Genome-wide association studies in a F1 tilapia population reveal novel genetic loci associated with salinity tolerance

Salinity tolerance is a complex trait of ecological and economic importance in tilapia aquaculture. To further dissect the genetic architecture underlying this trait, we performed a genome-wide association study (GWAS) using ddRAD-seq in an F1 tilapia population of GIFT tilapia, which is derived from selective breeding. Unlike previous studies localized to ~23 Mb on chrLG18, we identified 11 novel genome-wide significant SNPs spanning a 4.6 Mb region (24,593,966 to 29,240,173 bp) on chrLG18 associated with salinity tolerance. GO enrichment analysis of the genes within this QTL region on chrLG18 showed significant enrichment of genes involved in fatty acid metabolism. The significant associations with salinity tolerance for the two missense mutations, LG18_25,305,119 (c.C388T) and LG18_25,305,122 (c.A391G), in the slc25a24l gene have been confirmed by Sanger sequencing. Individuals homozygotes for the T allele of LG18_25,305,119 and G allele of LG18_25,305,122 demonstrated over 2-fold longer average survival times under high salinity challenge compared to the individuals with disadvantageous genotypes. The mutated 131th amino acid (I/V) in SLC25A24L corresponding to the location of the nonsynonymous SNP LG18_25,305,122 showed a strong association with habitat salinity differences when comparing orthologs between freshwater and marine fish species. Our findings provide novel insights into QTLs, candidate genes and mutations conferring enhanced osmoregulatory capacity in tilapia.