Aug 2026· Frontiers in Plant Physiology· 0 citations· 152 references
TL;DR
This review synthesizes current advances in understanding how light signaling interfaces with hormonal and epigenetic pathways to control seed fate decisions to 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.
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.
Plants integrate multiple environmental cues to decide the timing of seed germination. Light promotes germination primarily through photoreceptor phytochrome B (phyB), which eliminates the action of transcription factor PHYTOCHROME-INTERACTING FACTOR 1 (PIF1). Conversely, abiotic stresses typically elevate cytosolic Ca
2+
and inhibit germination. However, the coordination of light and calcium signaling during germination under stress conditions remains poorly understood. Here, we demonstrate that salt and osmotic stresses rapidly increase cytosolic Ca
2+
in imbibed seeds, and that the calcium sensor CALMODULIN-LIKE 20 (CML20) is crucial for germination tolerance to these stresses. CML20 directly interacts with PIF1 in a Ca
2+
-dependent manner, suppressing PIF1 self-association, oligomerization, and DNA-binding capacity. Moreover, phyB interacts with CML20 and PIF1 independently, promoting the assembly of the CML20-PIF1 complex and further reducing PIF1’s transcriptional activity. Genetic analyses reveal that PIF1 functions downstream of CML20, and that CML20 and phyB operate within the same pathway. Together, our findings define a phyB-CML20-PIF1 module, providing a rapid, reversible, and non-proteolytic mechanism to optimize seed germination under stress conditions.
Jing Kang, Jing Li, Xiao-Yan Liu et al.· Nature Communications· 0 citations
Background: Seed dormancy is crucial for plant survival and agricultural productivity, yet its molecular mechanisms, particularly the role of maternal effects, remain poorly understood. Methods: In this study, we applied a SWATH-based, label-free, quantitative shotgun proteomic mass spectrometry approach to investigate the temporal dynamics of dormancy establishment in Xanthium strumarium, a wild plant with two seeds in one burr that, despite sharing the same genetic and environmental conditions, exhibit distinct dormancy states. Results: Our data show that dormant seeds undergo coordinated metabolic suppression, marked by a decrease in energy metabolism, cell cycle arrest, and auxin signaling, explaining their smaller size. Simultaneously, dormant seeds exhibit metabolic re-prioritization towards fatty acid desaturation, cell wall modification, and an active epigenetic program stabilized by dormancy-promoting factors alongside a transcriptionally quiescent state in early–mid development. However, in the late developmental stage, molecular signaling pathways showed a recalibration distinguished by changes in seed metabolism (such as carbon–nitrogen reallocation, sulfur assimilation, and GABA production), hormonal fluctuations, and epigenetic regulation. Notably, previously reported high DOG1 transcript abundance, together with the absence of detectable DOG1 protein in the proteomic dataset, suggests that post-transcriptional mechanisms may contribute to DOG1 regulation. Conclusions: Based on these findings and the available literature, we propose a framework whereby dormancy establishment occurs in two phases: an early DOG1-mediated priming phase followed by a temperature-sensitive plasticity phase during seed maturation.
I. Nemati, Somayeh Gholizadeh, D. Elango et al.· Proteomes· 0 citations
Using a combination of genome-wide transcriptome, targeted hormonome and pharmacological approaches, this study showed that temporally resolved transcriptional regulatory networks integrating hormonal crosstalk underlie cold-induced modulation of seed dormancy and germination in wheat. Gene homoeologues (GHs) differentially expressed between cold-treated and untreated dormant seeds imbibed at optimal temperature (OT, 22°C) as well as between the same seed samples imbibed in cold and at OT represent distinct biological processes (BPs), indicating the role of coordinated activation/repression specific BPs in cold-mediated alteration of dormancy and germination. Our analyses highlighted that jasmonate (JA)-gibberellin (GA) synergism and JA-abscisic acid (ABA) or GA-ABA antagonism play roles in regulating dormancy release during imbibition of cold-treated dormant seeds at OT. The repression of germination in dormant seeds imbibed in cold compared to those imbibed at OT is associated with synergistic repression of seed sensitivity to JA and GA and activation of its sensitivity to ABA. Specific members of TaWRKY, TabHLH, TaMYB, TaNAC, TaERF, TaARF and TabZIP transcription factor families establish the transcriptional network involving specific GA, ABA and JA metabolism and signaling GHs and thereby the ABA-GA-JA crosstalk that enhance dormancy release during imbibition at OT after cold treatment and inhibition of germination during cold treatment.
Deepak Sharma, Tran-Nguyen Nguyen, Tuấn Anh Phạm et al.· Plant physiology and biochem...· 0 citations
Plants balance vegetative growth and stress responses through antagonistic phytohormone crosstalk, notably between abscisic acid (ABA) and cytokinin. However, the genetic architecture and molecular mechanisms driving this adaptive trade-off, particularly in perennial trees, remain elusive.
Integrating genome-environment and genome-wide association studies across 302
Populus tomentosa
accessions, we identify
PtoAG1
as a pleiotropic regulator of climate adaptation and stem growth. A naturally occurring frameshift mutation abolishes its repressor function, driving geographical niche differentiation by enhancing growth in humid habitats. Mechanistically,
PtoAG1
acts as a molecular rheostat. Under drought, ABA-activated PtoSnRK2.2 phosphorylates PtoMYB84 to transactivate
PtoAG1
. PtoAG1 then represses the cytokinin-signaling regulator
PtoRR12
, consequently releasing its inhibition of PtoSnRK2.2. This positive feedback further suppresses vegetative growth under stress while amplifying ABA responses via PtoAREB3. Concurrently, PtoAG1 directly represses
PtoAREB3
as a transcriptional brake to maintain signaling homeostasis. Evolutionary analyses reveal that
PtoMYB84
and
PtoAG1
constitute a tightly linked
cis
-regulatory module conserved across eudicots. Functional analysis on
AG1
orthologs in poplar,
Arabidopsis
, rice, and tomato demonstrates conserved cross-species utility: loss-of-function increases vegetative biomass but overexpression significantly boosts drought resilience.
Our study identifies a hierarchical crosstalk mechanism bridging ABA and cytokinin signaling to optimize environmental fitness. The evolutionarily conserved
MYB84
-
AG1 cis
-regulatory module establishes a versatile, translatable genetic target for precision breeding of climate-resilient and high-yielding crops.
This study identifies LdCDF2 as a hub linking GA signaling and biosynthesis and elucidates how the DELLA-LdCDF2 dual switch mediates GA self-amplification.
Xiaoman Zou, Hui Zhou, Sheng-Li Song et al.· Plant Physiology· 0 citations
The reproductive stage is a critical time in a plant’s life history when dealing with heat stress as the specific processes of meiosis, gametogenesis, anthesis, pollination, fertilization, and early seed development all occur within comparatively narrow temperature limits. Much of the importance of flowering is tied directly to temperature, both for the timing of reproductive transition and the ability for male and female reproductive tissues to survive exposure to damaging heat. Ambient-temperature sensing is linked to flowering via regulatory modules that involve phytochrome B, EARLY FLOWERING 3 (ELF3), PHYTOCHROME INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS T (FT), FLOWERING LOCUS M (FLM), SHORT VEGETATIVE PHASE (SVP), and the light–circadian components. Conversely, when temperature is harmful, protective responses involve other cellular mechanisms such as activation of heat-shock transcription factors (HSFs), heat-shock proteins (HSPs), endoplasmic-reticulum protein quality control, calcium and reactive oxygen species (ROS) signaling, antioxidant systems, hormone regulation, metabolic reprogramming, autophagy and DNA-repair pathways. Male reproductive development is often very sensitive, especially at meiosis, during formation of the tetrad, microspore development, during the maturation of pollen, and during the growth of the pollen tubes, although injury to pistils, ovules and the post-fertilization tissues may solely have an effect on the restriction of fertilization and seed set. Phenological heat escape and intrinsic reproductive thermotolerance are genetically separable but can be complementary aspects of adaptation, as revealed by natural allelic variation, QTL mapping, genomic prediction and marker assisted selection. This review summarizes molecular, genetic and physiological evidence, to propose that, to ensure stable yields at high temperatures, there is a need to coordinate optimization of reproductive timing, cell and development thermotolerance, and post-fertilization sink stability.
Sana Basharat, Muhammad Waseem, W. Saeed et al.· Stresses· 0 citations
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