Evaluation of DNA quality and molecular observation of Nile tilapia (Oreochromis niloticus) from Limpopo Province, South Africa

Abstract

In this study, the ability of the Quick-DNA™ Tissue/Insect Miniprep Kit and Chelex® methods to extract DNA from O. niloticus skin, muscle, and gill tissue was compared. The quantity and purity of the DNA were measured with a NanoDrop spectrophotometer. Based on the results obtained, it appears that the DNA extracted using the Kit has good quality based on A260/280 (1.67–1.98), and the Chelex method (1.52-1.81) was acceptable. ANOVA for the amount of nucleic acid revealed a significant difference between muscle and skin with gill tissue (P < 0.05). However, the skin of O. niloticus subjected to both methods was the best at extracting DNA (1.89-1.81). The extracted DNA was also studied by 28S ribosomal DNA and COI of mitochondrial DNA genes. Phylogenetic analysis based on 28S rDNA and COI of mtDNA placed the South African population of O. niloticus in a clade with other related species with a posterior probability value of 1.00. Finally, the molecular results showed that 28S ribosomal DNA is a suitable marker for the identification of O. niloticus. In conclusion, precise identification of O. niloticus is critical for breeding for farmers and commercial sectors.

Keywords

• DNA extraction
• Fish
• mtDNA
• Oreochromis niloticus
• Phylogeny
• rDNA