Phylogenetic relationship and variation among four strains of Small East African goats of Tanzania based on mitochondrial DNA

Objective: This study was conducted to determine the origin and phylogeography of four strains of Small East African (SEA) goat breed namely Pare, Gogo, Sonjo, and Sukuma. Methods: About 586 bp sequences of the first hypervariable (HV1) region within the mitochondrial DNA (mtDNA) displacement loop (D - loop) were analyzed in 142 individuals from SEA goat as well as Boer goat as reference breed. In addition, goat sequences from eight other African countries from the NCBI database were used for comparison. Results: A total of 154 polymorphic sites and 102 haplotypes were detected. The number of haplotypes ranged from 12 to 27 in Boer and Sonjo goats, respectively. Haplotype diversity ranged from 0.873 ± 0.039 (in Boer) to 0.994 ± 0.013 (in Gogo goats). The largest number of nucleotide diversity was found in Pare strain (0.030 ± 0.007) and the lowest in Gogo and Sonjo (0.023 ± 0.003). Three maternal haplogroups, A, B1B, and G were detected; haplogroup A being the most predominant with 116 individuals and 85 haplotypes. There was sharing of haplotypes among the Tanzania SEA goats, and the Kenya goats but not with goats from other African countries. Demographic expansion was detected in all SEA goat strains whereas background selection occurred only in Pare goats. Conclusion: The SEA and Boer goats have multiple maternal origins and are highly diverse from each other, though not strongly separated. There is sharing of haplotypes between the Tanzanian SEA goats and goats from Kenya. Population expansion occurred in all the SEA goat strains.