Salt tolerance candidate genes identified by QTL mapping, RNA-seq, and functional analysis in tilapia

Abstract

Salt tolerance in fish is crucial for aquaculture as it enhances survival and productivity in varying salinity conditions, thus expanding the range of viable farming environments and improving economic sustainability. Through QTL mapping and GWAS in a hybrid F₂ family of Mozambique and Nile tilapia, two large-effect QTL on chromosomes 11 and 18 were identified respectively. These two QTL explained a total of 39.9 % of the phenotypic variance. The identification of a QTL on LG11 suggests the presence of a previously unrecognized genetic factor contributing to salt tolerance. Comparative transcriptomic analysis of gill and kidney tissues between susceptible and tolerant tilapias highlights the importance of osmotic balance in regulation of salt tolerance in tilapia. Integration of QTL and RNA-seq data identified two candidate genes: acyl-coenzyme A thioesterase 5 (acot5) and sodium- and chloride-dependent taurine transporter (slc6a6) likely playing critical roles in such process. Functional analysis showed that over-expressing acot5 or slc6a6 in grouper kidney cells increased viability under salt stress by 4.46 % and 17.53 %, respectively. Subcellular localization revealed nuclear presence of ACOT5 and stress-induced nuclear translocation of SLC6A6. These findings highlight acot5 and slc6a6 as candidates for genetic manipulation and selection to enhance salt tolerance in tilapia, guiding genetic improvement efforts and promoting sustainable practices.