EPIGENETIC REGULATION OF GENE EXPRESSION IN PLANTS: MOLECULAR MECHANISMS, ENVIRONMENTAL INTERACTIONS AND APPLICATIONS IN CROP IMPROVEMENT

Abstract

Plant epigenetic regulation links DNA methylation, histone modifications, small-RNA pathways and chromatin remodeling to transcription, development and environmental response. This review critically evaluates original experimental evidence for these mechanisms and asks when environmentally induced states are causal, persistent and useful for crop improvement. Plant methylomes show that DNA methylation must be interpreted according to sequence context, genomic location and genetic background; promoter, gene-body and transposon-associated methylation are not equivalent. Genetic and targeted-manipulation studies support RNA-directed DNA methylation and histone/chromatin mechanisms, while heat-stress experiments provide strong evidence for short-term somatic memory at selected loci. Evidence for sexual transgenerational inheritance is more mixed: some parental stress experiments report descendant effects, but multigenerational drought work found few conserved methylation changes and limited association with phenotype. Natural epigenomic variation in crops is often linked to local sequence polymorphism, complicating claims of sequence-independent epialleles. We propose an evidence framework that separates molecular association, causal regulation, within-plant or clonal persistence, meiotic inheritance and field-level value. Translation should prioritise matched methylome, transcriptome and phenotype measurements; causal perturbation and rescue; genotype-aware controls; common-garden generation tests; and multi-environment validation. Targeted epigenome editing provides a route to test specific loci, but stability after editor removal, off-target effects, pleiotropy and breeding performance remain central gates. Plant epigenetics is therefore a credible source of mechanistic insight and candidate breeding variation, but its practical value must be established trait by trait rather than inferred from chromatin change alone.