Identification of SNPs in the NKA Gene of Scylla paramamosain and the Association Analysis with Low-Salinity Tolerance

The Na+/K+-ATPase (NKA) gene encodes a critical membrane transporter that maintains cellular ion homeostasis and plays a pivotal role in osmoregulation and salinity adaptation of aquatic organisms. In this study, we identified and validated SNP markers in the NKA gene associated with low-salinity tolerance in Scylla paramamosain. Four candidate SNPs (g.72037G>T, g.72122G>C, g.74293G>T, and g.74433G>T) were screened and genotyped in low-salinity tolerant and intolerant groups. Association analysis revealed that mutant genotypes at all four loci were significantly enriched in the tolerant group (p < 0.05), with odds ratios (OR) > 1. The tolerant group exhibited higher genetic diversity parameters than the intolerant group. Haplotype analysis showed the GGGG haplotype was dominant in the intolerant group, whereas the other haplotypes were mainly enriched in the tolerant group. The NKA expression in the mutant genotypes was significantly higher than that in the wild genotypes by qRT-PCR. For tolerant individuals, the fast-growing group exhibited higher mutation frequencies than the slow-growing group. Multi-locus analysis achieved substantially more discrimination accuracy than single-locus analysis. These findings demonstrated that these SNPs could be candidate molecular markers for breeding programs in S. paramamosain in low-salinity environments, helping to identify individuals with enhanced salinity tolerance and supporting sustainable aquaculture practices.