Mitochondrial DNA Sequence Analyses and Phylogenetic Relationships Among Two Nigerian Goat Breeds and the South African Kalahari Red

Abstract

The first hypervariable (HV1) region of mitochondrial DNA (mtDNA) of two popular Nigerian goat breeds: West African Dwarf (WAD) (n = 35) and Red Sokoto (RS) (n = 37) and one exotic breed: Kalahari Red (KR) (n = 38) imported from South Africa were sequenced to investigate sequence diversity, genetic structure, origin, and demographic history of the populations. A total of 68 polymorphic sites were found in 110 sequences that grouped into 68 haplotypes. Average haplotype and nucleotide diversities for all breeds were 0.982 ± 0.005 and 0.02350 ± 0.00213, respectively. Phylogenetic analysis revealed two mtDNA lineages (A and B). Lineage A was predominant and included all haplotypes from WAD and RS and 5 out of 11 haplotypes of KR goats. The remaining haplotypes (6) of KR belong to lineage B. The analysis of molecular variance revealed a high-within breed genetic variance of 82.4% and a low-between breed genetic variance of 17.6%. The three breeds clustered with Capra aegagrus as their wild ancestor. Mismatch distribution analysis showed that WAD, RS and haplogroup A have experienced population expansion events. The study has revealed very high diversity within the three breeds which are not strongly separated from each other based on mtDNA analysis. The information obtained on the genetic structure of the breeds will be useful in planning improvement and conservation programs for the local populations.

Keywords:

• Genetic diversity
• Goats
• Mitochondrial DNA
• Population expansions
• Population structure

ACKNOWLEDGEMENTS

We thank the Veterinary officers, Security officers and Technical staff of the Institute for their immense assistance, the initiative of the former Vice-Chancellor of FUNAAB, Professor O.O. Balogun, for the importation of the Kalahari Red goat from South Africa to Nigeria. We thank the Biosciences Eastern and Central Africa (BecA-ILRI Hub) for supporting the Scientific Paper-writing Workshop that prompted the writing of this paper and Dr. Chris Beadle (CSIRO Ecosystem Sciences, Australia) for his constructive comments.