The researchers compared triploid and diploid embryos across eight developmental stages, combining developmental observations with RNA sequencing and whole-genome bisulfite sequencing. DNA measurements confirmed the higher genomic content of the triploid group. Although the genome-wide dosage increase was substantial, the timing of major developmental milestones was comparable between the two groups, indicating preservation of overall developmental progression within this experimental system.

Global RNA-sequencing analysis showed that developmental stage, rather than ploidy, was the dominant source of large-scale variation in gene expression. In other words, the relative composition of the transcriptome changed more as embryos advanced through development than it did simply because an embryo was triploid. This result supports broad preservation of transcriptomic organization between the cold-shock-induced triploid embryos and their diploid controls.

That global pattern masked differences concentrated at particular stages. Stage-wise comparisons identified localized transcriptional divergence primarily at the blastula and heartbeat stages. Stage-by-ploidy interaction analysis further distinguished the developmental expression trajectories of triploid and diploid embryos in processes involving RNA processing, embryonic patterning, extracellular matrix organization and contractile development. These findings indicate that the molecular response to triploidy was not uniform across the sampled developmental stages.

Whole-genome bisulfite sequencing, performed at three stages, revealed extensive and bidirectional regional methylation differences between the groups. Some regions were more methylated in triploid embryos, while others were less methylated. The differentially methylated regions were not distributed randomly across the genome and showed particularly strong enrichment in CpG islands and promoters, indicating that the methylation differences were concentrated in defined genomic contexts.

The extensive methylation remodeling did not correspond to similarly widespread transcriptional divergence. Methylation–expression correlations were uniformly weak in promoter, gene-body, exonic and intronic contexts. Among genes that could be tested for both differences, only seven at the blastula stage and two at the heartbeat stage were both differentially methylated and differentially expressed. Those overlaps were not greater than expected if methylation and expression changes occurred independently.

Together, the results distinguish two patterns in cold-shock-induced triploid large yellow croaker embryos: broad preservation of developmental timing and relative transcriptome composition, alongside stage-specific transcriptional changes and structured methylation remodeling. The limited same-stage correspondence between methylation and expression argues against a simple interpretation in which most regional methylation differences directly accompany concurrent transcriptional changes in bulk embryos.

The study’s scope is important. It examined one fish species, one method of inducing triploidy and a defined series of embryo stages, so the findings do not establish a universal response to genome duplication across animals or other experimental systems. Analyses of whole embryos can also mask variation among individual cell types, and the observed relationships between methylation and expression do not demonstrate direct regulatory causation. Even with those limitations, the study provides a detailed developmental snapshot showing where triploid and diploid large yellow croaker embryos remained similar and where their molecular states diverged.

Subject of Research: Developmental, transcriptomic and DNA methylation responses in cold-shock-induced triploid large yellow croaker embryos

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

Article References: Long, F., Shao, W., Xiao, J., Chen, S., Chen, L., Li, Y., Weng, H., Pu, F., Zhou, T., Li, N., & Xu, P. (2026). Stage-resolved multi-omics reveals broad developmental preservation and localized molecular remodeling in cold-shock-induced triploid fish embryos. BMC Genomics. https://doi.org/10.1186/s12864-026-13490-4

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13490-4

Keywords: triploid embryos, large yellow croaker, cold shock, RNA sequencing, DNA methylation, genome dosage, embryonic development, epigenetic remodeling, multi-omics, Stage-resolved, reveals, broad