Stable and temporally shifted DNA methylation differences between 14-year-old Norway spruce epitypes under common garden conditions

Summary

DNA methylation can change DNA properties, affecting chromatin accessibility, gene expression, and phenotypic
variation. In clonal Norway spruce, warmer (WE) versus cooler (CE) embryogenic conditions produce phenotypically dif
ferent trees. This climatic memory, induced during embryogenesis, remains stable in the resulting epitype trees, and the
epigenetically altered timing of bud phenology persists between WE and CE epitypes even after decades under common
garden conditions. We examined DNA methylation patterns in 14-year-old epitypes throughout the annual developmental
cycle. Using targeted bisulfite sequencing, we screened for differential DNA methylation over a 3000 bp region in 2744
genes related to the epigenetic machinery, circadian clock, and phenology. Clustering DNA methylation differences in the
CG context clearly separated epitype trees, confirming epigenetic mark differences. Differences in methylation of cytosines
in all contexts were highly dynamic and varied markedly among annual developmental stages, suggesting the existence of
circannual clocks affecting methylation levels in the studied genomic regions. Most stable methylation marks were identified
in CG contexts, fewer in CHG and none in CHH contexts, consistent with differences in inheritance among methylation con
texts. We identified stable CG and CHG methylation marks in the promoter regions of 30 specific genes. Two ARGONAUTE
genes and 4 other genes exhibited stable marks across all time points for CE or WE, and putative embryo–adult transmission
for some genes. These findings indicate that DNA methylation marks maintained in genomic regions throughout the annual
cycle may contribute to an induced epigenetic memory established in embryos and later manifested as phenologically dif
ferent epitype trees.

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DOI : doi.org/10.1007/s00425-026-051...
NVA : hdl.handle.net/11250/5558407