Response of DNA methylation and gene expression to light treatments in Norway spruce Picea abies (L.) Karst.

Abstract DNA methylation is important for many developmental processes. Its role in plant’s adaptation to light conditions, however, remains unclear. In this study, we examined the DNA methylomes of Norway spruce ( Picea abies (L.) Karst.) under different light conditions, a combination of both light intensities (10, and 80 µmolm −2 s − 1 ) and light qualities (with or without far-red light). The result showed that both light intensity and quality affected seedling growth, with the former playing a major role. Both light intensity and quality drove genome-wide methylation changes, which varied among cytosine contexts (CG/CHG vs. CHH). The changes in light quality and intensity yielded a similar number of differentially methylated regions (DMRs), but light intensity was a major contributor in gene expression changes. At the genome-wide level, DNA methylation changes showed no consistent correlation with gene expression alterations. However, a subset of genes—particularly those involved in photosynthesis and circadian rhythms—exhibited coordinated methylation and expression changes, suggesting context-specific regulatory links. The findings indicate that DNA methylation may directly modulate photosynthesis and photoperiod genes and trigger an epigenetic memory, which in turn affects growth of Norway spruce seedlings in response to light conditions. In sum, our study provides a global picture of DNA methylation and gene expression under different light conditions in conifers and thus paves a way for future studies of light-directed gene regulation in plants.