Genomic analysis of a Nile tilapia strain selected for salinity tolerance shows signatures of selection and hybridization with blue tilapia (Oreochromis aureus)

Tilapia is a group of originally fresh water species, some of which can be tolerate a wide range of salinities and can be cultured in estuaries or brackish water ponds in polyculture with shrimp. Although the physiological processes that underly osmoregulation have been studied extensively, it is less clear how artificial selection produce adaptation to salinity stress. Here we studied the genomic architecture of an Indonesian saline-tolerant strain, called “Sukamandi”, which was selected for rapid growth in brackish water. We also investigated the impact of selection for salinity tolerance on the genome. Because the Sukamandi strain was potentially derived from hybridization between Nile tilapia (Orechromis niloticus) and blue tilapia (Orechromis aureus), we also searched for introgression signatures to understand their influence on salinity tolerance. Our results show that overall the Sukamandi strain is genetically much closer to Nile tilapia than to blue tilapia. Thirty-three salinity tolerance genes identified by Fst, enriched in ion transmembrane transport processes, such as MAPK3 activity, potassium ion homeostasis, ATPase activity and response to calcium ion. Comparing signatures of selection and introgression revealed that eight salinity tolerance genes, including caprin1a, nucb2a, abcb10, slc12a10.1, cacna1ab, ulk2, slc25a24 and cdh1 were strongly selected (top 1% signal windows) based on genome-wide scans, while five (slc12a10.1, zgc:153039, slc9a2, slc25a24, cdh1) out of thirty-three genes that have been introgressed from blue tilapia and selected (above top 5% signal windows) in the Sukamandi strain. Our findings not only contribute to understanding the evolution of salinity tolerance in fish, but, more generally, provide an interesting model for hybrid introgression in a farmed fish species.