Exploring candidate genes in a major QTL region associated with salinity tolerance in the skin of Nile tilapia based on transcriptomic analysis

Salinity is recognized to be a major environment factor that influences cellular hemostasis and functions in Tilapia. Previously, we identified a major quantitative trait locus (QTL) that associated with salinity tolerance at chrLG18 in tilapia. However, the causative functional genes within the QTL interval and their underlying molecular mechanisms in salinity tolerance remain unclear. In this study, we investigated the skin transcriptomic responses of the Nile tilapia GIFT line in response to three and a half months of salinity challenge with a concentration of 0, 17 and 27 ppt respectively, using RNA-seq. We detected 61, 1303 and 87 differentially expressed genes (DEGs) in three groups of comparison (ppt 0vs17, ppt 0vs27 and ppt 17vs27, respectively). These DEGs were mainly enriched in 5 pathway categories: apoptosis, cell junction, signal transduction, endocytosis and energy metabolism (p < .01). Colocalization of QTL intervals with the gene expression data revealed that three DEGs, nmrk2, ptprf and arhgef18a, were located within the major QTL region. In a red tilapia family, three SNPs in the gene ptprf were found significantly correlated with salinity tolerance. Our findings provide a DEG dataset for further identifying functional genes of salinity tolerance within the major QTL interval.