Identification of candidate functional SNPs and genes associate with salt tolerance in Siniperca chuatsi by an integrated analysis of genome-wide association and transcriptome study

Mandarin fish ( Siniperca chuatsi ) holds immense economic potential and promise within the realm of freshwater aquaculture. However, its limited ability for tolerating salinity has emerged as a pivotal obstacle impeding the growth of this industry. To address this challenge, our research conducted an integrative analysis of genome-wide association study (GWAS) and transcriptomic study to elucidate the genetic basis and molecular mechanisms of salinity adaptation in mandarin fish. For GWAS, a total of 1000 two‑month‑old fish (average body weight 18.25 ± 7.22 g) were used, and genome‑wide association analysis identified 44 salinity tolerance-associated SNPs, with 16 highly significant loci clustered on chromosomes 5, 13, and 21. Key loci including SNP 5:5591919 ( SLC4A upstream) and SNP 14:19975383 ( RAPGEF6 exon) exhibited strong phenotypic associations and were validated as potential molecular markers. Another 800 fish of the same age (average body weight 19.24 ± 7.31 g) were used for aquaculture experiments under varying salinity levels, and an additional experiment was conducted in which mandarin fish were reared at distinct salinity levels (0, 6‰, 15‰) for two months to further elucidate their molecular responses to salinity fluctuations. The results demonstrated that low salinity (6‰) promoted growth, whereas high salinity (15‰) significantly inhibited growth. Transcriptomic analysis revealed tissue-specific expression patterns, with gill showing extensive ion transport and signaling responses under high salinity, and muscle shifting from metabolic to osmoregulatory gene expression. Key candidate genes were identified through integrated analysis, with SLC4A1a showing salinity-dependent muscle expression and RAPGEF6 potentially acting as a signaling hub coordinating osmotic responses. These findings establish salinity tolerance as a polygenic trait involving coordinated regulation of ion transport and signal transduction pathways, with clear energy allocation trade-offs between growth and osmoregulation.