Genetic diversity and population analysis of farmed Nile tilapia based on ND1-mitochondrion DNA sequences

Abstract

The mitochondrial NADH dehydrogenase subunit 1 (ND1) gene was used to characterise maternal genetic diversity and broodstock connectivity in farmed Oreochromis niloticus in Ghana. Samples were obtained from thirteen aquaculture farms together with the Genetically Improved Farmed Tilapia (GIFT) breeding population. A near full-length ND1 fragment (1074 bp) was sequenced from 113 individuals and analysed using phylogenetic, haplotype and population genetic approaches. Phylogenetic analysis resolved two divergent African maternal haplogroups. The dominant haplogroup contained most farmed populations together with the O. niloticus reference sequence, indicating extensive sharing of maternal lineages across farms, whereas a second haplogroup contained GIFT-associated maternal lineages detected in several farm populations. Haplotype analysis identified 23 ND1 haplotypes, including one dominant and widely distributed haplotype shared across most farms and the GIFT population, together with multiple low-frequency population-specific haplotypes. Most farm populations exhibited moderate to high haplotype diversity but relatively low nucleotide diversity, consistent with hatchery-mediated propagation from a limited number of maternal founders. Hierarchical AMOVA further demonstrated strong mitochondrial differentiation between GIFT and predominantly local farmed stocks, while differentiation among Ghanaian farms was low, reflecting extensive broodstock connectivity within the national tilapia seed system. Overall, the study demonstrates that mitochondrial ND1 sequencing provides a practical approach for assessing maternal lineage structure, monitoring broodstock connectivity and supporting genetic management in tilapia aquaculture in Ghana.