Objective: The research was aimed at analysing single nucleotide polymorphisms and haplotypes on D-loop and Cyt-b regions of the mitochondrial DNA of tilapia fish.
Methods: Fifteen and thirteen tilapia fish were obtained from two populations, South-South (Domita farm) and South West (Odeda farm). DNA extraction from fish tissue was done using Quick-gDNATM mini prep kit
after which PCR amplification was carried out. Sequencing of the two mtDNA regions were done using forward primer 5’- GGATTYTAACCCYTRCCCC- 3’ and reverse 3’-AGTAAGTCAGGACCAAGCC-5’ for D-loop and
5’-GGATTTTAACCCTTACCCC-3’ and 3’AGTAAAGTCAGGACCAAGCC-5’ for Cyt-b region. 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 220.127.116.11.
Results: mtDNA polymorphism was highest in the D-loop of South-South (SS) population with 176 polymorphic sites, while South-West (SW) population had 162 polymorphic sites translating to 176, 162 and 144 SNPs with nonsynonymous substitutions higher 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-loop of SS and SW 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 SS than those from the SW as well as Cyt-b region of tilapia fish from SS. 28 haplotypes were identified among the tilapia from SS and SW with no shared haplotypes while 9 haplotypes were identified from the Cyt-b region with haplotypes 4, 5, 6 and 7 shared between species. Median joining network analysis revealed population-based clustering pattern. Demographic expansion was not significant using Tajima’s D and Fu’s F statistics.