Hidden genetic nature of epigenetic natural variation in plants

• We review plant natural epigenetic variation and transposon silencing.
• The mechanisms regulating gene expression and maintenance of genome integrity.
• Natural epigenetic variation is often associated with mutations and gene rearrangements.
• Mostly genetic basis of epigenetic natural variation has not been anticipated.

Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.