Epigenetic stress memory for predictive and heritable crop epibreeding

• Epigenetic memory allows plants to adapt according to earlier stress exposure • DNA methylation, histones, sRNAs, and TEs regulate plant stress tolerance • Epibreeding uses epiQTLs, EWAS, and priming to improve abiotic stress tolerance • CRISPR–dCas9 enables precise control of stress related genes in non-transgenic way Epigenetic regulation enables plants to rapidly adjust gene expression in response to abiotic stress through reversible and heritable mechanisms that determine stress memory and phenotypic traits. The objective of this review is to investigate the epigenetic modifications as functional and heritable resources for epibreeding of abiotic stress-tolerant crops and to present the developing tools that enable targeted manipulation of these modifications. Through recent studies across major crop systems, we identified that epigenetic mechanisms, including DNA methylation, histone modification, chromatin remodeling, and RNA pathways, consistently regulate stress adaptation and transgenerational tolerance. This review shows that stable epialleles, epigenetic quantitative trait loci (epiQTL), and epigenetically informed hybrids provide measurable links between epigenomic variation and stress-responsive phenotypes, enabling their incorporation into the epibreeding of crops. We further demonstrate that epigenetic fingerprinting, epigenome-wide association studies (EWAS), and CRISPR–dCas9-based epigenome editing provides broader approaches to examine epigenetic modifications. These tools facilitate beneficial epigenetic variation without altering the DNA sequence, enabling epibreeding of crops for enhanced abiotic stress tolerance.