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Frontiers in Plant Physiology ·

Volume 4 - 2026 | https://doi.org/10.3389/fphgy.2026.1894927

Epigenetic and metabolic regulation of drought stress memory in maize: from molecular mechanisms to field-applicable priming strategies

  • Bushra Quyoom1
  • Ajaz Ahmad Lone2
  • Zahoor Ahmad Dar2
  • Latif Ahmad Peer1*corresponding author
  1. 1Department of Botany, University of Kashmir, Jammu and Kashmir, India
  2. 2Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, India
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Abstract

Maize (Zea mays L.) is highly vulnerable to recurrent water deficits, particularly during vegetative-to-reproductive transition. Although physiological acclimation to drought is well documented, the capacity of maize to establish and transmit drought stress memory represents an underexplored frontier for climate-resilient agriculture. This review synthesizes the crop-specific epigenetic and metabolic mechanisms that govern drought priming and memory persistence in maize. We examine how initial osmotic stress triggers localized regulatory cascades, focusing on histone modifications (H3K4me2, H3K9ac, H3K27me3, and H3K36me3), DNA methylation dynamics, and transposable element regulation across the maize genome, where transposable elements comprise approximately 85% of the nuclear DNA. We detail the metabolic memory engram, which encompasses proline biosynthesis, carbon-nitrogen reallocation, and photosynthetic adjustments. Concurrently, we evaluate practical agronomic priming strategies—including hydropriming, osmopriming with CaCl 2 and PEG, chitosan priming, hormone priming (melatonin, SA, GA 3), and nanopriming—alongside emerging epigenetic biomarker screening platforms to identify drought-tolerant germplasms. By integrating molecular circuitry with field-applicable priming, this framework charts pathways for optimizing the memory yield equation. We explicitly identify critical knowledge gaps, including the limited direct measurements of proline biosynthetic enzyme kinetics (P5CS/P5CR) in primed versus unprimed maize and the largely uncharacterized phosphorylation states of PEPC under priming conditions, providing a roadmap for future research.

Keywords

1 Introduction

Global agriculture is facing accelerating climate pressures. The increasing frequency of extreme weather events, such as prolonged droughts, heatwaves, and erratic rainfall, exposes a critical limitation of conventional breeding: the pace of genetic adaptation often lags behind environmental change, creating an “adaptation debt” (Bell and Gonzalez, 2009; Vinton et al., 2022).

Maize (Zea mays L.) is particularly vulnerable to drought. As a C4 cereal crop, it supplies over 20% of food calories in parts of sub-Saharan Africa and, together with rice and wheat, provides at least 30% of food calories to more than 4.5 billion people worldwide (Shiferaw et al., 2011). In several countries (e.g., Malawi, Zambia, and Lesotho), maize contributes more than 50% of the daily caloric intake (FAOSTAT, 2024). Maize reproduction is exceptionally sensitive to water deficit during its critical flowering window, a period of 2–3 weeks that determines the final grain yield (Nuccio et al., 2015). Unlike model C3 dicots, such as Arabidopsis thaliana, maize possesses a genome dominated (~85%) by transposable elements (TEs), which creates unique challenges and opportunities for the epigenetic regulation of stress-responsive genes (Makarevitch et al., 2015; Schnable et al., 2009).

These unique biological characteristics, together with increasing climatic uncertainty, have intensified efforts to understand how maize adapts to recurrent drought stress. Among the proposed adaptive mechanisms, epigenetic stress memory has emerged as a promising process operating on ecological timescales. Epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNAs, play critical roles in enabling plants to adapt to environmental changes (Miryeganeh, 2025). Stress memory refers to the capacity of plants to “remember” prior encounters with environmental stress and mount faster, stronger, or more efficient responses when recurring stress occurs (Crisp et al., 2016; Hilker and Schmülling, 2019). Initial stress exposure “primes” the organism, triggering molecular, biochemical, and physiological changes that persist beyond the immediate stress period (Oberkofler and Bäurle, 2022). This review primarily focuses on within-generation (somatic) drought stress memory, whereby prior drought exposure modifies the response of the same plant to subsequent drought events during its lifetime. However, for context, it is useful to distinguish this from related phenomena in which stress-induced changes persist across generations. In some cases, this memory can persist for one or two generations following stress exposure, a phenomenon termed intergenerational memory. When effects are transmitted beyond the immediate progeny to subsequent generations not directly exposed to the stress, this is referred to as transgenerational epigenetic inheritance (TEI) (Herman and Sultan, 2011; Latzel et al., 2013). TEI provides a potential rapid-response system in which the parental environment shapes the offspring phenotype. However, the adaptive significance and stability of TEI under field conditions in crops like maize remain actively debated, and evidence for adaptive transgenerational effects in maize under drought is limited (Cao and Chen, 2024; Eichten and Springer, 2015; Quyoom and Peer, 2026).

Understanding how drought stress memory is established, maintained, and recalled requires examination of the molecular mechanisms that underpin these persistent responses. The molecular basis of epigenetic memory involves an integrated circuitry of small RNAs, DNA methylation, and histone modifications that may bypass meiotic reprogramming in certain contexts (Fitz-James and Cavalli, 2022; Zhang et al., 2018). Simultaneously, technological advances have enabled the genome-wide profiling of histone modifications, DNA methylation, and transcriptomes in crop plants (Forestan et al., 2020; Wang et al., 2021). Metabolomics has identified specific osmolyte fingerprints, including proline, raffinose family oligosaccharides, and myo-inositol, that correlate with drought-adapted states (Joshi et al., 2021; Obata et al., 2015). Translating these molecular and metabolic insights into practical applications, however, remains a critical challenge.

One promising approach for translating these molecular and metabolic insights into improved drought resilience is the development of priming and epigenetic screening strategies that can be deployed under field conditions. Seed priming, a pre-sowing treatment that partially hydrates seeds to initiate early metabolic processes followed by controlled drying, offers a low-cost, non-transgenic intervention to potentially “imprint” drought tolerance before planting (Marthandan et al., 2020). Epigenetic biomarker screening platforms, including methylation-sensitive amplified polymorphism (MSAP) and whole-genome bisulfite sequencing (WGBS), enable the identification of heritable epialleles associated with stress resilience (Bocchini et al., 2018; Eichten et al., 2013). Collectively, these molecular, epigenetic, metabolic, and physiological processes provide an integrated framework for understanding how maize perceives, stores, and recalls previous drought exposure, thereby linking cellular mechanisms with whole-plant adaptation and opportunities for crop improvement.

This review has three interconnected objectives. First, we synthesize the current knowledge of the molecular mechanisms of drought stress memory in maize, focusing on the crop-specific features of its TE-rich genome and C4 photosynthetic architecture. Second, we examine the metabolic adjustments associated with priming, including proline accumulation, carbon-nitrogen reallocation, and photosynthetic regulation. Third, we evaluate field-applicable priming strategies and epigenetic screening methods that translate mechanistic insights into practical tools for climate-resilient maize production. We conclude by explicitly identifying critical knowledge gaps—including limited data on proline biosynthetic enzyme kinetics and largely uncharacterized PEPC phosphorylation dynamics in primed plants—that define a research agenda for the coming years. Because the primary emphasis of this review is within-generation drought stress memory, Figure 1 presents a conceptual framework integrating the molecular, metabolic, and physiological processes underlying the establishment, maintenance, and recall of stress memory during sequential drought events experienced by a single maize plant.

Three-phase framework of within-generation drought stress memory in maize. This image illustrates drought stress memory occurring within a single maize plant during sequential drought–recovery–redrought cycles. It represents within-generation (somatic) stress memory and does not depict intergenerational or transgenerational inheritance, which are discussed separately in the text. The drought memory engram is established through a multi-scale regulatory loop. **(A)** Priming Phase: Initial water deficit triggers an ABA-mediated signaling cascade, activating SnRK2 kinases and ROS-scavenging enzymes. **(B)** Engram (Storage): Stress signals are recorded via chromatin remodeling (histone poising at *ZmP5CS* and *ZmPEPC* loci) and stable DNA methylation shifts at transposable elements (TEs). **(C)** Execution Phase: Upon recurrent stress, the “poised” molecular architecture enables super-induced transcription, leading to accelerated proline accumulation and optimized C4 metabolic flux, ultimately enhancing field-level resilience and yield protection in plants.
Figure 1. Three-phase framework of within-generation drought stress memory in maize. This image illustrates drought stress memory occurring within a single maize plant during sequential drought–recovery–redrought cycles. It represents within-generation (somatic) stress memory and does not depict intergenerational or transgenerational inheritance, which are discussed separately in the text. The drought memory engram is established through a multi-scale regulatory loop. (A) Priming Phase: Initial water deficit triggers an ABA-mediated signaling cascade, activating SnRK2 kinases and ROS-scavenging enzymes. (B) Engram (Storage): Stress signals are recorded via chromatin remodeling (histone poising at ZmP5CS and ZmPEPC loci) and stable DNA methylation shifts at transposable elements (TEs). (C) Execution Phase: Upon recurrent stress, the “poised” molecular architecture enables super-induced transcription, leading to accelerated proline accumulation and optimized C4 metabolic flux, ultimately enhancing field-level resilience and yield protection in plants.

2 Histone modifications in drought stress response and memory

Histone modifications play a key role in chromatin-based transcriptional regulation during stress. In maize, heat stress triggers genome-wide increases in H3K4me2 and H3K9ac at the promoter regions of heat shock factor and rRNA genes (Hou et al., 2019). Under drought conditions, natural antisense transcript (NAT) gene pairs exhibit elevated levels of H3K36me3, H3K9ac, and H3K4me3, with reduced levels of H3K27me3, indicating an open chromatin configuration (Xu et al., 2017). Collectively, these studies indicate that different abiotic stresses induce distinct combinations of histone modifications; however, activating histone marks are consistently associated with transcriptional activation of stress-responsive genes in maize.

While these studies established associations between activating marks and stress-induced transcription, Forestan et al. (2020) specifically addressed whether such chromatin changes persist after stress recovery. They provided a genome-wide map integrating transcriptomic and histone modifications in maize subjected to drought and recovery, identifying three categories of stress-memory genes: ‘transcriptional memory’ genes with stable expression changes after recovery, ‘epigenetic memory candidate’ genes retaining chromatin modifications without expression changes, and ‘delayed memory’ genes with delayed responses.

Dynamic regulation of histone marks also involves erasure mechanisms. Gao et al. (2026) characterized 27 ZmJMJ histone demethylases in maize, with ZmJMJ17a, ZmJMJ17b, ZmJMJ28, and ZmJMJ32 significantly induced under drought stress. However, whether these demethylases contribute specifically to drought memory or acute stress responses remains unknown. Collectively, these studies suggest that multiple activating histone marks accumulate at stress-responsive loci in maize, with some changes persisting after recovery, although causal links to functional memory phenotypes remain to be demonstrated. The persistence of activating histone marks across drought-recovery-redrought cycles is illustrated in Figure 2.

Epigenetic mechanisms underlying drought stress memory in maize. This image illustrates chromatin-based memory established and recalled within a single maize plant during sequential drought–recovery–redrought cycles. The drought episodes shown in panel B represent repeated stress events occurring within the same generation and do not depict intergenerational or transgenerational inheritance. **(A)** Chromatin-based memory at drought-responsive gene loci. The nucleosome core with wrapped DNA (blue helix) carries histone tail modifications, including activating marks (H3K4me2, H3K9ac, and H3K36me3) and repressive marks (H3K27me3). Upstream transposable elements (TEs) are silenced via RNA-directed DNA methylation (RdDM) and maintain methylated CpG/CHG sites (orange CH3). RNA polymerase II (Pol II) remains in a poised configuration at memory gene promoters, enabling rapid transcriptional reactivation during secondary stress. **(B)** Conceptual representation of the persistence and rapid re-establishment of activating histone marks across sequential drought–recovery–redrought cycles within the same generation. The bar heights are schematic and represent relative trends rather than exact quantitative measurements.
Figure 2. Epigenetic mechanisms underlying drought stress memory in maize. This image illustrates chromatin-based memory established and recalled within a single maize plant during sequential drought–recovery–redrought cycles. The drought episodes shown in panel B represent repeated stress events occurring within the same generation and do not depict intergenerational or transgenerational inheritance. (A) Chromatin-based memory at drought-responsive gene loci. The nucleosome core with wrapped DNA (blue helix) carries histone tail modifications, including activating marks (H3K4me2, H3K9ac, and H3K36me3) and repressive marks (H3K27me3). Upstream transposable elements (TEs) are silenced via RNA-directed DNA methylation (RdDM) and maintain methylated CpG/CHG sites (orange CH3). RNA polymerase II (Pol II) remains in a poised configuration at memory gene promoters, enabling rapid transcriptional reactivation during secondary stress. (B) Conceptual representation of the persistence and rapid re-establishment of activating histone marks across sequential drought–recovery–redrought cycles within the same generation. The bar heights are schematic and represent relative trends rather than exact quantitative measurements.

3 DNA methylation dynamics under drought stress

DNA methylation provides a relatively stable epigenetic mark because of its maintenance through DNA replication, making it a candidate for sustained memory mechanisms (Zhang et al., 2018). However, studies on stress-induced methylation changes in maize have yielded contrasting findings, highlighting the complexity of these dynamics.

3.1 Methylome stability versus stochastic variation

Wang et al. (2021) profiled DNA methylation in maize roots under water stress and found that drought-tolerant inbred lines maintained more stable methylomes than drought-sensitive lines, with increased methylation levels under stress and sequence-dependent inheritance patterns. In contrast, Eichten and Springer (2015) examined heat, cold, and UV stress in maize and found no evidence of consistent stress-induced methylation changes; instead, they observed low-rate stochastic variation in both control and stressed plants. These contrasting results suggest that methylome stability, rather than specific methylation changes, may help distinguish tolerant from sensitive lines, although stress type, tissue, and genotype likely influence outcomes.

3.2 Promoter demethylation is a mechanism of gene activation

Yan et al. (2025) provided a well-documented case linking specific promoter demethylation to drought tolerance. In drought-tolerant maize, demethylation occurred in the CpG island of the ZmGST2 promoter under drought stress, facilitating gene expression and enhancing drought resistance via improved ROS scavenging and root growth. The drought-sensitive inbred line failed to undergo this demethylation. This represents a clear example of how targeted demethylation can contribute to drought adaptation, although generalization to other loci requires further investigation.

3.3 Integration with ABA signaling

In addition to direct stress responses, DNA methylation changes have been observed in conjunction with ABA signaling. Sallam and Moussa (2021) identified demethylated transposable elements in an ABA-deficient maize mutant under drought stress, suggesting crosstalk between hormonal and epigenetic pathways. Whether these methylation changes are causal or correlative, and how they interact with other regulatory mechanisms, remains unclear.

Collectively, these studies indicate that DNA methylation dynamics contribute to drought responses in a locus-, genotype-, and stress-type-specific manner, although consistent stress-induced changes across environments remain elusive.

3.4 Emerging insights—N6-methyladenine dynamics

Beyond 5-methylcytosine, recent studies have revealed that N6-methyladenine (6mA), another DNA modification, shows dynamic patterns that correlate with heat stress responses in maize. Guo et al. (2025) found that 6mA is enriched in promoters, intergenic regions, and transposable elements, with inverse correlation to gene expression. Heat-tolerant inbred line B73 showed elevated 6mA levels upon heat stress, and mutation of the 6mA demethylase ZmALKBH1 enhanced its heat tolerance. Whether 6mA dynamics also contribute to drought stress memory in maize has yet to be determined and warrants further investigation.

4 Transposable element regulation and drought stress memory

TEs comprise approximately 85% of the maize genome, making their regulation particularly relevant to stress responses (Schnable et al., 2009). Rather than being merely “junk” DNA, TEs contribute to stress-responsive gene regulation through multiple mechanisms, including localized activation under abiotic stress (Liang et al., 2021), enhancer-like regulatory activity (Makarevitch et al., 2015; Noshay et al., 2021), and RNA-directed DNA methylation-mediated silencing (Mao et al., 2015), all of which can contribute to adaptive variation.

Studies investigating TE expression under abiotic stress have consistently found that genome-wide TE activation does not occur; instead, specific TE families generate transcripts only under stress. Liang et al. (2021) documented substantial genotypic variation in stress-responsive TE expression in response to heat and cold stress across multiple maize inbred lines, with activated TE families often containing small regions lacking DNA methylation, whereas fully methylated elements were rarely expressed. Genotypic variation in TE expression was driven by both genetic differences (presence/absence of TE copies) and epigenetic variation (methylation status), suggesting that TE expression is influenced by localized epigenetic variation rather than widespread demethylation.

Beyond TE activation, TEs can also provide regulatory variations for nearby genes. Makarevitch et al. (2015) found that between 4 and 9 different TE families were associated with upregulation of stress-responsive genes under each stress condition tested, affecting up to 20% of stress-upregulated genes and 33% of genes expressed only under stress. TEs inserted upstream of stress-responsive genes may provide local enhancer activity, and allelic variation in TE insertions is strongly correlated with stress-responsive gene upregulation. These findings align with those of Liang et al. (2021), demonstrating that TEs are not randomly activated, but rather that specific families and elements contribute to stress responses in a genotype-dependent manner. In addition to TE activation, the chromatin landscape of TE insertions can influence the expression of nearby genes. Noshay et al. (2021) identified TE insertions that interrupt or carry accessible chromatin regions (ACRs) in maize genomes, with nearly 20% of distal ACRs located within annotated TEs in the maize genome. TEs carrying ACRs were enriched for association with the higher expression of nearby genes, suggesting that TEs can create novel regulatory elements. TE polymorphisms affecting ACRs were associated with gene expression variation, highlighting the potential of TEs to rewire transcriptional responses.

A well-documented example that integrates these concepts involves a miniature inverted-repeat transposable element (MITE) inserted in the promoter of ZmNAC111, a NAC transcription factor gene. Mao et al. (2015) identified this MITE as significantly associated with natural variation in maize drought tolerance, repressing ZmNAC111 expression via RNA-directed DNA methylation (RdDM) and H3K9 dimethylation. Transgenic maize overexpressing ZmNAC111 showed enhanced drought tolerance and improved water-use efficiency, supporting the functional relevance of TE-mediated regulation in maize. MITE insertion appears to have occurred after maize domestication and spread among temperate germplasm, illustrating how TE variation can be selected for adaptive traits.

Collectively, these studies establish that TEs contribute to stress-responsive gene regulation through localized activation, enhancer-like activities and methylation-based silencing mechanisms. The MITE-ZmNAC111 case provides a direct link between TE variation and drought tolerance, although direct evidence for TE-mediated drought memory, distinct from acute stress responses, and the extent to which similar mechanisms operate at other loci remain to be determined.

Together, histone modifications, DNA methylation, and transposable element regulation define the upstream epigenetic landscape that governs transcriptional responsiveness during recurrent drought. The resulting transcriptional reprogramming influences downstream metabolic pathways involved in osmotic adjustment, carbon–nitrogen partitioning, and photosynthetic regulation, thereby linking chromatin-level regulation with whole-plant physiological acclimation.

5 Drought priming and metabolic memory

Transcriptional and physiological memory. Studies examining maize responses to repeated dehydration have established that prior stress exposure alters both gene expression and physiological parameters upon subsequent exposure. Ding et al. (2014) identified four transcriptional memory response categories in maize exposed to repeated dehydration, with patterns paralleling those in Arabidopsis thaliana, suggesting evolutionary conservation of this response. Extending these findings to physiology, Virlouvet et al. (2018) integrated transcriptome and physiological measurements across 14 parameters in maize seedlings and found that stomatal conductance and non-photochemical quenching displayed contrasting memory patterns, suggesting potential trade-offs between metabolic investment in cellular protection and photosynthetic efficiency. At the agronomic level, Kanojia et al. (2026) primed maize with the plant-derived biostimulant AgriPrime Stimulus (APS) and found that priming delayed drought-induced leaf senescence by preserving photosynthesis, strengthening cell wall biosynthesis, enhancing redox homeostasis (through increased proline, trehalose, and myo-inositol accumulation), suppressing senescence-associated genes, and modulating hormone balance. Collectively, these responses suggest that APS establishes a primed physiological state that improves osmotic adjustment, stabilizes cellular structures and membranes, maintains redox balance by limiting oxidative damage, and modulates hormonal signaling to delay senescence. This coordinated metabolic and regulatory reprogramming is proposed to enable plants to respond more rapidly and efficiently to drought stress, thereby enhancing drought resilience.

Proline accumulation and the question of endogenous biosynthesis. Proline is one of the most consistently observed osmoprotectants that accumulates in maize under drought conditions, although its accumulation alone is not necessarily indicative of drought resistance (Ibarra-Caballero et al., 1988; Khan et al., 2025). Notably, Ibarra-Caballero et al. (1988) also reported that exogenous ABA did not induce proline accumulation, indicating that proline content alone is not a reliable proxy for ABA-mediated drought adaptation. Accordingly, in this review, proline metabolism is considered as one component of a broader metabolic and regulatory network associated with drought acclimation rather than as an independent marker of stress memory or ABA responsiveness. Exogenous proline supplementation dramatically alleviates drought-induced reductions in maize growth: shoot and root fresh weights increase by 97% and 247%, respectively, under drought plus proline compared to drought alone, while H2O2 and MDA are reduced by 38% and 67%, and CAT, POD, and SOD activities are enhanced by 14%, 69%, and 144%, respectively (Khan et al., 2025). These data demonstrate the capacity of proline to mitigate drought damage. However, direct measurements of the expression and activity of the proline biosynthetic enzymes Δ¹-pyrroline-5-carboxylate synthetase (P5CS) and Δ¹-pyrroline-5-carboxylate reductase (P5CR) in primed versus unprimed maize remain limited. Specific enzyme kinetic parameters, such as modifications to the maximum velocity (Vmax), shifts in the Michaelis constant (Km) for glutamate, or stable post-translational modifications arising from priming, remain unknown. Resolving this enzymatic gap is a priority for verifying the biochemical basis of the proline-related metabolic memory.

Carbon–nitrogen metabolic integration during priming. In addition to osmolyte accumulation, drought priming reshapes carbon–nitrogen metabolism. In a two-year field study, Lai et al. (2026) found that mild drought combined with medium-to-high nitrogen maintained maize yields through enhanced leaf antioxidant capacity (increased POD activity and reduced MDA), sustaining photosynthesis and assimilate production. Multivariate analyses showed that carbohydrate metabolism, nitrogen metabolism, and hormone balance explained 44%, 19%, and 7% of the 100-grain weight variation, respectively, with interactions explaining an additional 19%. Similarly, Ren et al. (2021) demonstrated that melatonin-treated maize seedlings under drought conditions exhibited coordinated regulation of carbon and nitrogen metabolism, with higher photosynthesis, sucrose biosynthesis, nitrogen assimilation, and protein biosynthesis capacities. Complementing these findings, Xie et al. (2026) combined drought priming with moderate nitrogen application in summer maize and found that the synergistic treatment promoted proline accumulation and enhanced nitrogen metabolism enzyme expression, with nitrate reductase activity and aboveground nitrogen accumulation significantly increased. Root architecture metrics, including length density, surface area density, and dry weight density, increased by 31.6%, 22.5%, and 13.9%, respectively, suggesting that priming promotes osmolyte accumulation while enhancing resource acquisition through improved root development. These findings indicate that nitrogen availability modulates metabolic responses to water deficit and that priming agents, such as melatonin, may act through integrated carbon–nitrogen (C–N) pathways.

Collectively, these studies establish that drought priming in maize involves coordinated transcriptional, physiological, and metabolic changes. Recent conceptual frameworks have proposed that chromatin integrates metabolic and redox inputs to establish developmental thresholds, a paradigm termed the ‘epigenetic set-point’ (Peer, 2026). However, direct evidence linking specific enzymatic changes (particularly in proline biosynthesis) to priming-induced memory and the translation of such metabolic memory to yield protection under field conditions remains an important knowledge gap.

These metabolic adjustments represent the functional output of upstream transcriptional and epigenetic regulation. By sustaining cellular energy balance, osmotic homeostasis, and antioxidant capacity during recurrent drought, they support physiological acclimation, including the maintenance of photosynthetic performance under water deficit.

6 C4 photosynthetic regulation and PEPC in drought stress

The metabolic adjustments described above ultimately influence photosynthetic performance, the principal determinant of biomass accumulation and yield under drought. Among the enzymes linking metabolism with physiological function, phosphoenolpyruvate carboxylase (PEPC) occupies a central role in C4 photosynthesis. Its regulation under drought therefore provides an important mechanistic connection between metabolic memory and whole-plant physiological resilience. However, direct evidence for PEPC regulation in drought-primed maize remains limited, with most mechanistic insights derived from studies in heterologous systems.

PEPC expression and activity during drought. Studies on transgenic rice expressing maize C4-PEPC provide proof-of-concept evidence for potential epigenetic regulation of PEPC during drought. Liu et al. (2017) reported increased PEPC activity and transcript abundance, accompanied by rapid promoter demethylation and upregulation of PEPC kinase (PPCK) through Ca2+-, NO-, and H2O2-mediated signaling. However, because these observations were obtained in a transgenic C3 rice system rather than native C4 maize, they should not be interpreted as direct evidence for drought stress memory mechanisms in maize. Instead, they provide a useful experimental framework for investigating whether similar regulatory processes operate in the C4 photosynthetic context.

Similarly, Qian et al. (2015) reported higher PEPC activity, calcium content, protein kinase activity, and NO-associated signaling responses in transgenic rice overexpressing maize C4-pepc. Together, these studies demonstrate that maize PEPC can be functionally regulated in a heterologous system and suggest potential regulatory mechanisms. However, because rice lacks the Kranz anatomy and mesophyll–bundle sheath compartmentalization that define native C4 photosynthesis, these findings should be regarded as proof-of-concept rather than direct evidence for drought priming or stress memory mechanisms in maize.

PEPC kinetic properties and phosphorylation. PEPC activity is also regulated post-translationally via reversible phosphorylation. In maize, Tovar-Méndez et al. (2000) showed that both phosphorylated and non-phosphorylated PEPC exhibit high cooperativity in phosphoenolpyruvate (PEP) binding, with malate inhibition overcome by glycine or alanine. Černý et al. (2010) further demonstrated that dephosphorylation shifts PEPC from hyperbolic to sigmoidal kinetics, decreases maximal reaction rate, and increases sensitivity to L-malate inhibition. These studies have established phosphorylation as a key regulator of PEPC catalytic properties. Extending these biochemical findings to plant-level functions, Enyew et al. (2026) generated PEPC-protein kinase (PEPC-PK) mutant lines in maize. While maximum PEPC activity remained unchanged, PEPC in mutant plants was not phosphorylated under light and showed increased sensitivity to malate inhibition, although gas exchange and field biomass were not significantly altered, suggesting that additional regulatory mechanisms operate in planta.

Evidence gap: Phosphorylation of PEPC in primed maize. Although light-mediated regulation of PEPC-protein kinase (PEPC-PK) is well understood, direct analysis of the PEPC phosphorylation state or altered allosteric constants (Km and Ki) specifically induced by drought priming in maize is lacking. Few published studies have provided quantitative data on PEPC-PK activity levels or the specific in vivo phosphorylation status of Ser-15 during a second drought encounter. Reversible phosphorylation therefore represents a plausible—but unverified—mechanism that may contribute to metabolic memory in maize. Testing this hypothesis will require direct biochemical profiling of PEPC phosphorylation, enzyme kinetics, and PEPC-protein kinase activity in primed and unprimed maize during recurrent drought.

7 Seed priming protocols for field deployment

The molecular, metabolic, and physiological mechanisms discussed above collectively provide the biological foundation for developing field-applicable interventions. Among these, seed priming represents the most practical strategy for exploiting endogenous stress memory to improve drought resilience in maize. Seed priming, a pre-sowing treatment that partially hydrates seeds to initiate early metabolic processes followed by controlled drying, offers one such pathway (Marthandan et al., 2020).

Among the priming methods, hydropriming and osmopriming are the most widely tested. Hydropriming (typically 18–24 h soaking in water) improves germination, seedling vigor, and root proliferation under drought conditions, although the yield benefits are modest (Khan et al., 2015; Sudozai et al., 2013). CaCl2 osmopriming (ψs -1.25 MPa, 24 h) demonstrates stronger field validation: field trials report improved root development, grain yield, and economic returns under vegetative and terminal drought (Khan et al., 2015). PEG osmopriming has shown promise in experimental settings but requires field validation for maize.

Hormonal and chemical priming have also been shown to be effective. Melatonin priming (200-500 µM) consistently improves germination (>92%), seedling growth, proline accumulation, and antioxidant enzyme activities (SOD, POD, CAT) under PEG-induced drought (Kumari et al., 2026; Muhammad et al., 2023). Salicylic acid priming triggers H2S signaling, enhancing osmolyte biosynthesis and ROS homeostasis (Tu et al., 2025). Chitosan priming enhances germination and antioxidant defenses, though field validation remains limited (Kakar et al., 2023). Gelaw and Sanan-Mishra (2024) demonstrated that H2O2 and proline priming induced genotype-dependent responses, with priming reducing specific miRNA expression to increase the expression of target transcripts associated with osmolyte synthesis and ROS homeostasis.

Emerging approaches include nanopriming and biopriming, respectively. Nanopriming with AgNPs (40 mg/L) enhanced root architecture plasticity and activated stress-responsive transcriptional pathways, whereas CuO@SiO2 (20 mg/L) improved nutrient uptake-related gene expression and increased grain yield by 9–17% under drought (Chen et al., 2023; Zhu et al., 2025). Silicon quantum dots (Si QDs) have also been shown to outperform conventional Si nanoparticles (Zhao et al., 2026). Biopriming with Rhizobium and Pseudomonas improves agronomic and physiological parameters under terminal drought, offering an eco-friendly and commercially feasible option for drought management (Nawaz et al., 2020).

Figure 3 summarizes the comparative effectiveness of different seed priming strategies and presents an integrated two-tier screening pipeline for identifying drought-resilient maize germplasm.

Practical tools for drought resilience in maize. **(A)** Comparative effectiveness of seed-priming methods for enhancing drought tolerance. Performance scores are composite indices that integrate germination percentage, seedling vigor, and grain yield under water-limited conditions relative to unprimed controls. CaCl<sub>2</sub> osmopriming demonstrates the strongest multi-site field validation, with documented improvements in root development, grain yield, and economic returns (Khan et al., 2015). Melatonin priming shows promise in controlled environments but requires further validation in field studies. Hydropriming is effective for germination and early vigor but is less effective for yield traits under severe drought. **(B)** An integrated two-tier screening pipeline combining laboratory-based epigenetics and root phenotyping with multi-environment field validation. Tier 1 employs cost-effective methods (MSAP, WGBS, hydroponic PEG screening, and targeted histone ChIP) to evaluate 200–600 accessions. Candidate lines advance to Tier 2 for multi-site field trials (2+ locations, 2–3 seasons) with managed drought stress (50–60% field capacity), assessing yield components (ASI, NDVI), and physiological traits (Pn, gs, RWC). Validated lines proceed to breeding programs as donor germplasms with associated epigenetic biomarkers. Abbreviations: MSAP, methylation-sensitive amplified polymorphism; WGBS, whole-genome bisulfite sequencing; PEG, polyethylene glycol; ChIP, chromatin immunoprecipitation; FC, field capacity; ASI, anthesis-silking interval; NDVI, normalized difference vegetation index; Pn, net photosynthetic rate; gs, stomatal conductance; RWC, relative water content; PGPR, plant growth-promoting rhizobacteria.
Figure 3. Practical tools for drought resilience in maize. (A) Comparative effectiveness of seed-priming methods for enhancing drought tolerance. Performance scores are composite indices that integrate germination percentage, seedling vigor, and grain yield under water-limited conditions relative to unprimed controls. CaCl2 osmopriming demonstrates the strongest multi-site field validation, with documented improvements in root development, grain yield, and economic returns (Khan et al., 2015). Melatonin priming shows promise in controlled environments but requires further validation in field studies. Hydropriming is effective for germination and early vigor but is less effective for yield traits under severe drought. (B) An integrated two-tier screening pipeline combining laboratory-based epigenetics and root phenotyping with multi-environment field validation. Tier 1 employs cost-effective methods (MSAP, WGBS, hydroponic PEG screening, and targeted histone ChIP) to evaluate 200–600 accessions. Candidate lines advance to Tier 2 for multi-site field trials (2+ locations, 2–3 seasons) with managed drought stress (50–60% field capacity), assessing yield components (ASI, NDVI), and physiological traits (Pn, gs, RWC). Validated lines proceed to breeding programs as donor germplasms with associated epigenetic biomarkers. Abbreviations: MSAP, methylation-sensitive amplified polymorphism; WGBS, whole-genome bisulfite sequencing; PEG, polyethylene glycol; ChIP, chromatin immunoprecipitation; FC, field capacity; ASI, anthesis-silking interval; NDVI, normalized difference vegetation index; Pn, net photosynthetic rate; gs, stomatal conductance; RWC, relative water content; PGPR, plant growth-promoting rhizobacteria.

8 Epigenetic biomarker screening for drought-resilient germplasm

Parallel advances in epigenomics have enabled the identification of heritable epigenetic variations associated with drought adaptation. Several platforms are available, each with distinct trade-offs between resolution, cost and throughput. Epigenetic modifications, including DNA methylation and histone acetylation, have been identified as key regulators of stress-responsive pathways in maize (Peer et al., 2025).

DNA methylation-based method. Methylation-sensitive amplified polymorphism (MSAP) is a PCR-based method that detects methylation differences at CCGG sites using the isoschizomers HpaII and MspI. MSAP is cost-effective, requires modest equipment, and can screen multiple samples simultaneously, making it suitable for initial epigenetic diversity surveys in maize germplasm collections. However, the limitations of this approach include surveying only a small fraction of the genome (CCGG sites) and providing a limited sequence context (Eichten et al., 2013). Bocchini et al. (2018) used MSAP to examine epigenetic changes in selenium-biofortified maize under drought, identifying differential methylation patterns in genes encoding phytoene synthase (PSY), sorbitol dehydrogenase (SDH), and alcohol dehydrogenase (ADH).

Whole-genome bisulfite sequencing (WGBS) provides single-base resolution maps of DNA methylation across the entire genome. Wang et al. (2021) used WGBS to profile DNA methylation in maize roots subjected to water stress. Genome-wide DNA methylation profiling has identified thousands of differentially methylated regions (DMRs) that vary among inbred lines, populations, and stress treatments (Eichten et al., 2013). Many DMRs are heritable across generations, suggesting stable epialleles that could be targets of selection. DMRs are frequently located near or within the transposable elements. However, to date, the literature has reported few validated epigenetic loci or DMRs that are causally and reproducibly associated with drought adaptation across multi-environment field trials. This represents a critical evidence gap between epigenetic correlations and causation.

Histone modification biomarker. In addition to DNA methylation, specific histone marks may serve as molecular memory indicators. Forestan et al. (2020) characterized genome-wide histone modifications (H3K4me2, H3K9ac, and H3K36me3) in maize subjected to mild, prolonged drought followed by recovery. The identification of “epigenetic memory candidate” genes—with stress-induced chromatin changes persisting in the absence of transcriptional changes—suggests that specific histone marks could serve as molecular memory indicators. Hou et al. (2019) demonstrated that short-term heat stress induces genome-wide increases in H3K4me2 and H3K9ac levels, providing candidate histone marks that may be explored as indicators of stress-primed states, although drought-specific validation is needed.

Transposable element methylation as an adaptive marker. Transposable elements are also promising biomarker targets. Mao et al. (2015) identified a miniature inverted-repeat transposable element (MITE) inserted in the ZmNAC111 promoter associated with natural variation in drought tolerance via RNA-directed DNA methylation (RdDM) and H3K9 dimethylation. This TE insertion status could serve as a predictive marker for drought resilience across germplasm. More recently, Bubb et al. (2025) used long-read chromatin fiber sequencing (Fiber-seq) to comprehensively identify accessible chromatin regions (ACRs) and CpG methylation across the maize genome, revealing stereotypical ACR patterns at young TEs that degenerate with evolutionary age. They further identified TE enhancers characterized by simultaneous hyper-CpG methylation and chromatin accessibility, representing a novel plant-specific epigenetic signature with potential biomarker applications.

Collectively, these approaches offer a toolkit for screening drought-resilient germplasm, although the translation from correlative epigenetic marks to causal biomarkers requires further validation across field environments.

9 Evidence gaps and future directions

To move maize drought memory from laboratory characterization toward field-scale application, several knowledge gaps must be systematically resolved.

9.1 Critical knowledge gaps

Several critical knowledge gaps require systematic resolution to move maize drought memory from laboratory characterization toward field-scale application (Table 1).

Table 1. Critical knowledge gaps in drought stress memory research in maize.

GapDescriptionPriority
P5CS/P5CR enzyme kineticsDirect measurements of proline biosynthetic enzyme activities in primed vs. unprimed maize are largely absentHigh
PEPC phosphorylation dynamicsFew studies report PEPC phosphorylation state or PEPC-PK activity in drought-primed maizeHigh
Post-translational memory engramsPersistent modifications on metabolic enzymes remain largely undocumentedHigh
Field validation of chemical primingMost SA, melatonin, Se, Zn priming studies lack multi-environment field trialsHigh
Validated drought-adaptive DMRsFew epigenetic loci have been causally validated for drought tolerance across environmentsHigh
Tissue-specific spatial dynamicsMost studies use whole-leaf samples; C4 cell-type specific memory is unexploredMedium
Transgenerational stabilityHeritability of priming-induced changes across generations is unclearMedium
Landrace epigenomic dataLimited profiling of climate-resilient landraces from drought-prone regionsMedium

9.2 Methodological priorities

Addressing these gaps requires a coordinated, multidisciplinary systems biology approach.

  • Time-resolved enzyme assays to track P5CS, P5CR, PEPC, and PPDK activities across drought-recovery-redrought cycles.
  • Quantitative phosphoproteomics to compare phosphorylation profiles in primed versus unprimed lines.
  • Stable isotope metabolic flux analysis (¹³C-MFA) to trace carbon routing through C4 cycle and amino acid synthesis pathways.
  • Cell-type-specific multi-omics using laser-capture microdissection to map memory between mesophyll and bundle sheath cells.
  • Functional validation via CRISPR/Cas9 to knock out or overexpress candidate memory genes (ZmJMJ32, ZmWRKY106, ZmP5CS).

9.3 Translational opportunities

Decoding the maize metabolic engram may enable four pathways for climate-smart agriculture:

  • Epi-priming agronomic protocols using precise chemical elicitors or nano-priming agents.
  • Breeding for memory capacity by screening landraces for natural variation in memory retention.
  • Targeted epigenome editing using CRISPR-dCas9 platforms to investigate “smart memory” architectures.
  • Predictive crop growth modeling integrating memory kinetics to optimize irrigation scheduling.

A summary of key experimental studies on priming strategies and the molecular, metabolic, physiological, and epigenetic mechanisms underlying drought stress memory in maize is provided in Tables 2 and 3.

Table 2. Summary of priming strategies for enhancing drought tolerance and stress memory in maize.

Priming strategyKey FindingExperimental approachCitation
Micronutrient primingPriming with 0.075 mM Se + 10 mM Zn, or 6 mM Si + 0.075 mM Se + 10 mM Zn, or coating with Si+Se+Zn (0.732 g Si + 0.014 g Se + 2.875 g Zn.kg-1 seed) improves germination percentage, speed of germination, root dry weight, seedling dry weight, and seedling growth rate under PEG-induced drought (10% PEG)RCBD split-plot; PEG-induced drought(Ikasari et al., 2025)
Micronutrient primingCombined Se (0.075 mM) + Zn (10 mM) seed priming for 24 h improved germination percentage (+52%), promptness index (+54%), vigor index (+35%), emergence index (+42%), relative water content (+27%), antioxidant enzyme activities (CAT + 69%, GPX + 116%, SOD + 48%, APX + 39%), and increased shoot Se (+154%) and Zn (+114%) concentrations in maize under drought stress (60% field capacity)Pot experiment; 60% field capacity (FC)(Nawaz et al., 2021)
NanoprimingSeed priming with iron oxide nanoparticles (n-Fe2O3) at 75 mg L-¹ improved leaf water status (RWC + 13%, water potential +44%), photosynthetic water-use efficiency (+64%), intrinsic water-use efficiency (+17%), enhanced SOD and POD activities, reduced H2O2 and MDA accumulation, and improved yield traits including cob length (+59%), kernel rows per cob (+27%), and 100-kernel weight (+33%) in maize under drought stressSplit-plot field experiment under well-irrigated and deficit irrigation (drought) conditions(Mazhar et al., 2024)
NanoprimingCopper nanoparticle (nano-Cu0) priming (69.4 µM) increased drought tolerance by maintaining shoot biomass (78% biomass reduction vs. 87% in control), enhancing anthocyanin, chlorophyll, and carotenoid contents, reducing O2•- and H2O2 accumulation through increased SOD and APX activities, improving recovery after re-watering, and increasing total seed number and grain yield in maize under drought stressGreenhouse pot experiment with drought and recovery (re-watering) assays(Van Nguyen et al., 2022)
Chemical primingSeed priming with 2% KCl (2–10 h) improved cob yield under drought in the open-field trial, whereas most other priming agents, durations, and concentrations had no significant effects on the measured growth, physiological, or yield traitsOpen-field and screen-house drought trials(Radda et al., 2024)
Chemical priming (foliar)Foliar application of glycine betaine (GB; 11.5 g L-¹) was the most effective treatment for improving drought tolerance, increasing grain yield (+60.49%), biological yield (+41.10%), free proline (+57.08%), total soluble sugars (+61.23%), and relative water content (+23.42%). Salicylic acid (SA; 140 mg L-¹) was most effective in enhancing APX (+91.89%), GR (+125.64%), and SOD (+23.54%) activities, whereas Zn (4 g L-¹) also improved grain yield (+19.98%) but was less effective than GB and SAControlled pot experiment (CRD); 50% field capacity drought stress(Shemi et al., 2021)
Chemical pretreatment (priming/presoaking)Optimal pretreatment concentrations were GA (10 mg L-¹), NaCl (50 mM), and PEG (15%). Priming with 15% PEG enhanced seedling shoot and root biomass, whereas presoaking with water, NaCl (50 mM), or PEG (15%) significantly increased hundred-grain weight. The authors concluded that, when immediate sowing is possible, presoaking is preferable to priming for improving yield performanceLaboratory germination, greenhouse pot, and field experiments(Tian et al., 2014)
Biostimulant seed primingPlant-based biostimulant priming produced genotype-dependent drought responses. Red chicory (RC) extract was the most effective priming treatment, increasing the number of drought-tolerant genotypes under stress. The study identified Nostrano di Storo, Marano, Mais da Polenta Chatillon, and Spinato di Mortara as relatively drought-tolerant during germination and assessed ROS accumulation together with expression of antioxidant- and drought-related genes (including MSD3.4, CAT1, and PMP3g)Laboratory soil-based germination screening with molecular analyses(Wazeer et al., 2025)
Stress primingTwo cycles of combined heat (33/25 °C) and drought (50–60% soil water-holding capacity) priming enhanced tolerance to subsequent severe combined stress by increasing antioxidant enzyme activities (SOD, POD, CAT, GR, APX), promoting osmolyte accumulation (soluble sugars and proline), and reducing oxidative damage (O2-, MDA, and membrane injury index, MII). ROC analysis identified SOD and POD as reliable indicators of heat stress (AUC 0.94–0.97), GR and soluble sugars (SS) as indicators of drought stress (AUC 0.92–0.96), and SOD, GR, and proline as indicators of combined heat and drought stress (AUC 0.91–0.96)Controlled growth chamber pot experiment(Ru et al., 2023)
Stress primingTwo cycles of drought–rewatering induced a super-compensation effect, increasing photosynthetic rate (Pn, +10.12%), stomatal conductance (Gs, +5.61%), proline (+343.49%), soluble protein (+26.12%), and root length (+21.05%). Repeated drought–rewatering enhanced drought adaptability through improved antioxidant defense (SOD and POD), osmotic regulation, and faster physiological recovery following rewateringRainfall-shelter pot experiment under field conditions(Gao et al., 2024)

Table 3. Molecular, metabolic, physiological, and epigenetic mechanisms underlying drought stress memory in maize.

MechanismKey FindingExperimental approachCitation
Proline metabolismProline accumulated only in green leaves of intact maize seedlings under drought stress. Accumulation required fully developed chloroplasts and systemic plant organization, was not correlated with drought resistance, and was not induced by exogenous ABA in detached leaves or callus tissuesPhysiological study using intact seedlings, detached leaves, etiolated seedlings, and callus cultures(Ibarra-Caballero et al., 1988)
Proline metabolismFoliar application of proline (30 mM) alleviated drought-induced reductions in K+, Ca2+, N, and P uptake in maize grown at 60% field capacity, with 30 mM being more effective than 60 mM in promoting nutrient accumulationPot experiment with foliar proline application under controlled water regimes (60% field capacity)(Ali et al., 2008)
Proline metabolismFoliar application of proline (30 mM) improved seed composition by increasing seed sugar, oil, protein, moisture, fiber, and ash contents. It also enhanced seed oil antioxidant quality by increasing α-, γ-, δ-, and total tocopherols, flavonoids, phenolics, carotenoids, and DPPH radical scavenging activity under drought stressField experiment with foliar proline application and seed quality analysis(Ali et al., 2013)
Proline metabolismProline accumulation in the embryo axis was directly proportional to osmotic stress intensity, with different maize hybrids accumulating different proline levels under the same water limitation. Trehalose content decreased in both the embryo axis and endosperm during germination under low osmotic potential, suggesting its utilization as an energy source rather than as an osmoprotectantSeed germination under PEG-induced osmotic stress(Queiroz and Cazetta, 2016)
Proline metabolismProline content in both the embryo and endosperm was higher in backcrosses than in the parental inbred lines and the drought-tolerant population (DTP). Embryo proline was higher in backcrosses with a greater proportion of exotic germplasm (BC1). In contrast, phenolic content and DPPH radical scavenging activity were generally lower in DTP than in adapted inbred lines and tended to decrease in the backcrossesSeed biochemical analysis of embryo and endosperm(Kravić et al., 2009)
Carbon–nitrogen metabolismSupplemental nitrogen (1 mM → 2 mM NO3-) upregulated genes involved in sucrose metabolism (ZmSPS1, ZmSuSy1, ZmINVs, ZmSUT2, ZmSTP2, ZmSUC2, ZmSWEET14) and starch metabolism (ZmSS1, ZmAGPase1, ZmAMY1, ZmBAM1), increased soluble sugars, sucrose and starch accumulation, enhanced photosynthetic activity, and promoted spatial carbon partitioning across leaves, leaf sheath, and rootsHydroponic experiment with supplemental nitrogen, biochemical assays, spatial carbon analysis, and qRT-PCR(Amoah et al., 2026)
PEPC regulationFirst full-length cDNA cloning and characterization of maize root-form PEPC. Compared with the C4-form enzyme, root-form PEPC exhibited ≤1/10 the Km for PEP and Mg2+, ~1/2 the Km for HCO3-, 3.6-fold greater sensitivity to L-malate inhibition (Ki 0.12 vs 0.43 mM), lacked activation by glucose-6-phosphate and glycine, and phosphorylation reduced L-malate sensitivityFull-length cDNA cloning, recombinant expression, and enzyme kinetic characterization(Dong et al., 1998)
PEPC regulationLight-dependent phosphorylation of maize C4-form PEPC at Ser-15 is mediated by PEPC-protein kinase (PEPC-PK). Phosphorylation is dependent on light intensity, and the PEPC-PK gene had not yet been identified at the time of the studyPEPC-protein kinase purification, kinase assays, and antibody-based phosphorylation detection(Ueno et al., 1998)
PEPC regulationLight activation of PEPC kinase and PEPC does not require a functional Calvin cycle. In the Rubisco-deficient bsd2-m1 maize mutant, which lacks appreciable carbon fixation, PEPC sensitivity to malate inhibition decreased and PEPC kinase activity increased with increasing light intensity, similar to wild-type plantsRubisco-deficient mutant analysis, enzyme assays, immunoblotting, and PEPC kinase activity measurements(Smith et al., 1998)
PEPC regulationModerate leaf dehydration affects PEPC activity/regulation similarly across three C4 grass subtypes (NADP-ME, NAD-ME, PEPCK); PEPC phosphorylation state (judged by L-malate inhibition) increases with water deficit in all three species, potentially promoting CO2 assimilation under stress; changes in decarboxylases are small and species-specificComparative drought experiment with enzyme activity assays and PEPC phosphorylation analysis (L-malate inhibition assay)(Carmo-Silva et al., 2008)
PEPC regulationThe phosphomimic maize PEPC mutant (S15D) exhibited a lower Km (higher affinity) for PEP than the wild-type enzyme while maintaining similar allosteric regulation, including activation by glycine and inhibition by L-aspartate and L-malateSite-directed mutagenesis, recombinant protein expression, and enzyme kinetic analysis(Das et al., 2020)
Transcriptomics/Histone regulationRNA-seq revealed that drought-tolerant genotype-specific DEGs were enriched in glycolysis/gluconeogenesis, osmotic regulation, ROS scavenging, transport, cell wall modification, and defense pathways, whereas susceptible genotype-specific DEGs were enriched in photosynthesis, histone, and carbon fixation pathways. The study also identified 428 previously reported lncRNAs, of which ~22% were putative transposable element-associated lncRNAs (TE-lncRNAs)Comparative RNA-seq and physiological analysis of drought-tolerant and susceptible maize seedlings(Waititu et al., 2021)

10 Conclusion

Drought stress memory in maize emerges from the coordinated interaction of epigenetic regulation, metabolic reprogramming, and physiological acclimation rather than from any single mechanism. Histone modifications, DNA methylation dynamics, and transposable element-associated regulatory networks establish the epigenetic framework that reprograms drought-responsive gene expression, driving metabolic adjustments and physiological acclimation that ultimately enhance drought resilience. These epigenetic processes are reinforced by metabolic adjustments, including proline accumulation, carbon–nitrogen reallocation, and sustained photosynthetic competence, which collectively enhance stress resilience. Among current translational approaches, seed priming provides the most immediately applicable strategy for exploiting stress memory, with CaCl2 osmopriming showing the strongest evidence under field conditions. However, the molecular basis linking priming-induced phenotypes to stable epigenetic memory remains insufficiently resolved. Addressing this gap will require integrated biochemical, phosphoproteomic, and cell-type-specific multi-omics studies, together with rigorous multi-environment field validation. Such efforts will facilitate the development of maize cultivars and management strategies that exploit endogenous stress memory to improve drought resilience under increasingly variable climatic conditions.

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Footnotes

Edited by: Claudia Cocozza, University of Florence, Italy

Reviewed by: Temesgen Assefa Gelaw, Debre Birhan University, Ethiopia

Mujo Hasanović, University of Sarajevo - Institute for Genetic Engineering and Biotechnology, Bosnia and Herzegovina

Statements

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding

The author(s) declared that financial support was not received for this work and/or its publication.

Author contributions

BQ: Resources, Data curation, Writing – review & editing. AL: Supervision, Writing – review & editing. ZD: Supervision, Writing – review & editing. LP: Methodology, Validation, Project administration, Conceptualization, Supervision, Writing – original draft, Visualization, Writing – review & editing.

Acknowledgements

The authors acknowledge the use of PaperPal and Grammarly for language polishing and proofreading. All content has been reviewed and approved by the authors.

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Citation

Quyoom, B., et al. (2026). Epigenetic and metabolic regulation of drought stress memory in maize: from molecular mechanisms to field-applicable priming strategies. Frontiers in Plant Physiology, Volume 4. https://doi.org/
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4 - 2026

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Copyright © 2026 Quyoom, Lone, Dar and Peer.

License: https://creativecommons.org/licenses/by/4.0/

*Correspondence: Latif Ahmad Peer

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