Engineering resilience in woody plants: multi-omics, genome editing, and microbiome strategies to boost abiotic stress tolerance

Abstract

Woody plants are critical to human well-being, serving as major sources of biomass and increasingly recognized as promising biofuel resources. They contribute to climate regulation and act as long-term carbon sinks, while also mitigating pollution, flooding, and noise, and providing essential habitats for wildlife. However, recent climatic extremes have underscored the vulnerability of woody species to abiotic stress. In this review, we propose a conceptual framework for stress-adapted woody crops that links physiological responses to resilience biomarkers and outlines strategies to enhance abiotic stress tolerance. We synthesize findings on the sensing structures, physiological networks, and molecular dynamics of woody plants under environmental challenges. Mechanisms of resistance and recovery are examined at both the organismal and cellular levels. We further discuss the integration of genomics, systems biology, and genome-editing technologies to develop climate-resilient woody crops. While many of these emerging tools remain underutilized, their potential is greatly amplified when combined with machine learning-based analyses of genomic data, offering a roadmap for engineering stress-resilient traits and implementing actionable “therapeutic” frameworks. This review highlights recent advances and proposes future directions for improving woody plant performance under abiotic stress.

1 Introduction

The foundational components of forests and various ecosystems on our planet comprise woody plants, encompassing trees, shrubs, and lianas. These long-lived organisms play a pivotal role in sustaining a substantial portion of Earth’s terrestrial biodiversity, serving as vital habitats and food sources for a wide range of microbes, epiphytes, and both invertebrate and vertebrate species (Crowther et al., 2015; Rogers and McAvoy, 2018). Throughout human history, billions of people have relied on trees and shrubs for essential resources such as shade, food, fuel, medicine, and tools, while also contributing to watershed maintenance and climate regulation (Beech et al., 2017). Consequently, woody species hold immense importance from scientific, ecological, economic, social, cultural, and aesthetic perspectives (Watson et al., 2018).

Environmental habitats are often characterized by a primary abiotic constraint that predominantly influences plant performance. Although woody plants generally exhibit low absolute poly-tolerance to dual stressors (Laanisto and Niinemets, 2015), recent research indicates that the degree of poly-tolerance is significantly affected by the interaction with additional environmental stressors (Laanisto and Niinemets, 2015; Puglielli et al., 2023). This highlights the importance of viewing poly-tolerance strategies as relative and dynamic trait rather than absolute one (Puglielli et al., 2021b). In natural ecosystems, where multiple abiotic (and biotic) stressors co-occur, plant performance thus emerges from intricate environmental interactions rather than single-factor effects (Laanisto and Niinemets, 2015).

Abiotic stressors —such as high temperatures, drought, flooding, and salinity—represent major constraints to plant growth and productivity (Vaughan et al., 2018; Rankenberg et al., 2021). These pervasive environmental pressures profoundly affect the distribution, morphology, and function of plant species, particularly for sessile organisms such as woody plants. As perennial and long-lived species, woody plants continually modulate their strategies for resource acquisition, allocation, and conservation in response to environmental fluctuations (Leotta et al., 2023; Puglielli et al., 2023). Accordingly, their adaptive responses to abiotic stress in natural ecosystems reflect a long-term integration of diverse environmental signals, positioning woody plants as valuable models for studying plant responses to multiple abiotic stressors (Puglielli et al., 2021b).

A major challenge of the post-genomic era is understanding the function of genes within complex biological systems. Although many gene functions remain uncharacterized, their roles can often be inferred their interactions with known components, enhancing our systems-level understanding of plant biology. High-throughput omics technologies—including genomics, transcriptomics, proteomics, and metabolomics—have accelerated the discovery of novel genes and their roles in stress responses. Furthermore, decoding genotype-to-phenotype interactions requires comprehensive genome-scale network reconstructions that capture the dynamic complexity of cellular processes. As these integrative approaches continue to evolve, they not only deepen our understanding of stress-responsive networks but also provide a foundation for designing strategies that translate molecular insights into applied outcomes. Building upon these advances, a conceptual framework is proposed to illustrate how physiological responses, resilience biomarkers, multi-omics data, genome editing, and microbiome engineering can be integrated into a unified strategy for developing stress-resilient woody crops (Figure 1). Within this framework, physiological and biochemical traits represent measurable indicators of adaptation, while multi-omics approaches—including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics—provide comprehensive insights into the molecular mechanisms that regulate these responses.

Figure 1

Because single omics analyses often fail to capture the complexity of stress adaptation, integrated multi-omics approaches are increasingly used to connect molecular layers and identify key genes, proteins, and metabolites involved in tolerance pathways (Singh et al., 2024; Varadharajan et al., 2025). Supported by bioinformatics, systems biology, and machine learning (ML) tools, such integration enables functional annotation, network reconstruction, and discovery of biomarkers or targets for crop improvement. Finally, genome editing technologies [e.g., CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated protein)] and microbiome engineering translate these discoveries into practice, enabling precise manipulation of plant and microbial systems to enhance resilience and resource-use efficiency (Zhang et al., 2024; Srikanth et al., 2025). Together, these interconnected layers form a comprehensive systems biology strategy for the rational design of climate-resilient woody crops.

In this review, we provide an overview of recent advances in transcriptomic, metabolomic, proteomic, and integrated multi-omics approaches for investigating the responses of woody crop species to abiotic stress. We emphasize key perspectives, offered by systems biology and omics-enabled research, particularly those elucidating how woody plants perceive, respond to, and adapt under environmental stress conditions.

2 The woody plants physiologic system: sensing structure and network

Plants, as highly sensitive and adaptive organisms, continuously engage in a competitive struggle for environmental resources, involving both above- and below-ground components. They possess a remarkable capacity to evaluate their surroundings and make energy-efficient decisions to accomplish specific physiological tasks (Khan et al., 2018; Imran et al., 2021). Through sophisticated strategies that optimize resource acquisition, plants demonstrate the ability to differentiate self from non-self and adjust their behavior based on environmental cues (Khait et al., 2019; Ninkovic et al., 2021).

Like all long-lived species, woody plants must make numerous decisions throughout their lifespan, many of which are governed by environmental inputs. Abiotic stressors such as nutrient deficiency, water scarcity, temperature extremes, and heavy metal toxicity can severely disrupt plant physiology (Skalak et al., 2021; Xu et al., 2022). Plants respond to such stimuli at both the cellular and organismal levels, integrating signals that coordinate overall growth and developmental processes (Lamers et al., 2020; González Guzmán et al., 2022). These responses are mediated through intricate signaling networks that detect and decode environmental messages (Figure 1). Although the plasma membrane is generally regarded as the primary site for “cellular decision-making,” signal perception and integration also occur across multiple intracellular locations (Kaur et al., 2019). Key organelles such as the cell wall, chloroplasts, mitochondria, endoplasmic reticulum, and peroxisomes significantly contribute to the sensing of environmental cues, including abiotic stressors (Zhu, 2016; Zhang et al., 2018). The physiological responses of woody plants to abiotic signals, along with associated downstream signaling events, have been extensively documented (Fernández-Escobar, 2019; Gao et al., 2019; Puglielli et al., 2021a, 2023; Yao et al., 2021). However, the precise mechanisms underlying the initial perception of such signals remain elusive. All cues—abiotic or otherwise—require interpretation to be distinguished from non-informative molecules (noise) and recognized as components of meaningful messages (Witzany, 2006; Imran et al., 2021). These interpretations, executed by the plant, may result in either effective or ineffective responses. When correctly decoded, the message elicits a targeted physiological adjustment; conversely, misinterpretation can lead to maladaptive or null responses. To prevent inappropriate reactions to transient signals, many plants require repeated stimulus inputs before committing resources. This behavioral pattern indicates a form of memory, where past stimuli are retained to enhance the specificity, speed, or intensity of future responses (Karban, 2021). Although plants lack a nervous system, accumulating evidence suggests they are capable of learning and memory in a functional sense.

Recent studies have proposed candidate mechanisms for the perception of various abiotic stressors (Zhu, 2016; Imran et al., 2021; Skalak et al., 2021; Xu et al., 2022). Primary sensory pathways transduce external physicochemical changes—such as fluctuations in temperature, nutrient availability, and water potential—into internal biological signals. While perception mechanisms have been partially elucidated for certain stress types, the fundamental sensors for many abiotic stimuli remain unidentified. Moreover, in the absence of well-defined ligands, the concept of an “abiotic stress sensor” remains ambiguous. Future research is essential to elucidate the molecular and structural basis of abiotic signal perception and sensing in woody species.

3 Physiological, metabolic, and molecular responses of woody plants to abiotic stresses

Woody plants initiate a suite of physiological, metabolic, and molecular responses when subjected to abiotic stressors such as drought, salinity, extreme temperatures, and heavy metal pollution. These stressors influence key processes including photosynthesis, ion homeostasis, and hormone signaling, which in turn modulate gene expression. Collectively, these responses manifest at both the genotypic and phenotypic levels (Table 1) (Lukatkin et al., 2017; Li et al., 2023). Abiotic stressors—non-living environmental factors that negatively impact plant growth and productivity—pose significant challenges to woody plants. Among the most detrimental are drought, salinity, and high temperatures (Krasensky and Jonak, 2012; Li et al., 2023). Woody plants respond to such stresses through morphological, physiological, and metabolic adjustments, which may include tissue injury, altered anatomy, inhibited germination, reduced vegetative and reproductive growth, premature senescence, and in severe cases, mortality (Lobo et al., 2022).

Photosynthesis is particularly sensitive to environmental stress. In response to drought and salinity, stomatal closure serves to minimize water loss and enhance water use efficiency; however, this action also impairs gas exchange and disrupts the balance between photosynthesis and photorespiration. The efficiency of photosystem II (PSII) is closely tied to leaf water status (Ahmad and Wani, 2014; Li et al., 2023). Sub-lethal heat stress can inhibit photosynthesis by destabilizing membranes and inducing protein denaturation and aggregation (Zhou et al., 2023). Drought-related decreases in Rubisco content and alterations in membrane-bound protein composition further compromise carbon assimilation (Durand et al., 2011). Both stomatal and metabolic limitations are implicated in reduced photosynthetic performance under abiotic stress (Ahmad and Mohd, 2014). Components such as ATP synthesis, RuBP regeneration, and Rubisco activity are particularly vulnerable (Mizrachi and Myburg, 2016; Lobo et al., 2022).

The reprogramming of metabolic pathways to establish a new physiological equilibrium is essential when environmental stress conditions perturb plant growth. This adaptive process, commonly referred to as acclimatization, is a hallmark of stress tolerance. From a metabolomics standpoint, acclimatization involves at least three distinct classes of compounds (Le Gall et al., 2015; Lobo et al., 2022). The first group comprises protective substances that assist directly in stress mitigation, such as antioxidants and osmoprotectants. The second group includes metabolic byproducts that accumulate as a result of disrupted homeostasis under abnormal growth conditions. The third group consists of signal transduction molecules—such as phytohormones and secondary metabolites—critical for initiating and sustaining stress-responsive signaling cascades (Lobo et al., 2022; Zandalinas et al., 2022).

Among the principal metabolites involved in abiotic stress responses are sugars such as sucrose, trehalose, and fructan; polyols such as mannitol, myo-inositol, and sorbitol; and amino acids such as proline and ectoine. These compounds function predominantly as osmoprotectants, stabilizing cellular structures and osmotic balance under extreme conditions including salinity, drought, and desiccation (Zandalinas et al., 2022). Moreover, low temperatures are known to influence gene expression and alter the levels of endogenous hormones and metabolites, including protective proteins and sugar content (Janmohammadi et al., 2015). In addition, small signaling molecules such as methyl salicylate, jasmonic acid (JA), and methyl jasmonate, which are synthesized in response to abiotic stress, act as systemic signals that mediate defense activation and acclimation in woody plants (Li et al., 2023).

The phenylpropanoid pathway plays a pivotal role in the woody plant defense response and is commonly activated under abiotic stress conditions. This pathway leads to the biosynthesis of lignin, a structural polymer that enhances mechanical strength and reduces permeability (Devireddy et al., 2021; Zandalinas et al., 2022). Abiotic stress frequently induces cell wall degradation, which is associated with a decrease in polysaccharide content and a concomitant increase in cell wall hydrolase activity. At the same time, the biosynthesis and remodeling of the cell wall are downregulated through the suppression of key enzymes such as phenylalanine ammonia-lyase (PAL), 4-coumarate CoA-ligase (4CL), cinnamoyl-CoA reductase (CCR), caffeate O-methyltransferase (COMT), caffeoyl-CoA 3-O-methyltransferase (CCoAOMT), trans-cinnamate 4-hydroxylase (C4H), and ferulate 5-hydroxylase (F5H) (Le Gall et al., 2015). These molecular and enzymatic changes collectively reduce cell wall expansion and cell extensibility, thereby limiting water loss and preventing structural collapse under adverse environmental conditions (Zandalinas et al., 2022).

Woody plants possess intricate and interconnected molecular mechanisms to counteract or mitigate the damage induced by unfavorable environmental conditions. Central to these adaptive responses are transcription factors (TFs), which regulate gene expression in response to abiotic stress by binding to cis-regulatory elements within the promoter regions of target genes or other functional modular DNA structures. Plant genomes harbor a rich repertoire of TF families, including dehydration-responsive element binding proteins (DREB), basic region/leucine zipper motifs (bZIP), APETALA2/ethylene-responsive element binding factors (AP2/ERF), WRKY, myeloblastosis (MYB), and no apical meristem (NAC)/NAM-ATAF-CUC (NAC) proteins. These TFs act either directly or indirectly to coordinate diverse stress response pathways (Banerjee and Roychoudhury, 2017).

Among these, WRKY TFs are particularly significant in regulating responses to salt-induced stress. For instance, Xu et al. (2018) reported the regulatory relevance of WRKY proteins in salt tolerance mechanisms. In a study by Jiang et al. (2021), the WRKY gene PalWRKY77 was isolated and characterized in Populus alba var. pyramidalis. Under salt stress conditions, PalWRKY77 expression was repressed, resulting in decreased salt tolerance. This gene was found to act as a negative regulator of the abscisic acid (ABA) signaling pathway, revealing a mechanism in which ABA signaling suppresses PalWRKY77, thereby heightening the plant’s sensitivity to salinity stress. At the cellular level, the management of ionic homeostasis is a critical factor in plant resilience to salinity. This involves several pathways, including Na⁺/H⁺ antiporters in the plasma membrane and tonoplast, cation channels, and various co-transporters, all of which are tightly regulated (Llanes et al., 2021). According to Martínez-Alcántara et al. (2015), a pivotal plant response to salinity is the maintenance of intracellular Na⁺ exclusion, thereby preserving cellular ionic equilibrium. This is accomplished through the concerted action of genes encoding plasma membrane and vacuolar H⁺-ATPases, vacuolar H⁺-pyrophosphatases, and cation/proton antiporters at both plasma and vacuolar membranes (Ma et al., 2016). These molecular components form the core of the plant’s salt stress mitigation toolkit.

High-temperature stress, another major abiotic factor, also profoundly impacts the genomic landscape of woody plants. It affects various regulatory layers including gene expression, signal transduction pathways, epigenetic modifications, genome stability, mutation rates, and the management of heat shock proteins (HSPs). These changes collectively drive alterations in both physiological and biochemical functions (Singh et al., 2022). Among the transcriptional regulators, HSFs have emerged as critical components in mediating heat tolerance. These TFs modulate the expression of heat-responsive genes either independently or in coordination with other regulatory proteins, thereby modulating plant adaptation to thermal stress. Extensive comparative analyses across species have demonstrated the structural and functional complexity of HSF families in woody plants exposed to elevated temperatures (Haider et al., 2022).

In addition to transcriptional regulation, epigenetic mechanisms—notably DNA methylation and histone modifications—play important roles in regulating stress-inducible genes under heat stress conditions. DNA methylation, involving the addition of a methyl group to cytosine residues, modulates gene responsiveness and enhances thermal stress adaptation (Sun et al., 2022a). Interestingly, plants exposed to high temperatures often exhibit reduced global methylation levels relative to unstressed controls, a phenomenon thought to facilitate flexible gene expression and enhance stress memory (Correia et al., 2013).

4 Abiotic stress and resiliency biomarker changes in woody plants

The environmental impacts of the climate crisis on plants in general, and on woody plants in particular, are unequivocal (Matyssek et al., 2017). Fluctuations in temperature and precipitation patterns—already underway and projected to intensify by the end of the 21st century due to the accelerating water cycle—are negatively affecting plant biomass, yield, and overall productivity (Raza et al., 2019). Seasonal shifts driven by altered climate variables are disrupting soil humidity and evapotranspiration rates, often leading to premature withering of plants (Raza et al., 2019). As a result, plant vulnerability to abiotic stressors such as drought, salinity, heat, and heavy metals is steadily increasing (He et al., 2018). These stressors constrain optimal plant performance by impairing growth, disturbing photosynthesis, and deregulating biochemical pathways (Chaudhry and Sidhu, 2022). The escalating severity of climate-related events underscores the urgency of deciphering plant response mechanisms at the molecular level. This complexity is particularly pronounced in woody plants—especially gymnosperms—due to their relatively unexplored genomes. Moreover, the polygenic nature of agronomically valuable traits complicates genomic characterization (Mizrachi and Myburg, 2016). In this context, biomarkers offer valuable tools to advance understanding. The identification and application of omics-based biomarkers can facilitate the assessment of molecular responses in woody plants under abiotic stress. Resilience biomarkers are measurable molecular and microbiological indicators that reflect the ability of woody plants to tolerate, adapt to, and recover from abiotic stresses. They include: i/specific stress-responsive genes and TFs (e.g., DREB, NAC, WRKY, HSP) that control protective pathways (Qian et al., 2023; Zeng et al., 2024; Wang and Xu, 2025). For instance, NAC TFs act as key regulators in networks related to stress and plant development. In woody plants, they regulate various biological processes, such as secondary wall formation, senescence, seed dormancy, and fruit ripening, mainly by regulating hormonal interactions and transcriptional cascades (Zhang et al., 2025a); ii/key metabolites such as proline, glycine betaine, and flavonoids, act as osmoprotectants and antioxidants. The phenylpropanoid pathway being essential for the development of climate-resilient crops by producing over 8,000 metabolites, including flavonoids and lignin, that contribute to tolerance against biotic and abiotic stresses (Rossi et al., 2016; Ninkuu et al., 2025); and (iii) microbiological signatures—notably rhizosphere bacterial and fungal communities—that contribute to stress mitigation through hormonal modulation and improved resource uptake (Anli et al., 2020; Toubali et al., 2020; Fassih et al., 2024; Sharma et al., 2025). In this context, these biomarkers form the basis for integrating multi-omic analyses (transcriptomic, metabolomic, and microbiomic data) with genomic engineering approaches (e.g., CRISPR/Cas-mediated gene editing) and phenotypic evaluation of resilience traits in woody plant species.

4.1 Omics approaches in woody plants under abiotic stress

Woody plants deploy a variety of molecular, metabolic, and physiological mechanisms to tolerate abiotic stresses, which can be comprehensively characterized and analyzed using omics approaches. These mechanisms include the regulation of key gene expression, the accumulation of protective metabolites, and the adjustment of physiological processes (Table 2). Advancements in next-generation high-throughput omics technologies provide unprecedented opportunities to investigate how woody plants perceive, respond, and adapt to diverse abiotic stressors. The increasing availability of multi-layered omics data—including genomics, transcriptomics, proteomics, metabolomics, and epigenomics—offers extraordinary opportunities to elucidate the molecular mechanisms underlying stress tolerance. Sequencing data generated through these platforms enable detailed insights into how vital physiological and metabolic processes are molecularly modulated under stress conditions (Jamil et al., 2020; Saleem et al., 2025). Multi-omics integration combines datasets from multiple high-throughput platforms to offer a holistic perspective of complex biological systems (Figure 1). This integrative strategy has been widely applied in crops to dissect the molecular basis of abiotic stress tolerance and accelerate the development of resilient varieties. In woody plants, such integration is particularly valuable for linking molecular-level responses to long-term adaptive traits. Notably, omics integration is most effective when applied to early plant life, such as the seedling stage, enabling the detection of early molecular responses. In Quercus ilex, a non-targeted multi-omics integration approach revealed early drought responses and allowed the identification of key transcriptional regulators (Guerrero-Sánchez et al., 2022). Multi-omics integration pipelines have emerged as powerful frameworks for uncovering regulatory interactions and adaptive pathways across molecular layers. Transcriptomic analyses based on RNA sequencing (RNA-seq) and single-molecule real-time (SMRT) Isoform sequencing (Iso-seq) have been utilized to assess drought-induced molecular alterations in Populus species (Jia et al., 2017; Zhang et al., 2019; Wang et al., 2021a). Similarly, in Vitis vinifera and Camellia sinensis transcriptomics profiling and cDNA library construction have revealed stress-responsive gene expression patterns (Zhang et al., 2017; Guan et al., 2018; Daldoul et al., 2022). At the protein level, proteomic analyses—often integrated with transcriptomics —have been used to examine adaptive responses to heavy metal stress in Populus alba, Citrus grandis, and Vitis vinifera (Szuba and Lorenc-Plucińska, 2018; Chen et al., 2021; Wu et al., 2021). Similar integrative strategies have been applied in oil palm under drought and salinity stress, where combined transcriptomics, proteomics, and metabolomics identified key enzymes and metabolites highly correlated (r ≥ 0.9) with cysteine and methionine metabolism pathways (Bittencourt et al., 2022; Leão et al., 2022). It has been reported that the combination of transcriptomic, proteomic, and metabolomic data has enabled the identification of enriched protein hubs and key candidate genes underlying drought-sensitive ‘quantitative trait loci (QTL) hotspots’ (Kudapa et al., 2024). This illustrates that multi-omic integration not only clarifies molecular responses, but also identifies potential regulatory networks and biomarkers for stress tolerance. The integration of multi-omic data allows us to understand more precisely the regulatory networks and physiological and molecular mechanisms that regulate woody plants’ responses to abiotic stress.

The integration of data from different omic layers, particularly transcriptomic and metabolomic data, is a major challenge in the study of stress responses in woody plants. Differences in nature, scale, and temporal dynamics between gene expression and metabolic profiles complicate the establishment of direct causal relationships between genes, biochemical pathways, and observed phenotypes (Acharya and Mukhopadhyay, 2024). Variations in signal intensity, metabolite coverage, or normalization between analytical platforms add biases that may limit inter-study comparability (Zhang, 2024). In addition, woody tissues exhibit marked cellular heterogeneity and metabolic gradients related to xylem and phloem differentiation, making the interpretation of integrated data particularly complex (Hsieh et al., 2025). To overcome these obstacles, advanced statistical and computational approaches, such as Partial Least Squares (PLS), which identifies the most correlated variables between heterogeneous datasets, and the DIABLO method (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies), designed for supervised multi-block integration and biomarker discovery, are increasingly being used to robustly link transcriptomic and metabolomic signatures to stress tolerance mechanisms (John Martin et al., 2024). These methods, combined with ML algorithms, enable the identification of co-regulated gene and metabolite modules, paving the way for a systemic and integrated understanding of woody plant adaptation to adverse abiotic conditions.

4.2 Molecular control of abiotic tolerance mechanisms in woody plants

4.2.1 Drought stress

Transciptomic profiling enables the dissection of regulatory gene networks activated under drought stress. In Populus simonii, drought stress induced expression changes in TFs such as ERF1 and RD26, associated with phytohormone biosynthesis and reactive oxygen species (ROS) generation (Jia et al., 2017; Ali et al., 2025). In Populus trichocarpa, drought-induced RNA-binding proteins and differential histone H3 acetylation (H3K9ac) modifications have been reported (Wang et al., 2021a). In hybrid poplar (P. deltoides cultivars ‘55/65’ × ‘Imperial’), differentially expressed genes (DEGs) were linked to isoprene biosynthesis and ABA-dependent signaling pathways (Zhang et al., 2019). Based on these findings, recent transcriptomic studies conducted on Vitis vinifera have further reinforced the central role of ABA-regulated transcriptional networks in coordinating abiotic stress tolerance. Comparative analyses have revealed that increased expression of ABA biosynthetic and signalling genes, including NCED, PYR/PYL/RCAR, and SnRK2, promotes the activation of ABA-responsive TFs such as AREB/ABF, bZIP, and NAC (Li et al., 2021). These transcriptional regulators not only govern the expression of stress-responsive genes but also modulate secondary metabolism, particularly the biosynthesis of flavonoids and phenolic compounds, thereby establishing a functional link between stress adaptation and enhanced tolerance in woody species. Members of the AP2/ERF family (OsERF71, ZmDREB39, TkERFs, TaAP2-10) are induced at the transcriptional level by ABA or osmotic stress, highlighting their conserved role in drought tolerance (Xie et al., 2019). Furthermore, the ZmEREB160 gene has been shown to enhance drought resistance through the upregulation of the ABI2, ABI5, and DREB2A genes, key components of the ABA signalling pathway. Similarly, in Pinus massoniana, the expression of the PmAP2/ERF gene was modulated by exogenous ABA treatments under water stress, with PmAP2/ERF96 showing tissue-specific induction in resistant lines, suggesting that AP2/ERF genes play an important role in integrating hormonal signalling in stress adaptation (Sun et al., 2022b).

4.2.2 Salinity stress

Transcriptomic analyses in Vitis vinifera have revealed DEGs implicated in ROS scavenging, ion transport, HSP modulation, and phytohormone signaling under salt stress (Guan et al., 2018). In wild grapevine (V. vinifera subsp. sylvestris), upregulation of glycolytic and flavonoid biosynthesis pathways was observed in response to ROS overaccumulation (Daldoul et al., 2022). In Camellia sinensis, DEGs associated with polyphenol and caffeine biosynthesis suggested a potential decline in product quality under salinity. Additional DEGs were linked to galactosyltransferase, tetrapyrrole-binding, and proline, carbohydrate, and gamma-aminobutyric acid (GABA) metabolism (Zhang et al., 2017).

Further, salinity stress induces multiple post-translational modifications (PTMs) in proteins, including phosphorylation, glycosylation, methylation, ubiquitination, and acylation (Benny et al., 2020; Zhang et al., 2022). Extracellular salts bind to glycosyl inositol phosphoryl ceramides on the plasma membrane, altering its permeability and triggering Ca²⁺ influx via ion channels (Kumari et al., 2021; Bachani et al., 2022; Zhao et al., 2023). This Ca²⁺ accumulation activates the salt overly sensitive (SOS) pathway, which modulates physiological and metabolic responses (Yang and Guo, 2018; Ding et al., 2020; Jiang et al., 2021). Additionally, Ca²⁺-dependent protein kinases (CDPKs) interact with calcineurin B-like proteins (CBL-CIPK complexes) to activate NADPH oxidases (e.g., RbohD), leading to H₂O₂ accumulation that functions as a diffusible signaling molecule coordinating intercellular stress responses (Bilska et al., 2019; Iqbal et al., 2020; Wei et al., 2020; Llanes et al., 2021; Ravi et al., 2023; Chen et al., 2024). It is important to note that TFs constitute a conserved regulatory layer that controls downstream gene expression under salinity conditions. In triticale, the AP2/ERF genes (TRINITY_DN567174_c7_g3 and TRINITY_DN582605_c6_g1) were significantly upregulated under saline stress conditions, highlighting their role in ROS-mediated signalling (Deng et al., 2020). Seven differentially expressed genes encoding WRKY were upregulated, consistent with the involvement of WRKY in salt tolerance in Gossypium hirsutum (Yao et al., 2011). Similarly, bHLH (basic helix–loop–helix) TFs, including ILR3 homologues, were upregulated, suggesting their conserved function in enhancing salt tolerance (Zhang et al., 2025b). The application of KEGG enrichment analysis further identified the MYB, NAC, bHLH, WRKY, and MADS TF families, indicating a coordinated network of TFs orchestrating stress adaptation (Liu et al., 2022b; Pang et al., 2024; Li et al., 2025b). Collectively, these suggest a hierarchical regulatory model: conserved Ca²⁺-dependent and ROS-mediated signalling activate central TFs, which then intervene in species-specific metabolic and developmental adjustments to optimise salinity tolerance (Kesawat et al., 2023; Yu et al., 2024).

4.2.3 Heavy metals toxicity

Multi-omics technologies applied to woody plants offer valuable insights into how these species tolerate heavy metal stress. For instance, in response to chromium (Cr) toxicity, Populus alba (white poplar) exhibited adaptive proteomic responses, including the activation of ROS-scavenging pathways, DNA repair systems, and protection of the photosynthetic apparatus (Szuba and Lorenc-Plucińska, 2018; Al-Obaidi et al., 2024). In pomelo (Citrus grandis) seedlings exposed to copper (Cu) stress, modulation of heavy metal-responsive genes was associated with reduced Cu uptake. The plants mitigated Cu toxicity by limiting vacuolar Cu release into the cytoplasm and by overaccumulating Cu-chelating compounds, such as lignin, metallothioneins, and total phenolics, thereby enhancing detoxification (Wu et al., 2021). In grapevine (V. vinifera), Cu stress induced expression of several detoxification-related genes and proteins, including the P-type ATPase (HMA5), ABC transporters, dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR), supporting Cu stress tolerance (Chen et al., 2021).

Heavy metal toxicity elicits diverse plant detoxification mechanisms, including immobilization, chelation, sequestration, and compartmentalization of metal ions into cellular organelles (Mustafa and Komatsu, 2016; Riyazuddin et al., 2021). Such stress conditions also trigger overproduction of ROS, which in turn activate antioxidant defenses and expression of stress-responsive genes, notably TFs. The WRKY TF family, one of the largest in woody plants, is characterized by a highly conserved WRKY domain (Dong et al., 2020). For example, PsnWRKY genes from P. simonii and P. nigra were upregulated under cadmium (Cd) stress (Zhao et al., 2015), highlighting their role in ROS regulation and enhanced tolerance to metal toxicity (Wu et al., 2022b).

Beyond their involvement in stress signaling, WRKY TFs have been shown to enhance photosynthetic performance under metal stress (Zhang et al., 2020b). Their expression is correlated with reduced malondialdehyde (MDA) levels in leaves—an indicator of lipid peroxidation and oxidative damage (Liu et al., 2019; Chen et al., 2023). Moreover, metal-induced accumulation of soluble sugars has been linked to the WRKY75 gene, which appears to function as a key regulator in sugar-mediated stress mitigation (Wu et al., 2022a; Cao et al., 2023). Collectively, the presence and activity of WRKY TFs in the leaves of woody plants help lower oxidative pressure (i.e., MDA and H₂O₂ accumulation), enhance antioxidative defenses, and reduce physiological damage caused by metal toxicity (Jiang et al., 2021; Wu et al., 2022a).

4.2.4 Heat stress

Small HSP (sHSPs) are universally conserved across all living organisms and play a critical role in plant thermotolerance (Yang et al., 2017; Guan et al., 2018; Waters and Vierling, 2020; Kumar et al., 2021b). In woody plants, most studies have focused on cytoplasmic class I sHSPs, which are central to the heat stress response. Functional characterization has revealed thermotolerance-enhancing roles for ThHSP18.3 in Tamarix hispida (Gao et al., 2012), RcHSP17.8 in Rosa chinensis (Jiang et al., 2020), PtHSP17.8 in P. trichocarpa (Li et al., 2016), MsHSP16.9 in Malus sieversii (Yang et al., 2017), and CsHSP17.2/CsHsfA2 in Camellia sinensis (Wang et al., 2017a; Zhang et al., 2020a). Overexpression of RcHSP17.8 has been shown to increase heat resistance, enhance proline accumulation, and decrease electrolyte leakage (Jiang et al., 2020). Similarly, PtHSP17.8 overexpression improved root elongation and survival under high-temperature conditions (Li et al., 2016). CsHSP17.2 acts as a molecular chaperone to preserve photochemical efficiency and protein synthesis, while also neutralizing ROS and activating heat-responsive (HR) genes (Wang et al., 2017a).

Recent findings also highlight the importance of class II and III cytoplasmic sHSPs in woody plants. For example, SpHSP17.3, a class II sHSP gene from Sorbus pohuashanensis, is upregulated under thermal stress (Zhang et al., 2020c; Pré et al., 2023). Regulation of sHSP expression is largely governed by HSFs. The heat shock response (HSR), coordinated by the HSF/HSP transcriptional module, represents a conserved evolutionary strategy for responding to elevated temperatures (Pal and Sharma, 2021). Heat shock elements (HSEs) in gene promoters enable rapid transcriptional responses via HSFs (Andrási et al., 2021). Among these, HSFA1s serve as master regulators, activating downstream TFs such as HSFA2 and DREB2A (Tian et al., 2020c; Albertos et al., 2022).

HSFs exert their effects primarily by regulating both HSP expression and ROS-scavenging enzymes, which are critical for maintaining protein homeostasis and oxidative balance under heat stress (Tian et al., 2020c; Kumar et al., 2021a). In Populus euphratica, PeHSF directly binds HSE motifs in the promoter of PeWRKY1, establishing a transcriptional feedback loop to fine-tune heat responses (Zang et al., 2019). Interestingly, HSPs can also interact directly with HSFs to modulate their stability and activity, further reinforcing this regulatory network.

Epigenetic mechanisms such as DNA methylation, histone modifications, and mRNA processing play a vital role in modulating gene expression and maintaining genomic stability under heat stress (Liu et al., 2015). DNA methylation, specifically the formation of 5-methylcytosine via cytosine methylation, is one of the most studied epigenetic responses. Under heat stress, plants often exhibit reduced global methylation levels, which is associated with enhanced transcriptional plasticity (Sun et al., 2022a). For example, in P. simonii, methylation levels dropped from 38.93% at 25 °C to 28.61% at 42 °C (Ci et al., 2015). These epigenetic shifts likely contribute to dynamic gene regulation and thermotolerance.

4.3 Applications of machine learning in predicting stress responses and genomic design

Machine learning (ML) is now establishing itself as a key tool for studying and improving woody plants, offering new insights into understanding and predicting their responses to abiotic and biotic stresses. This tool is transforming omics data analysis by enabling the modeling of complex physiological responses of plants to abiotic and biotic stresses, identifying functional loci, and optimizing gene editing tools. By mobilizing approaches that integrate multi-omic data—including genomic, transcriptomic, metabolomic, and epigenomic data—from woody plants such as Populus, Eucalyptus, and Pinus. ML models can be used to model the tolerance and sensitivity of genotypes to various environmental stresses with greater accuracy than traditional statistical methods (Xu et al., 2021; Chandrashekar et al., 2024). These approaches are particularly effective for identifying loci with complex effects and for genomic prediction of quantitative traits such as growth, wood density, and resistance to environmental stresses. Recent work on Populus deltoides has shown that integrating ensemble algorithms and data from GWAS/QTL mapping significantly improves the detection of adaptive loci and the performance of genomic selection models (Zhou et al., 2025). At the same time, the application of ML shows promise in the design of genetic editing tools, particularly for predicting the efficacy and specificity of CRISPR guide RNAs, using models that exploit sequence and chromatin structure features. This highlights the importance of considering a wide range of sequential and genomic features in order to improve prediction models (Elkayam et al., 2024; Bhardwaj et al., 2024). Together, these advances illustrate the potential of ML to integrate omic and genetic information in a mechanistic and applied perspective, paving the way for innovative strategies for improving and managing woody plants in the face of environmental change. However, future work will focus on refining these models and exploring their applicability in different genomic contexts.

5 Approaches to conceptualizing and improving woody plants’ abiotic stress

To meet the growing challenges posed by climate change and global food insecurity, recent plant breeding programs have increasingly focused on enhancing stress tolerance—particularly abiotic stress tolerance—in both herbaceous and woody plants. This focus is critical for harnessing non-arable lands and expanding the cultivation frontier to support a rapidly growing population. Research in this domain is essential for achieving sustainable, resilient, and productive agriculture.

Harnessing genetic resources for abiotic stress tolerance in woody plants involves a combination of conventional breeding techniques—such as hybridization, clonal selection, and pedigree analysis—alongside advanced molecular breeding tools, including marker-assisted selection (MAS) and QTL mapping. Furthermore, cutting-edge genome editing tools such as CRISPR/Cas9, and platforms derived from Next-Generation Sequencing (NGS), offer new avenues for precise genetic improvement. Complementarily, understanding the interaction between woody plants and their associated microbiomes opens up possibilities for engineering microbial consortia that can be integrated with gene-editing strategies to further enhance abiotic stress tolerance (Table 3).

5.1 Genome editing events conferring tolerance to abiotic stress in woody plants

Gene editing has emerged as a transformative molecular tool for dissecting gene function and engineering targeted genetic modifications. It enables precise manipulation of alleles to introduce beneficial variation, and can be applied to modify traits related to abiotic stress tolerance in woody plants. Major genome-editing platforms include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the widely adopted CRISPR/Cas systems.

ZFNs consist of a zinc finger DNA-binding domain fused to the non-specific cleavage domain of the FokI endonuclease (Carroll, 2011; Chivukula et al., 2025). These proteins create site-specific double-stranded breaks (DSBs) and introduce mutations during DNA repair. ZFNs have been successfully used to target endogenous genes in woody species such as Populus and Malus domestica (apple) to generate transgenic lines (Lu et al., 2016; Dullah et al., 2024; Chivukula et al., 2025). However, the practical application of ZFNs is limited due to off-target effects, complex design protocols, and high cost.

TALENs, the second generation of gene editing tools, are derived from the TALE proteins of the bacterial genus Xanthomonas. These proteins naturally function as transcriptional activators during pathogenesis. TALENs consist of TALE DNA-binding domains linked to FokI, and offer higher specificity and editing precision than ZFNs (Lu et al., 2016; Thapliyal et al., 2023). Despite their efficiency, TALEN application in plants is constrained by their large size and high delivery costs.

The CRISPR/Cas system, originally discovered in bacteria and archaea as a defense mechanism against viruses, represents the third and most advanced generation of gene editing. CRISPR allows for highly efficient, cost-effective, and precise editing of target sequences using custom-designed guide RNAs (gRNAs). The CRISPR/Cas9 system, in particular, has shown superior editing capability in comparison to ZFNs and TALENs (Imran et al., 2021; Chang, 2022; Min et al., 2022; Thapliyal et al., 2023; Bhardwaj et al., 2024). Given the heterozygous genomes and extensive single nucleotide polymorphisms (SNPs) found in woody perennials, CRISPR enables targeted mutagenesis at multiple loci through multiplexed gRNAs to generate biallelic mutants (Tsai and Xue, 2015; Thapliyal et al., 2023).

Recent classifications divide CRISPR-Cas systems into two major classes, six types, and 33 subtypes, each with unique features and target recognition mechanisms (Makarova et al., 2022; Alqahtani et al., 2024). CRISPR/Cas9 functions by employing the Cas9 endonuclease, directed by a gRNA, to introduce DSBs at precise genomic loci. Variants such as dCas9 (catalytically inactive Cas9) tethered to transcriptional activators or repressors allow modulation of gene expression without altering DNA sequence (Thapliyal et al., 2023; Cai et al., 2023). Such systems are also being explored for epigenetic editing, enabling modification of gene expression patterns without permanent genetic changes (Wang et al., 2016; Kovalev et al., 2025).

In addition, CRISPR/SaCas9 enables targeted allele replacement or recombination, while newer tools such as CRISPR/dCas9-Spo11 facilitate intra-chromosomal recombination and precise genome restructuring without segregation drag (Sarno et al., 2017; Thapliyal et al., 2023). These innovations parallel advances seen in model systems like rice and are now being translated to woody plants to produce genetically variable lines via genome-wide insertions and deletions (indels) (Babitha et al., 2020; Thapliyal et al., 2023).

Ultimately, CRISPR-based gene editing offers a stable, efficient, and precise method for modifying gene expression in woody plants. It enables gene knock-out, gene knock-in, or cis-regulatory modulation, thereby facilitating the engineering of desirable traits such as abiotic stress tolerance (Elorriaga et al., 2014; Thapliyal et al., 2023; Erdoğan et al., 2023; Ajithkumar et al., 2025). The continued refinement and application of these tools promise to transform tree breeding strategies by enabling the direct and heritable manipulation of complex traits in long-lived woody species.

5.2 Application of conventional breeding to enhance abiotic stress tolerance in woody plants

Conventional breeding approaches remain essential for generating novel genetic variation, conserving wild germplasm, and facilitating sexual hybridization between genetically diverse parental lines. Within these programs, methods such as crossing, clonal selection, hybridization, and mutation-based selection have long been employed to improve agronomically important traits, including abiotic stress tolerance.

Significant progress has been made in enhancing abiotic stress tolerance in woody plants through conventional breeding. For instance, in Germany, frost-resistant Douglas firs were developed via inter-varietal crosses between the two principal American varieties (Flachowsky et al., 2009). In Morocco, the olive cultivars “Haouzia” and “Menara” were released for commercial cultivation following rigorous clonal selection procedures (Zaher et al., 2011). In China, the variety Jinyefoxilan, derived from a cross between Olea europaea subsp. europaea var. frantoio and O. europaea subsp. cuspidata (Yunnan isolate), demonstrated enhanced abiotic stress tolerance, increased vegetative vigor, and delayed flowering compared to the female parent. These findings provide a foundation for marker-assisted breeding targeting O. europaea subsp. cuspidata (Niu et al., 2020). However, the advancement of stress-tolerant cultivars has been constrained by the prolonged juvenile phase of woody plants. Although combining desirable traits through crossing is theoretically feasible, the development of abiotic stress-tolerant cultivars remains underrepresented in current olive breeding programs. Most efforts have instead focused on yield optimization and adaptability to mechanized harvesting systems (Dutta et al., 2022). Since the 1960s, olive crossbreeding programs have emerged across several countries (Dabbou et al., 2012; Lavee, 2013; Trapero et al., 2013; Arias-Calderón et al., 2015; Ozdedmir et al., 2016), largely aiming to enhance oil content and harvestability. Only a few programs have focused on disease resistance (e.g., Verticillium wilt and Xylella fastidiosa) or on biotechnological integration (Rugini and De Pace, 2016; Rallo et al., 2018). Notably, no major initiatives have specifically targeted abiotic stress resilience.

Rootstock selection and interspecific hybridization offer alternative pathways to enhance tolerance, yet their efficiency remains constrained by the long reproductive cycles of woody crops. For example, large-scale citrus breeding programs require the screening of thousands of progenies to identify elite hybrids (Caruso et al., 2020b), underscoring the high resource demand of these strategies. Mutation breeding—whether spontaneous or induced through agents such as ethyl methanesulfonate (EMS), gamma rays, or UV—has contributed to generating variability and occasionally improving abiotic stress tolerance (Khah et al., 2024). However, its success is often limited by the recessive nature of induced mutations and the complexity of polygenic stress-response traits (Van Harten, 1998; Khah et al., 2024).

In the genomics era, these conventional approaches are being transformed and complemented by molecular and computational tools that enable a more predictive and efficient breeding process (Table 3). Recent advances in pan-genomics allow exploration of genetic diversity beyond a single reference genome, uncovering resistance genes and QTLs associated with both biotic and abiotic stress adaptation (Dolatabadian et al., 2022). Epigenomic studies further reveal the importance of DNA methylation and histone modifications in regulating gene expression and transgenerational stress memory, opening new avenues for the selection of beneficial epialleles (Lloyd and Lister, 2022).

Moreover, integrated multi-omics approaches—combining transcriptomics, proteomics, and metabolomics—provide a systems-level understanding of physiological responses, of plant exposed to diverse stress conditions (Wang et al., 2021b; Ge et al., 2021; Balotf et al., 2022). When coupled with precision genome editing tools such as CRISPR/Cas, these advances offer unprecedented potential to accelerate breeding cycles and generate “climate-smart” cultivars that combine productivity with resilience in the face of climate change.

5.3 QTL mapping and marker-assisted selection (MAS)

Conventional breeding methods aimed at enhancing abiotic stress resistance in woody plants often rely on phenotypic selection based on gene expression. However, these approaches are constrained by factors such as epistatic interactions, time-intensive evaluation periods, and strong environmental dependency. In contrast, selection based on phenotypic and genotypic markers offers a more efficient, precise, and rapid alternative. To enhance tolerance against abiotic stress, breeding strategies should emphasize the utilization and pyramiding of multiple resistance genes and QTLs. Marker-assisted selection (MAS) provides a powerful tool to overcome many limitations inherent in conventional breeding.

Robust genetic analysis and MAS are foundational to modern breeding programs. MAS has enabled the construction of high-density genetic maps to facilitate the detection of QTLs through marker-locus-trait associations (Ru et al., 2015). Various molecular markers—including isozymes, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), sequence-characterized amplified regions (SCARs), and single nucleotide polymorphisms (SNPs)—have been leveraged to improve selection efficiency and precision (Zaher et al., 2011; Andert and Mumme, 2015; Krueger et al., 2015; Al-Khateeb et al., 2019; Magon et al., 2023).

Although isozyme markers initially played a pivotal role in tree improvement programs (Escandón et al., 2021), DNA-based markers have since revolutionized breeding for abiotic stress tolerance in woody plants. These markers are particularly valuable in selecting for low-heritability traits. In Quercus spp., for example, SSR and SNP markers have been extensively used to investigate drought tolerance (Nagamitsu et al., 2019). The authors employed nuclear SSRs to study Quercus mongolica and Q. dentata, revealing their adaptive responses to coastal versus inland environments in northern Japan. Similarly, Pina-Martins et al. (2019) identified SNPs located within trehalase and peroxidase genes associated with drought tolerance in Quercus suber. Moreover, in Q. robur and Q. petraea, SNP markers facilitated the mapping of candidate drought-resistance genes—marking a first in linkage map construction for Quercus species (Porth et al., 2005; Sun et al., 2024).

In viticulture, where grafted propagation predominates, rootstock improvement is a key target for enhancing abiotic stress tolerance. While scion selection mainly focuses on yield and quality, rootstocks are selected for traits like drought tolerance and mineral nutrient uptake efficiency. For instance, in Vitis amurensis—a highly cold-tolerant species—17 genes involved in cold signal transduction were identified, suggesting distinct mechanisms for chilling versus freezing tolerance (Wang et al., 2021c). A genome-wide association study (GWAS) further revealed a phosphoglycerate kinase gene potentially involved in bud resistance to winter freezing (Magon et al., 2023).

QTL mapping, typically conducted using biparental populations, remains central to identifying markers linked to target traits. In Populus, Du et al. (2022) mapped 208 QTLs related to drought tolerance in an F1 population derived from the cross between ‘Danhong’ and ‘Tongliao 1’. One such marker, np2841, associated with QTL qDLRWC-LG10-1, was linked to relative leaf water content. In total, 187 candidate genes were annotated across QTL regions for five drought-related traits. Many of these candidate genes were consistent with previous functional studies in model species such as Arabidopsis thaliana (Bastiaanse et al., 2017). Two notable candidate genes—Potri.003G171300 and Potri.012G123900—were functionally annotated using the Populus trichocarpa reference genome. Furthermore, five core regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) associated with drought tolerance were identified through co-expression network analysis in Populus (Du et al., 2022).

5.4 Genetic engineering and genome editing to improve woody crops for abiotic stress tolerance

Genome editing enables precise modifications of specific genomic sequences to enhance desirable traits in crops, including tolerance to abiotic stress (Limera et al., 2017). These technologies aim to edit, delete, or replace defined DNA sequences at targeted loci within the genome. While ZFNs and TALENs have significantly advanced genome-editing efficiency, their application at novel genomic targets requires labor-intensive protein engineering or redesign, limiting their scalability and broad deployment (Cox et al., 2015). In contrast, the CRISPR/Cas system has revolutionized genome editing due to its simplicity, cost-effectiveness, and ease of customization (Yang et al., 2020). The CRISPR/Cas9 system functions by introducing DSBs through the endonuclease Cas9 guided by a synthetic single-guide RNA (sgRNA) that binds a complementary genomic region (Concha and Papa, 2022). These breaks are repaired via non-homologous end joining (NHEJ) or homology-directed repair (HDR), enabling precise gene disruption or correction. CRISPR/Cpf1 (also known as Cas12a) has emerged as a more efficient alternative to Cas9 in some systems due to its smaller size and distinct protospacer adjacent motif (PAM) recognition (Gong et al., 2021).

CRISPR-based targeted mutagenesis is now actively employed to improve abiotic stress tolerance in woody plants (Riaz et al., 2021; Jiang et al., 2021; Clemens et al., 2022; Thapliyal et al., 2023) For instance, in grapevine, the Epidermal Patterning Factor-Like 9 (EPFL9) gene—which regulates stomatal development—was disrupted using CRISPR/Cas9. This modification led to reduced stomatal density in gene-edited lines, thereby enhancing intrinsic water-use efficiency and highlighting the potential of stomatal density manipulation for climate resilience in perennial species (Clemens et al., 2022). In another study, VaPAT1 (Phytochrome A Signal Transduction 1) was shown to mediate cold tolerance in grapevines by modulating jasmonic acid (JA) biosynthesis. CRISPR/Cas9 knockouts of VaPAT1 impaired cold responses, confirming its regulatory role (Wang et al., 2021c). Similarly, the cold-responsive VaDof17d gene—part of the DNA-binding with One Finger (Dof) family—was edited via CRISPR/Cas9. The mutant plants exhibited decreased cold tolerance and reduced raffinose accumulation under stress, suggesting a direct link between Dof gene function and sugar-mediated cold acclimation (Wang et al., 2021c). CRISPR/Cas9 has also been instrumental in elucidating salt stress pathways in poplar. PalWRKY77, a member of the WRKY transcription factor family, was disrupted using CRISPR/Cas9, resulting in enhanced salt tolerance in poplar seedlings (Jiang et al., 2021). Normally, PalWRKY77 suppresses ABA-responsive genes and alleviates ABA-induced growth inhibition, rendering plants more salt-sensitive. Its disruption leads to elevated ABA signaling, conferring improved stress responses.

Additionally, epigenetic regulation has been targeted to enhance drought tolerance. The AREB1-ADA2b-GCN5 protein complex has been implicated in histone acetylation-mediated gene activation under drought conditions in Populus spp. Using CRISPR/Cas9, Zhou et al. (2020) knocked out PdNF-YB21, a gene encoding a subunit of the NF-Y transcription factor complex, which led to diminished root growth and reduced drought resistance. Conversely, overexpression of PdNF-YB21 enhanced root development and drought tolerance, underscoring its critical role in drought adaptation mechanisms in poplar. A summary of gene editing strategies applied to enhance abiotic stress tolerance in woody plants is presented in Table 4. It connects the targeted genes to specific biomarkers and experimental outcomes, showing how gene editing approaches translate into measurable improvements in stress resilience.

These studies collectively demonstrate that CRISPR-based genome editing holds transformative potential for understanding gene function and accelerating the development of woody crops with enhanced resilience to abiotic stress. The application of these tools in long-lived perennials is poised to reshape breeding strategies by enabling precise, heritable, and rapid improvements in stress tolerance traits.

Despite the recent advancements in CRISPR/Cas technologies for genetic improvement in crops, several limitations remain that hinder their widespread application in woody plants (Wang et al., 2022). The most commonly used enzyme, Streptococcus pyogenes Cas9 (SpCas9), requires a protospacer-adjacent motif (PAM) sequence—specifically 5’-NGG-3′—directly adjacent to the 20-nucleotide target site. This PAM requirement restricts editing efficiency by limiting targetable genomic regions (Wang et al., 2022). Although targeted mutagenesis aims to disrupt genes in a sequence-specific manner, overcoming PAM dependency remains a significant technical challenge. In woody forest species, applying CRISPR/Cas genome editing faces additional constraints, including extended generation times, limited availability of mutant resources, and low transformation efficiency (Fan et al., 2015; Thapliyal et al., 2023; Cao et al., 2024). To improve delivery and enhance efficiency in these species, tailored vector systems must be considered. Vectors for CRISPR/Cas delivery include plasmid-based, viral, and non-viral systems, each with specific advantages and limitations (Wang et al., 2022).

Viral vectors—such as Bean yellow dwarf virus and Tobacco mosaic virus—have been used to deliver CRISPR components in plants (Varanda et al., 2021; Li et al., 2022a; Mahmood et al., 2023). However, their limited capacity to carry large genomic sequences, including Cas enzymes, and the potential to trigger plant immune responses, reduce their effectiveness in woody species. In contrast, non-viral vectors such as inorganic nanoparticles, carbon nanotubes, liposomes, peptide-based nanoparticles, and nanoscale polymeric materials offer promising alternatives. These vectors exhibit low toxicity, retain biological activity, and can traverse plant cell barriers effectively, thereby enhancing the feasibility of CRISPR/Cas-mediated genome editing in challenging plant systems (Wang et al., 2022).

Despite significant advances in cutting-edge technologies such as CRISPR/Cas9 and multi-omic approaches, their application to woody crops continues to face several structural and biological limitations: i/ the long generation cycles of trees significantly delay phenotypic evaluation, making it difficult to assess modified traits such as wood density, flowering time, or stress resistance within a short time frame. The integration of accelerated breeding programmes, including early-flowering lines, somatic embryogenesis, and in vitro screening systems, could help shorten these timeframes (Min et al., 2022; Pak and Li, 2022); ii/ transformation inefficiency remains a major obstacle, as many woody species are refractory to Agrobacterium-mediated transformation or lack effective tissue culture protocols. Advances in nanotechnology-based delivery systems, protoplast transfection, and new promoters adapted to woody species could improve transformation success rates (Cao et al., 2024; Ramakrishnan et al., 2025); iii/ beyond technical constraints, regulatory barriers and public acceptance continue to influence the practical adoption of genetically modified trees (Ghimire et al., 2023). In several regions, genetically modified organisms are subject to the same strict regulations as transgenic plants, delaying their deployment in the field (Ghimire et al., 2023); iv/ although research into genetic editing of trees is progressing favorably for certain genotypes despite current constraints, the commercialization of these trees remains a long-term prospect. Phenotypic validation of modified traits—such as wood quality, stress tolerance, or flowering behavior—will still require several years, if not a decade. Large-scale trials in various environments, combined with intellectual property considerations, regulatory approvals, and mass propagation processes, will further extend the timeline. Under the most optimistic conditions, it will likely take one to two decades before genetically modified woody crops have a significant commercial or ecological impact (Nelson, 2023); v/ the transferability of these technologies is hampered by significant interspecific genomic divergence: trees have large, highly heterozygous, and often polyploid genomes, which complicates the identification of precise targets for genetic editing (Min et al., 2022; Chen and Zhao, 2024); vi/ the scaling up of multi-omics platforms faces technical constraints, as little homogeneous biological material is obtained, and different woody tissues produce data that is difficult to combine and interpret (Schaart et al., 2021; Wang et al., 2023); vii/ species dependence remains a major obstacle: transformation and regeneration protocols vary considerably from one taxon to another, thus limiting the uniform application of CRISPR/Cas9 (Pak and Li, 2022; Thapliyal et al., 2023). These constraints slow down the transfer of results obtained on model species such as Populus or Arabidopsis to economically important species such as Eucalyptus or Quercus (Fan et al., 2015; Cao et al., 2024; Zhou et al., 2025). Recent advances in nanotechnology offer transformative potential for genome editing in woody crops. Traditional transformation systems—such as Agrobacterium-mediated or biolistic methods—often face challenges due to lignified tissues, low regeneration efficiency, and recalcitrance to tissue culture (Haque et al., 2018; Kumar et al., 2023a). Nanoparticle vectors, including carbon nanotubes, mesoporous silica nanoparticles, and lipid-based nanocarriers, provide a promising alternative for DNA, RNA, or CRISPR/Cas component delivery with minimal tissue damage (Demirer et al., 2019; Shehzad et al., 2025). These nanoparticles can penetrate plant cell walls without mechanical wounding, enhance transgene expression efficiency, and bypass genotype-dependent barriers (Duan et al., 2021). For example, single-walled carbon nanotubes functionalized with polyethyleneimine have enabled plasmid DNA delivery into mature leaves and somatic cells, eliminating the need for tissue regeneration (Demirer et al., 2019; Shehzad et al., 2025). Additionally, stimuli-responsive nanocarriers (e.g., pH or light-sensitive) are being designed to control release kinetics and improve genome editing precision (Khan and Mathesh, 2025). Such approaches could revolutionize transformation protocols for recalcitrant woody species like Populus, Eucalyptus, and Malus domestica, facilitating stable and transient gene editing for enhanced abiotic stress tolerance (Li et al., 2024b). Thus, nanoparticle-mediated systems address key transformation bottlenecks, offering scalable, species-independent tools for woody crop improvement.

5.5 Next,-generation sequencing-based tools to improve abiotic stress tolerance in woody plants

Developing abiotic stress-tolerant cultivars with high yields and superior nutritional quality requires a multidimensional approach that combines conventional breeding with advanced genomic tools. A comprehensive understanding of genome architecture and genetic variation is central to this effort. Prior to the advent of high-throughput technologies, genome sequencing was based primarily on Sanger sequencing, which, although accurate, was not scalable (Valencia et al., 2013; Kumar et al., 2024). The successful sequencing of Arabidopsis and Oryza sativa genomes stimulated broader efforts to sequence a wide range of crops and model species (Sun et al., 2022a).

The evolution of sequencing technologies, accelerated by computational advances, has led to NGS platforms, which are cost-effective, rapid, and scalable (Satam et al., 2023). NGS enables simultaneous sequencing of millions of DNA fragments, providing insights into genome structure, polymorphisms, gene expression profiles, and epigenetic modifications. Recent innovations have further enhanced accuracy, reduced sequencing costs, and enabled high-throughput data analysis. In tandem with automated phenotyping, NGS has revolutionized crop improvement by facilitating the identification of reference genomes, enabling genomic selection, and supporting QTL mapping and genotyping-by-sequencing (GBS) for marker-assisted breeding (Singh et al., 2022).

NGS has been applied to various woody plants. For example, Populus tomentosa was among the first non-model woody species sequenced using NGS (Chen et al., 2013). In olive (O. europaea), three chloroplast genomes were sequenced and characterized in 2020 (Niu et al., 2020). Similarly, the chloroplast genome of Plukenetia volubilis was sequenced and annotated in 2018 (Hu et al., 2018). In bamboo, which significantly suffers under abiotic stress, the availability of genomic data has allowed the classification of TF families central to stress responses (Zheng et al., 2020; Huang et al., 2021; Ashraf et al., 2022). For instance, PeLAC, a TF highly expressed in bamboo stems, was found to contain an ABA-responsive element (ABRE) in its promoter, mediating transcriptional regulation in response to ABA and gibberellic acid (GA) (Ashraf et al., 2022). Additional transporters and hormone-responsive genes linked to auxin biosynthesis and signaling—such as PhIAA, PhPIN, PhPILS, PhAFB, and PhLAX—have also been identified (Wang et al., 2017b). Moreover, the tonoplast intrinsic proteins (TIPs) in bamboo were found to enhance abiotic stress tolerance by regulating water homeostasis (Ashraf et al., 2022). In Cinnamomum migao, a combination of transcriptomics and NGS revealed key regulatory genes involved in the biosynthesis of terpenoids, compounds linked to stress mitigation. A total of 70,427 isoforms were annotated, and differentially expressed transcripts (DETs) implicated in the biosynthesis of sesquiterpenoids, diterpenoids, and monoterpenoids were identified (Ju et al., 2023). The integration of NGS into woody plant research enables deep exploration of genetic traits associated with abiotic stress responses. These genomic resources lay the foundation for gene discovery, functional genomics, metabolic engineering, and precision breeding, positioning NGS as a central tool for future improvement of stress-resilient woody crops.

5.6 Abiotic stress effects and engineering the woody plant-microbial interactions

Periods of drought, salinity, or elevated temperatures induce notable alterations in the soil microbiome due to the critical influence of moisture and temperature on microbial growth, community structure, and metabolic activity (Islam et al., 2020). Denardin et al. (2020) and Flórián et al. (2019) demonstrated that shifts in soil moisture levels significantly impact both microbial diversity and function. Moreover, temperature increases during drought episodes have been associated with reductions in microbial biomass and changes in microbial abundance associated with woody plant rhizospheres. In parallel, reduced inputs of labile carbon and nitrogen into the rhizosphere under drought conditions may contribute to declines in microbial phyla such as Verrucomicrobia, Proteobacteria, and Acidobacteria (Pérez Castro et al., 2019). Drought conditions can suppress microbial respiration by up to 30%, as reported by Schimel (2018), thereby impairing soil microbial functionality.

Pérez Castro et al. (2019) also identified drought-induced shifts in the root microbiome, characterized by an increased prevalence of Actinobacteria and other Gram-positive taxa, which tend to replace the previously dominant Gram-negative populations. Among these, Firmicutes were also found to be more abundant under drought stress (Chodak et al., 2015). The proliferation of Actinobacteria under arid conditions may be attributed to their enhanced ribosome production, as suggested by Barnard et al. (2013). In addition, Planctomycetes have been identified as one of the few Gram-negative phyla capable of tolerating drought conditions, possibly due to their unique cellular characteristics—including the absence of peptidoglycan in their cell walls, intracellular compartmentalization via inner membranes, and typically larger genomes (Buckley et al., 2006; Klimek et al., 2025).

To survive drought, soil microbes adapt by modulating their intracellular osmotic potential through the biosynthesis of compatible solutes or osmolytes. These include amino acids such as glutamine, glutamic acid, proline, and taurine, which play essential roles in protein synthesis and water retention within microbial cells during reduced soil moisture and water potential (Kakumanu et al., 2019).

Similarly, salinity exerts detrimental effects on the soil microbial community due to its associated osmotic stress, ionic toxicity, and nutrient imbalances (Mukhtar et al., 2018). Soil salinity, defined by the concentration of dissolved salts, influences both osmotic pressure and the ionic composition—particularly sodium content—of the soil exchange complex, thereby affecting microbial functionality and soil systemic stability (Yan et al., 2015; Sree et al., 2025). High salt concentrations lower the solute potential of soil water, leading to osmotic stress and cellular dehydration—a process known as plasmolysis, which can ultimately cause microbial cell death (Yan et al., 2015; Sree et al., 2025). To counteract osmotic stress, microbes and plants often accumulate osmolytes; however, the biosynthesis of these molecules requires significant metabolic energy and investment of carbon skeletons, leading to reduced microbial growth and activity (Chakraborty et al., 2020). Numerous studies confirm that salinity not only suppresses microbial activity but also alters community composition and relative abundance (Imhoff et al., 2021; Ma et al., 2024; Gong et al., 2025). Notably, fungi tend to be more susceptible to salinity than bacteria, resulting in a shift in the microbial ratio favoring bacteria in saline soils (Pérez-Jaramillo et al., 2016; Tian et al., 2024).

In addition to drought and salinity, flooding significantly influences soil microbial communities by altering soil pH, redox potential, and nutrient dynamics (Ravanbakhsh et al., 2017; Dutta et al., 2022). Grzyb et al. (2020) reported a reduction in fungal populations, including fungal pathogens, due to the anaerobic conditions created during prolonged soil saturation. Flooding conditions promote a shift in microbial dominance from aerobic to anaerobic taxa, as obligate aerobes progressively decline (Furtak et al., 2020). Furthermore, Sánchez-Rodríguez et al. (2018) observed that freshwater-induced flooding decreased the abundance of Gram-negative bacteria while increasing that of Gram-positive bacteria.

Hydrological saturation affects microbial cell integrity by facilitating the rapid influx of water, which increases turgor pressure and may lead to cell lysis (Rosenblueth et al., 2018). To adapt to fluctuating solute concentrations under flooding, bacteria regulate intracellular osmolarity and enhance cell wall rigidity. Initially, they activate aquaporins to control the influx and efflux of water and small molecules. During transient osmotic stress, potassium transporters such as Kup, KdpFABC, and TrKA are upregulated. Under sustained osmotic pressure, the proVWX-encoded ATP-binding cassette (ABC) transporter system facilitates the uptake of osmoprotectants such as glycine betaine and proline or enables the biosynthesis of glycine betaine from extracellular choline (Ajeng et al., 2020). Collectively, these results illustrate that abiotic stresses impose profound changes in the composition and functionality of soil and root microbiomes associated with woody plants. These disturbances compromise essential interactions between plants and microbes involved in nutrient acquisition, osmotic regulation, and defence activation. Understanding these stress-induced microbial dynamics provides an essential basis for the development of innovative biotechnological interventions aimed at restoring or enhancing microbial functionality. In this context, the integration of multi-omic tools and genetic editing technologies has opened new avenues for engineering interactions between woody plants and microorganisms to mitigate the adverse effects of abiotic stresses and promote sustainable resilience.

The plant microbiome, or phytomicrobiome, encompasses the complex communities of microorganisms—comprising bacteria, fungi, archaea, and protists—that inhabit different plant compartments. Plant microbiome which include growth-promoting bacteria (PGPB) such as Acinetobacter, Alcaligenes, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Clostridium, Enterobacter, Flavobacterium, Paenibacillus, Pseudomonas, and Rhizobium, plant growth promoting actinobacteria (PGPA) including Actinophytocola, Nocardiopsis, Pseudonocardia, and Streptomyces, plant growth promoting fungi (PGPF) such as Aspergillus, Fusarium, Gliocladium, Humicola, Penicillium, Phoma, and Trichoderma, and plant growth promoting cyanobacteria (PGPC) like Anabaena, Aphanothece, Calothrix, Lyngbya, Microcoleus, Nostoc, and Oscillatoria, play a critical role in plant growth and nutrition, productivity, production of growth-promoting substances, and resilience to stress, including in woody species (Panda and Das, 2024). Certain endophytic fungi exhibit strong associations with the roots of woody plants, contributing to abiotic stress alleviation and enhancing nitrogen fixation efficiency (Tian et al., 2020a; Chaudhary et al., 2021). Paenibacillus spp. have been identified as common endophytes in woody plants such as Quercus robur (Vaitiekūnaitė et al., 2021), Handroanthus impetiginosus (Yarte et al., 2022), and Eucalyptus urophylla (de França Bettencourt et al., 2021) are reported to produce indole-3-acetic acid (IAA), potentially aiding in stress mitigation. Frankia, a nitrogen-fixing actinobacterial genus, forms actinorhizal nodules and promotes growth and abiotic stress tolerance in numerous woody species including Hippophae tibetana, Alnus rubra, Casuarina glauca, and Elaeagnus angustifolia (Tian et al., 2020b). Furthermore, the microbiomes of woody plants improve stress tolerance through others specific molecular mechanisms, including 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, which breaks down ACC—a precursor of ethylene—to reduce its accumulation and mitigate the negative effects of abiotic stress on root growth, as reported by Moreno-Valencia et al. (2024) on Pine Seedlings. At the same time, the neutralization of ROS by antioxidant enzymes (such as catalase, peroxidase, and superoxide dismutase) protects plant cells from oxidative damage as reported on microbial inoculated date palm by many authors (Anli et al., 2020; Toubali et al., 2020). The biofilm formed by plant microbiome, increases physical, chemical, and biological stress resistance, and the associated extracellular polymeric substances (EPS) stabilize the soil (Panda and Das, 2024). This complex and highly structured microbial community is essential to plant and soil health. Microbiome engineering draws on these functions to design synthetic consortia combining strains with complementary functions, such as nitrogen fixation by Frankia in actinorhizal plants (Alnus, Casuarina) that enhances plant tolerance in degraded soils (Bhattacharyya et al., 2024), or PGPR such as Pseudomonas stutzeri and Bacillus subtilis in Populus, which improve growth under saline stress and ROS management (Li et al., 2025a). However, the field application of such bioinoculants faces major challenges related to the ecological stability of introduced microbiomes, host specificity that determines plant-microbe compatibility, and complex integration with genetic editing approaches (e.g., CRISPR-Cas) designed to synchronize host-symbiote functions (Jones et al., 2024; Sen et al., 2025). Still, recent advances in synthetic biology and predictive microbial ecology offer promising prospects for designing stable and adaptive microbiomes capable of supporting the resilience of woody ecosystems in the face of climate change.

Plant-associated microbes can be categorized based on their location: rhizospheric (root-associated), epiphytic (surface-dwelling), or endophytic (internal colonizers) (Compant et al., 2019; Dastogeer et al., 2020). These interactions significantly influence plant sustainability (Chaudhary et al., 2021). Understanding the plant–microbiome interface paves the way for harnessing gene-editing tools to engineer synthetic microbial consortia that enhance stress resilience.

In these interactions, microbes and their host plants often share secondary metabolite biosynthesis and terpenoid pathways, creating a direct link between microbial activity and host plant metabolomics (Adeniji et al., 2020; Chauhan et al., 2023). Although omics technologies have enabled detailed dissection of microbial diversity and host interaction pathways in woody plants, the precise regulatory mechanisms modulating plant defense in response to beneficial microbes remain incompletely understood.

In recent decades, genetic engineering technologies have been deployed to improve crop productivity by manipulating the resident microbial community. Recombinant DNA technology has played a central role in agricultural biotechnology (Wang et al., 2003; Thakor and Charles, 2025), and RNA interference (RNAi) has emerged as a potent tool to modulate gene expression post-transcriptionally. Small RNAs, including siRNAs and miRNAs, are pivotal in fine-tuning developmental processes such as branching, plant height, organ size, and inflorescence structure (Chaudhary et al., 2021).

With the advent of CRISPR/Cas9 and related gene-editing systems (Ren et al., 2022; Sen et al., 2025; Kovalev et al., 2025), genome editing has become more accessible and efficient. The Cas9 endonuclease, guided by a single guide RNA (gRNA), introduces precise double-strand breaks at targeted genomic loci, which can be exploited for insertion or deletion mutagenesis. This technology has demonstrated significant promise for agricultural applications, including the modification of plant-associated microbial traits (Chikkaputtaiah et al., 2017; Bhardwaj et al., 2024; Sen et al., 2025). These tools not only facilitate functional genomics studies at the transcriptional level but also enable targeted engineering of desired plant traits such as improved nutrient acquisition or resistance to microbial pathogens. Furthermore, genetically modified microbes developed using CRISPR-based methods can potentially overcome limitations associated with field establishment and persistence of beneficial inoculants (Qiu et al., 2019).

Nevertheless, the introduction of transgenic or genetically engineered microbes into agricultural systems remains controversial. One limitation lies in the ecological unpredictability of releasing genetically identical microbial clones, which may have limited adaptability and survivability in field conditions. Additional concerns involve horizontal gene transfer between microbial populations, which raises environmental and biosafety issues (Pradhan et al., 2024). Rigorous monitoring of genetically modified organisms (GMOs) is required to assess their behavior and persistence in agroecosystems. However, such monitoring demands substantial resources, including specialized personnel and high biosafety standards, making implementation costly. Moreover, strict regulatory frameworks and legislative bans in several countries currently restrict the widespread application of genetically modified microorganisms in open-field agriculture. Addressing these challenges requires science-driven policy reforms that balance innovation with ecological stewardship.

6 Future directions

Breeders are increasingly turning to fundamental biological sciences and advanced biotechnological tools to address persistent challenges that conventional breeding approaches have failed to fully resolve. Future breeding strategies should prioritize expanding the genetic and cytoplasmic diversity of newly developed woody plant varieties, targeting not only enhanced resistance to abiotic stresses but also to biotic stresses, especially in the context of accelerating climate change. This integrated perspective provides deeper insights into the molecular mechanisms that underlie species specificity and stress adaptation.

Ongoing advancements in molecular gene-editing technologies are enabling researchers to navigate the complexity of woody plant genomes more effectively, thereby accelerating efforts toward their genetic improvement. The current body of data and scientific knowledge highlights the promising potential of genome editing tools—particularly CRISPR-based platforms—for the efficient development of elite woody genotypes. This is especially valuable for geneticists working with classical breeding and clonal propagation methods across multiple vegetative generations. Genome editing thus represents a transformative opportunity to usher woody plant science into a new era of precision enhancement.

CRISPR-mediated gene editing holds immense potential to revolutionize the woody plant sector by conferring enhanced resistance to multiple stressors—including abiotic stress—and by facilitating the engineering of complex traits associated with yield optimization. Genetic resources can be more precisely characterized, and their adaptive traits strategically manipulated through genome editing to support the development of more resilient and productive cultivars. Beneficial alleles or allele combinations may be identified and conserved, or synthetically introduced, for future breeding programs. Moreover, superior stress-tolerant phenotypes can be created through targeted mutagenesis or allelic modifications using precision gene-editing approaches. In addition to direct sequence alterations, the physiological robustness and abiotic stress resilience of woody plants can be further strengthened through the targeted introduction of epigenetic marks and key TFs that modulate gene expression. These regulatory elements can fine-tune transcriptional responses under fluctuating environmental conditions, ultimately contributing to more stable and adaptive phenotypic outcomes.

The development of engineering strategies aimed at strengthening plant tolerance to environmental stresses is not only a scientific challenge, but also an essential lever for the sustainability of agroforestry and food systems. By improving the resilience of woody plants to abiotic stresses, these approaches contribute directly to the achievement of several United Nations Sustainable Development Goals (SDGs). In particular, they support SDG 2 (Zero Hunger) by promoting stable and sustainable crop production; SDG 13 (Climate Action), by strengthening the adaptation of ecosystems to environmental disturbances; and SDG 15 (Life on Land), through the preservation of genetic diversity and the sustainable management of forest resources. Thus, stress tolerance engineering, supported by multi-omic tools and ML, is fully in line with an integrated vision of sustainability, linking biotechnological innovation, food security, and climate impact mitigation.

Conventional selection of woody plants faces considerable challenges due to their long generation cycles, genetic complexity, and limited availability of stress-tolerant genetic material. These factors slow down and make uncertain the improvement of stress resilience, particularly in rapidly changing environmental conditions.

New technologies such as CRISPR and other genome editing tools offer faster and more precise ways to introduce beneficial traits. They can target specific genes related to drought or salinity tolerance, helping scientists develop improved varieties without the long waiting times required by traditional breeding. Integrating these technologies with omics data, AI-based trait prediction, and advanced phenotyping platforms could further accelerate the discovery of key genes for stress adaptation.

Future studies on CRISPR-modified woody plants should focus on the need to bridge the gap between laboratory results and real-world field conditions. To date, most successes in improving drought, salinity, or heat tolerance have only been demonstrated in controlled environments. However, these plants may behave differently when grown in natural, changing climatic conditions. To take this further, researchers need to conduct field trials with modified trees, use standard methods to measure their growth and stress tolerance, and monitor for any side effects over time. Regulation is also a major challenge.

Another major challenge is regulation, rules for genetically modified trees are not yet clear or consistent across countries, slowing down testing and commercialization. Future work should focus on harmonizing these rules, improving communication between scientists and regulators, and establishing systems that ensure safety and transparency. Close collaboration between researchers, environmental experts, and policymakers will be essential to integrate innovations from laboratories into sustainable agroforestry practices capable of coping with abiotic stresses.

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