Plants maintain DNA methylation landscapes with high fidelity. Multiple pathways are coordinated to maintain DNA methylation patterns over many millions of cell divisions, reproductive generations and even evolutionary timescales. As DNA methylation maintenance is typically a robust and accurate process, scenarios in which the fidelity of methylation patterns is compromised represent compelling opportunities to gain a deeper understanding of DNA methylation stability. In this review, we discuss recent research that sheds light on two points of failure for DNA methylation maintenance: plant aging and tissue culture. In both cases, loss of DNA methylation is associated with the activation of transposable elements, potentially causing further genetic instability. We propose that uncovering the precise relationship between epigenetic instability, tissue culture, and somaclonal variation is crucial and timely, as epigenetic and genetic instability in tissue culture undermines the core strategy of gene editing to generate new genetic variants with high precision.
Transposable elements (TEs) constitute a major fraction of eukaryotic genomes and represent one of the most abundant classes of repetitive sequences in plants. Recent advances in sequencing technologies, together with the increasing availability of telomere-to-telomere and pan-genome assemblies, have enabled comprehensive characterization of TE sequences, revealing their complex architectures, structural variation, and evolutionary dynamics across diverse plant species. Because TE mobilization can compromise gene function and genome integrity, plants have evolved sophisticated epigenetic mechanisms to restrict TE activity. In turn, TEs have co-evolved diverse strategies to evade host silencing, reflecting a continuous evolutionary arms race between host genomes and their mobile elements. Beyond their traditional view as genomic parasites, accumulating evidence now demonstrates that TEs are major drivers of genome innovation by providing novel protein-coding modules, cis-regulatory elements, and structural variation that reshape chromatin organization and gene regulatory networks. In this review, we highlight recent advances in our understanding of how TEs promote regulatory innovation, environmental adaptation, and genome evolution in plants.
During plant sexual reproduction, the paternal epigenome is remodelled as it progresses from meiocyte to sperm cell and, after fertilization, to the zygote. In flowering plants, sperm cells retain a condensed chromatin state, specialized histone variants and a relatively stable DNA methylation landscape, whereas the companion vegetative cell undergoes chromatin decondensation, DNA demethylation and transposon reactivation. These contrasting epigenetic states are associated with small RNA production and reinforce genome integrity in the male germline. Following fertilization, sperm-specific histone variants are rapidly removed, and DNA methylation is also reinforced during embryogenesis, a process that may involve mobile maternal small RNAs. We present recent advances in our understanding of the regulation of chromatin states and DNA methylation during male gametogenesis, and discuss how paternal epigenetic information is transmitted, reset or re-established in the early embryo.
For decades, salinity research has sought to identify the molecular determinants of salt tolerance by comparing plants under non-saline and saline conditions. This strategy has profoundly advanced our understanding of stress sensing, signalling, and physiological responses. However, the persistent gap between the discovery of salt-responsive genes and the development of crops with improved field performance suggests a need to reconsider how stress responses are interpreted in relation to tolerance. I argue that salinity does not activate a single “tolerance programme”. Rather, salt tolerance is an emergent performance outcome arising from the integrated action of multiple physiological and developmental processes that sustain growth, reproduction, and recovery across variable saline environments. Consequently, the magnitude of a plant’s response to salinity does not necessarily reflect its capacity to maintain performance and may itself depend on the experimental context. This perspective proposes that binary stress-control experiments remain valuable for uncovering mechanisms of environmental responsiveness but should increasingly be complemented by experimental frameworks that evaluate performance across environmental gradients, developmental stages, and recovery phases. Such a framework aligns stress biology more closely with ecological reality and the mechanisms that ultimately determine agricultural performance.
