Evaluation of Single Nucleotide Polymorphisms and Genetic Diversity of Tilapia Fish Using Mitochondrial D-Loop and Cyt-B Regions

Abstract

The research was aimed at analysing single nucleotide polymorphisms (SNPs) and genetic diversity on D-loop and Cyt-b regions of the mitochondrial DNA of tilapia fish. Fifteen and thirteen tilapia fish were obtained from two populations, South South (Domita farm) and South West (Odeda farm), Nigeria. DNA extraction was performed using Quick-gDNA^TM mini Prep kit followed by PCR and sequencing of the two mtDNA regions. Statistical analyses were carried out on the aligned sequenced data using MEGA version 6.06, Dnasp 5.1, Codon code aligner 6.06 as well as NETWORK 4.6.1.1. MtDNA polymorphism was highest in the D-loop of South-South population with 176 polymorphic sites, while South-West population had 162 polymorphic sites translating to 176, 162 and 144 SNPs with higher non-synonymous substitutions than synonymous substitutions. Haplotype diversities (Hd) were 1.00 ± 0.024 and 1.00 ± 0.030 while nucleotide diversities were 0.168 ± 0.086 and 0.161 ± 0.084 for D[1]loop of South-South and South-West populations, respectively. For Cyt b region, haplotype and nucleotide diversities were 0.91 ± 0.003 and 0.051 ± 0.016. Positive selection was more on mtDNA D-loop of tilapia sampled from South South than those from the South Westas well as Cyt-b region of tilapia fish from South South, while demographic expansion was not significant. Higher SNPs were revealed in mtDNA D-loop when compared with mtDNACyt-b region of the tilapia fish.