Genome-wide DNA methylation responses to salinity stress in skin of GIFT tilapia as revealed by whole-genome bisulfite sequencing

In euryhaline fish frequently exposed to salinity shifts, epigenetic mechanisms are expected to play a crucial role in facilitating adaptation. Nile tilapia Oreochromis niloticus is recognized for its rapid growth and adaptability to low-salinity environments. The GIFT strain of the tilapia is suggested to be a good candidate for culture in brackish water. Recently, the mechanisms underlying salinity challenge in tilapia have received increasing attention. In this study, the dynamics of DNA methylation in the skin tissue of GIFT tilapia in response to high salinity stress were explored by integrating whole-genome bisulfite sequencing (WGBS) with published transcriptomic and genetic data. DNA methylation was enriched in heterochromatin and correlated positively with the density of transposable elements (TEs). A notable increase in CpG methylation level was detected, especially in the body of TEs, possibly due to the downregulated expression of DNA demethylases. Among the 10,514 differentially methylated regions (DMRs), 6346 showed hypermethylation, and 4168 displayed hypomethylation, with a marked prevalence on the chromosome LG3. Integration of methylation data with the skin transcriptome data unveiled a significant negative correlation (p < 0.05) between methylation levels in promoter regions and gene expression. Colocalization of differentially expressed genes (DEGs) and differentially methylated promoters (DMPs) identified 69 candidate genes. Additionally, 17 DMRs were overlapped with or near to the 24 SNPs on chromosome LG18:24,543,912 to 29,002,006 that significantly associated with salinity tolerance, highlighting candidate genes like mtcl1, nfatc4, pex19, kirrel1b, acot4, and pard3ab acting in adaption to high salinity. The methylation differences and expression changes of the candidate gene acot4 under high salinity stress were confirmed through BS-PCR and qRT-PCR. This investigation offers novel gene resources for further functional study on tilapia's adaptation to salinity changes from the genetic and epigenetic perspectives.