microsatellite loci. In addition, 24
goats of the South African Boer breed were used as reference. Observed heterozygosity (Ho) ranged from
0.583 ± 0.04 for Sukuma to 0.659 ± 0.030 for Gogo, while expected heterozygosity (He) ranged from 0.632 ±
0.16 for Sukuma to 0.716 ± 0.16 for Boer. Five loci deviated from Hardy–Weinberg equilibrium (HWE) across
populations. The mean number of alleles ranged from 4.75 ± 1.58 for Pare to 6.88 ± 3.00 for Sukuma. The
mean inbreeding coefficient (F IS ) ranged from 0.003 in Sonjo to 0.148 in Sukuma. The differentiation
coefficient (F ST ) was highest (0.085) between Boer and Sukuma and lowest (0.008) between Gogo and
Sonjo. The largest genetic distance (0.456) was found between Sukuma and Boer, while the smallest (0.031)
was between Gogo and Sonjo populations. Pare, Gogo, and Sonjo populations, formed one cluster, while
Sukuma and Boer populations formed two separate clusters. From the findings, it can be concluded that the
SEA goats in this study showed high in population genetic variation, which implies that there is good scope
for their further improvement through selection within populations. The Sukuma population, which has fairly
high inbreeding, is moderately differentiated from Pare, Sonjo, and Gogo goat populations, which showed a
high level of admixture. Conservation and improvement strategies of the goats should be designed with first
priority being on Sukuma goats.
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