Stage-resolved multi-omics reveals broad developmental preservation and localized molecular remodeling in cold-shock-induced triploid fish embryos

Abstract Background Increased genome dosage can alter cellular and regulatory states, yet how vertebrate embryos maintain coordinated developmental progression following a whole-genome dosage increase remains unclear. Results Here, we examined developmental, transcriptomic, and DNA methylation patterns during cold-shock-induced triploid embryogenesis in large yellow croaker ( Larimichthys crocea ). Triploid embryos exhibited approximately 1.51-fold higher DNA content and reached major developmental stages at times comparable with diploid controls. Across eight stages, developmental stage rather than ploidy dominated global RNA-seq variation, indicating broad preservation of relative transcriptome composition. Stage-wise comparisons identified localized transcriptional differences concentrated primarily at the blastula and heartbeat stages. Stage-by-ploidy interaction analysis revealed distinct developmental expression trajectories involving RNA processing, embryonic patterning, extracellular matrix organization, and contractile development. Whole-genome bisulfite sequencing at three stages revealed extensive and bidirectional regional methylation differences. Relative to analyzable genomic windows, differentially methylated regions showed non-random enrichment across genomic contexts, including particularly strong enrichment in CpG islands and promoters. However, methylation–expression correlations across promoter, gene-body, exonic, and intronic contexts were uniformly weak. Among RNA-testable differentially methylated genes, only seven genes at the blastula stage and two at the heartbeat stage were also differentially expressed, and these overlaps were not greater than expected under independence. Conclusions Cold-shock-induced triploid embryos therefore retain broadly preserved developmental progression and relative transcriptome organization while exhibiting localized transcriptional differences and extensive, genomically structured methylation remodeling. The limited same-stage correspondence between methylation and expression indicates that regional methylation differences are not broadly associated with concurrent transcriptional divergence in bulk embryos.