Seed germination: light-hormone-epigenome crosstalk at the dormancy-to-growth transition

Abstract

Seed dormancy and germination represent a critical developmental transition that determines plant fitness, ecological adaptation, and agricultural productivity. This switch is governed by the integration of environmental cues with endogenous hormonal networks, most notably the antagonistic balance between abscisic acid (ABA), which enforces dormancy, and gibberellins (GA), which promote germination. Among environmental signals, light acts as a central informational cue regulating germination timing through phytochrome-mediated pathways. A key component of this network is PHYTOCHROME-INTERACTING FACTOR 1 (PIF1), a transcriptional regulator that maintains dormancy in darkness by promoting ABA biosynthesis and signaling while suppressing GA accumulation. Light perception through phytochromes triggers rapid degradation of PIF1, leading to a hormonal reprogramming that shifts the balance toward GA dominance and initiates germination. Crucially, this light-hormone signaling module is strongly integrated with epigenetic regulation, where chromatin remodeling, DNA methylation, histone modifications, and small RNAs dynamically regulate the accessibility of key dormancy- and germination-related genes. This multilayered regulatory architecture enables environmental inputs to be converted into stable or reversible developmental states during the dormancy-to-growth transition. In this review, we synthesize current advances in understanding how light signaling interfaces with hormonal and epigenetic pathways to control seed fate decisions. We further highlight how additional environmental cues, including temperature, nitrate availability, and smoke-derived signals, converge on the ABA–GA regulatory axis to fine-tune germination responses. Additionally, we discuss emerging mechanistic gaps and translational opportunities for improving seed performance, reducing pre-harvest sprouting (PHS), and enhancing crop resilience under changing climatic conditions. Collectively, we propose an integrated framework in which light, hormonal, and epigenetic networks function as a coordinated regulatory system ensuring germination occurs only under favorable environmental conditions.