Identification of a Novel QTL on LG16 Associated with Acute Salt Tolerance in Red Tilapia (Oreochromis spp.) Using GWAS

Culturing saline tilapia has become a new trend in the aquaculture due to the scarcity of freshwater resources. In this study, the genetic basis controlling for salt tolerance were investigated by using a ddRAD-seq-based GWAS in 288 individuals with extreme salt tolerant traits from half-sib families of red tilapia. 12 genome-wide significant SNPs and 6 chromosome-wide significant SNPs associated with acute salt tolerance were identified. Two QTLs on LG18:25,593,701-7009020 and on LG16:19,735,164-21,231,391 were defined. It is noteworthy that the QTL on LG16 is a novel QTL associated with acute salt stress. Near the significant SNP sites, we identified candidate genes sik1, ltb4r2b, pnp5b and kirrel1b with differential transcript expression under salt stress. Furthermore, significant physiological differences in serum osmolality and ion concentrations were confirmed between the tolerant group and sensitive group under 4.5 h of 22 ppt stress. The sensitive group had much higher serum osmolality (osmolality: 642.20 +/- 6.30 mOsm/kg) and higher concentrations of sodium and chloride ions (sodium: 317.67 +/- 5.03 mmol/L and chloride: 316.43 +/- 8.28 mmol/L) than the tolerant group (547.60 +/- 15.44 mOsm/kg, p(osmolality) = 0.0002; sodium: 280.53 +/- 9.13 mmol/L, p(sodium) < 0.0242; chloride: 266.00 +/- 12.00 mmol/L, p(chloride) < 0.0184). However, the lowest bicarbonate concentration was detected in the sensitive group at 22 ppt (2.53 +/- 0.30 mmol/L), which was significantly different from both the sensitive group at 0 ppt (p = 0.0008) and the tolerant group at 22 ppt (p = 0.0164). Our research laid the foundation for exploring the genetic mechanisms of acute salt tolerance and osmoregulation in red tilapia and for developing strains of red tilapia adapted to saltwater.