Genetic diversity and effect of selection at the mitochondrial hypervariable region in major Nigerian indigenous goat breeds.

Mitochondrial DNA (mtDNA) hypervariable region 1 ( HV1) sequences of three Nigerian indigenous goat breeds; West African Dwarf (WAD), Red Sokoto (RS) and Sahel were used to investigate the genetic diversity and effect of selection between and among these populations. Deoxyribonucleic acid (DNA) of Nigerian indigenous chicken was extracted from blood samples collected and preserved on Fast Technology for Analysis (FTA) paper. The extracted DNA were amplified and sequenced with predefined mitochondria (mtDNA) primer sets for HV1. Eighty-seven (87) polymorphic sites were found in 115 sequences which were grouped into 92 haplotypes. The mean haplotypic and nucleotide diversity were found to be 0.996±0.002 and 0.092±0.04 respectively. Genetic variation within population and between populations accounted for 97.26% and 2.74% of the total maternal variation respectively, with FST value of 0.0274. The Tajima's (D) and Fu's (F) test of neutrality were significant (P<0.05) and negative with the mean value of -1.12 and -21.34 respectively which is an indication of population expansion. The result further revealed that the WAD and RS goats are closely related with less genetic distance value of 0.01, and high genetic distance value (0.02) was observed between RS and Sahel goats and WAD and Sahel goats. Selection analysis result shows that there is more positive selection site (6 sites) to negative site (5 sites) among the Nigerian goats, which signifies how diverse they are as well as how nature has being trying to confer genetic fitness to these breeds.