Genetic differences and selection signatures of four Nile Tilapia (Oreochromis niloticus) populations as determined by whole-genome resequencing

Oreochromis niloticus is a globally significant farmed fish species that plays a vital role in China’s aquaculture industry. Long-term artificial breeding practices, including inbreeding, have led to reduced genetic diversity and germplasm degradation. To compare genetic differences between wild and Chinese farmed populations, we collected 60 samples from three wild populations—Alexandria, Egypt (AlT), Ismailia, Egypt (IsT), and Saint Louis, Senegal (SeT)—and a domesticated population (QlT) from Wuxi, China. Whole-genome resequencing was employed to analyze genetic diversity, population structure, and selection signatures across these four populations. The results revealed that the SeT population exhibited the highest genetic diversity and showed significant divergence from the IsT population. Principal component, phylogenetic reconstruction, and genetic clustering analyses consistently demonstrated distinct genetic separation among the four populations. Kinship analysis indicated close genetic relatedness between IsT and AlT, and revealed gene flow between AlT and SeT. Selective sweep analyses identified regions under selection in six pairwise comparisons (AlT/IsT, AlT/QlT, AlT/SeT, IsT/QlT, IsT/SeT, and QlT/SeT), with the JAK-STAT signaling pathway showing the highest enrichment. This pathway is associated with immune regulation and growth in O. niloticus. Further analysis of differentially selected genes identified key candidates (ifngr2, clcf1, cish, ak7, nme6, pde2a, pde4d, and adcy8) in the JAK-STAT and purine metabolism pathways, suggesting strong selection for disease resistance and reproductive traits in breeding programs. In summary, these results add to the database of O. niloticus genetic resources, and will be useful for the development of genetic breeding strategies and germplasm characterization methods.