The studies on fish genetic diversity and its conservation in Nigeria are still at its preliminary stages. The country needs to document the diversities of all the water bodies and also embark on a DNA barcoding project for rapid identification of the enormous populations and consequent deposition in the global genebank for references. All molecular studies usually start with the isolation, purification, and recovery of DNA and this usually depends on the types of tissue, mode of sample collection, the medium of storage, duration of storage, and used extraction protocols. The current study embarked on fish collection in four major freshwater habitats as a preliminary study to a proposed fish barcoding project and to comparatively determine the extraction protocol that will be cost-effective, fast, safe, and yield adequate molecular materials for downstream amplification, cloning, and sequencing reactions. In the current study, three DNA extraction protocols, Zymo Research Kit (ZR), modified conventional SNET method, and modified Urea-SDS Method were compared to establish the best DNA extraction method from freshwater fishes. Sixty-two (62) fish samples were collected belonging to 16 different families, 23 Genera, and 32 Species. The average yield of the three protocols in terms of concentration (ng/μL: Purity) are: ZR (30.59: 1.58); UREA, (705.49: 1.75) and SNET (562.22: 1.73). Hence, in terms of DNA concentration recovery, the sequence of the best method is UREA > SNET > ZR, and the same trend followed in the case of Purity. Statistical tests did not show any significant difference when the extraction protocols were compared among fish families. Cytochrome B gene was successfully amplified on the DNA template to confirm their suitability for further studies. The result of the study can be concluded that among the best DNA extraction methods, UREA protocol can be recommended for fish DNA extraction, this is not only cost-effective, but also gave quality yield and adequate for downstream analysis.
