© 2020 The Author(s). This open access article is distributed under a Creative Commons Attribution (CC-BY) 3.0 license. Genetics and Biodiversity Journal Journal homepage: http://ojs.univ-tlemcen.dz/index.php/GABJ Original Research Paper Abubakar GR. Ezewudo EA. Egena SSA. Usman A 1 Department of Animal Production, Federal University of Technology, P.M.B 65, Minna, Niger State, Nigeria. Corresponding author: Egena, S.S.A; Nigeria. Email: acheneje.egena@futminna.edu.ng Article history; Received: 12 March 2020; Revised: 20 May 2020; Accepted: 10 June 2020 Abstract The study assessed genetic diversity of four Nigerian sheep populations namely; Balami, Yankasa, Ouda and West African Dwarf (WAD) making use of blood sample. Extracted DNAs were used to study polymorphism at the β-lactoglobulin gene locus using RLFP-PCR process. Results revealed the percentage polymorphic locus was 100% while Shannon’s information index, observed homozygosity, expected heterozygosity, unbiased expected heterozygosity and fixation index were 0.656, 0.516, 0.464, 0.477 and -0.075, respectively. The gene flow (Nm) for all the population was estimated to be 7.65. The pairwise Fst was low and within the range of 0.0004(between Balami and WAD) to 0.0520 (between Balami and Yankasa). Variation within and between the populations of sheep shows that a large proportion of the observed variance (98% at p < 0.01) occurred within the breeds while only 2 % of the variance (p < 0.01) was contributed due to differences among the breeds. The nearest genetic distance was between the Balami and WAD (0.001) and between Ouda and the WAD (0.001). Phylogenetic analysis revealed three clusters. The present study showed that effort should be made to prevent the wearing away of the genetic make-up of the sheep populations considering the negative fixation index. Keywords: Cluster analysis; fixation index; RLFP; PCR; sheep; indigenous Introduction Milk and milk products from ruminants like sheep and goat could play vital roles in the agricultural sector of most countries (Selvaggi et al., 2015) particularly the developing ones if given more attention. The milk of sheep is mainly used in cheese making (Selvaggi et al., 2014a). This may not be unconnected with its peculiar composition and properties which makes it suitable for specific productive purposes (Selvaggi et al., 2014b). β -lactoglobulin, representing 60 to 65% of the total protein in milk, is the major whey protein in ruminant milk (Selvaggi et al., 2015). It was the first protein in which polymorphism was first reported and it is made up of 162 amino acids forming stable dimers in milk (Kontopidis et al., 2004). β -lactoglobulin gene is located on ovine chromosome 3 and it is one of the particular genes affecting milk traits in sheep (Selvaggi et al., 2015). The effect of the gene is felt in the mammary gland in pregnant animals and during lactation in a tissue-specific manner (Selvaggi et al., 2015). The gene is reported to be highly polymorphic in cattle; 12 polymorphic types are found in cattle and the A and B types are the most frequent. The difference in the polymorphic forms is commonly linked to differences in milk protein yield and value (Selvaggi et al., 2015). In sheep, three alleles A, B and C have been observed, their difference brought about by one or more amino acid changes. For example, the variant A differs from the variant B only at position 20 (Tyr → His) in the amino acid sequence (Selvaggi et al., 2015). A new and rare variant (C) was discovered by Erhardt (1989); the author opined that this type is a kind of variant A but with an exchange at location Genetic diversity of Nigerian Indigenous Sheep breeds at the β- Lactoglobulin gene locus