Stability of DNA methylation across clonal generation in Lemna minor. Stability of temperature-induced DNA methylation changes across clonal generation in the common Duckweed Lemna minor L.

While some DNA methylation variants are transgenerationally stable in plants, DNA methylation modifications that are specifically induced by environmental exposure are typically transient and subject to resetting in germ lines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germ lines, and may thus be more conducive to long-term inheritance of epigenetic marks. This, however, has been poorly explored. Taking advantage of the rapid clonal reproduction of Lemna minor, we tested the hypothesis that exposure to high temperature environments triggers DNA methylation changes in the genome that can subsequently persist over multiple clonal generations once the stress signal removed. Using a reduced representation bisulfite sequencing approach, we show that high temperature stress induces changes in DNA methylation profiles both in CG and CHG contexts but not in CHH. A subset of the induced CHG variants persisted for many clonal generations (3-12) once the stress removed. Structural annotations of differentially methylated cytosines and loci showed that induced and inherited CHG variants are enriched within TEs. Our results corroborate the hypothesis that partial DNA methylation patterns can be stably inherited, over a large number of generations, in clonal plant lineages. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result indicates potential for long-term modulation of stress responses in asexual plants and vegetatively propagated crops.