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

Abstract

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.

Sequencing, polymorphism and phylogenetic characterisation of KiSS-1 gene in two Nigerian indigenous goat breeds

“…Among the twelve breeds sequences used for this analysis Guanzhong and Xinong Saanen had 100 percent nucleotide identity having the closest value of 0.000 and the highest was observed at 0.574 between Red Sokoto and Guanzhong, Xinong Saanen, Lehzi black. Based on the polymorphisms earlier reported in this study we observed a low pair-wise distance of 0.003 between Red Sokoto and Sahel goat breeds which compares favourable with findings of other studies estimate for Red Sokoto and Sahel (Murital et al, 2015;Udeh, 2015;Ajibike et al, 2016;Ajayi et al, 2016;Ojo et al, 2017). The low genetic distance estimates obtained between Red Sokoto and Sahel from different molecular markers could be attributed to migration, high degree of miscegenation or high gene flow, geographical adaptation.…”

Effect of feeding diets containing levels of ginger (<i>Zingiber officinale</i>) on digestibility and nitrogen balance of red Sokoto bucks

“…Goats play an important role in the life of small-holder farmers via their ability to convert lowcost feed resource to high value products (meat and milk) (Aregawi et al, 2013). Goat is one of the most important, adaptable and geographically widespread livestock species, which provides a good source of meat, milk and other by-products and is therefore referred to as "poor man's cow" (Ajibike et al, 2016). The role of goats in providing protein to humans is increasingly being recognized.…”