Genetic Differentiation of Clarias gariepinus From Nigerian's Rivers Benue and Donga Using Single Nucleotide Polymorphism

ABSTRACT Clarias gariepinus (Burchell, 1822), a cornerstone of aquaculture in Nigeria, faces threats to its genetic integrity due to indiscriminate breeding and environmental degradation. This study investigates the genetic differentiation of C. gariepinus broodstocks from Rivers Benue and Donga using single nucleotide polymorphism (SNP) markers derived from the mitochondrial 16S rRNA gene. A total of 30 specimens were collected, with 29 successfully sequenced and analyzed. DNA was extracted, and amplification was performed using species-specific primers. BioEdit and MEGA X were used for sequence alignment, SNP identification, and phylogenetic analysis. Results revealed high sequence similarity (99.0–100%) with the C. gariepinus reference genome (NCBI: KT001082.1), confirming species identity. Low sequence divergence was observed, reflecting high genetic homogeneity within this population. Nucleotide composition was slightly A–T rich, and the transition/transversion bias was R = 2768.32. Only one SNP (T/C at locus 431) differentiated the three haplotypes identified, while the Tajima’s relative rate test showed no significant differences in evolutionary rates among haplotypes (χ² = 0.00; p = 1.000). In conclusion, the low haplotypic diversity and absence of functional mutations reflect genetic homogeneity among the populations studied. However, complementary analyses using DNA markers are required to fully understand the genetic differentiation in C. gariepinus. Keywords: Clarias gariepinus, single nucleotide polymorphism, mitochondrial RNA, genetic diversity, Rivers Benue and Donga