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Review

Ethylene-Triggered Rice Root System Architecture Adaptation Response to Soil Compaction

by
Yuxiang Li
1,2,†,
Bingkun Ge
1,2,†,
Chunxia Yan
2,
Zhi Qi
2,
Rongfeng Huang
1,3 and
Hua Qin
1,3,*
1
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2
Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Science, Inner Mongolia University, Hohhot 010021, China
3
National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agriculture 2025, 15(19), 2071; https://doi.org/10.3390/agriculture15192071
Submission received: 8 July 2025 / Revised: 26 September 2025 / Accepted: 29 September 2025 / Published: 2 October 2025
(This article belongs to the Special Issue Crop Responses and Adaptations to Environmental Stresses: New Insights and Approaches)
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Versions Notes

Abstract

Soil compaction is a major constraint on global agriculture productivity. It disrupts soil structure, reduces soil porosity and fertility, and increases mechanical impedance, thereby restricting root growth and crop yield. Recent studies on rice (Oryza sativa) reveal that the phytohormone ethylene serves as a primary signal and functions as a hub in orchestrating root response to soil compaction. Mechanical impedance promotes ethylene biosynthesis and compacted soil impedes ethylene diffusion, resulting in ethylene accumulation in root tissues and triggering a complex hormonal crosstalk network to orchestrate root system architectural modification to facilitate plant adaptation to compacted soil. This review summarizes the recent advances on rice root adaptation response to compacted soil and emphasizes the regulatory network triggered by ethylene, which will improve our understanding of the role of ethylene in root growth and development and provide a pathway for breeders to optimize crop performance under specific agronomic conditions.

1. Introduction

Soil compaction is a common problem in modern agriculture. It causes a significant reduction in crop yields, with reductions reaching up to 30% under typical conditions [1]. The negative effect becomes more serious when combined with other stresses, such as salinity, flooding, and drought [2,3,4]. Compacted soil has higher bulk density and lower porosity. These changes restrict water infiltration and aeration in the soil, making it harder for roots to penetrate and access resources [5,6,7]. As a result, plant development is limited, and crop yield decreased. In addition to its physical effects, soil compaction also affects soil biodiversity. It reduces the diversity and activity of soil microbes and increases the risk of soil-borne diseases, leading to ecological and environmental imbalance [8,9]. To alleviate the impact of compaction, comprehensive management measures are needed, such as reducing tillage, controlled traffic farming, and subsoil management. However, these methods are costly, time-consuming, and ineffective for deeper soil layers [6,10].
Soils with high moisture are more susceptible to compaction during field tillage [11]. This makes it important to study how crops respond to such conditions. Rice (Oryza sativa), a major monocotyledonous crop and model species, is susceptible to soil compaction due to it growing in a water-saturating environment [12]. Rice is an annual cereal crop with a typical fibrous root system, which consists of seminal root, a dense mass of crown roots, and lateral roots. Crown roots arise post-embryonically from stem nodes and constitute the major root system of rice. It supports the aerial organs of the plant, facilitates water and nutrient uptake from the soil, and enhances soil exploration. The number, angle, and branching capacity of crown roots profoundly impact root system architecture and subsequent aboveground biomass accumulation. Anatomically, rice roots comprise epidermis, cortex, endodermis, and stele, with aerenchyma frequently formed in the cortex to facilitate oxygen transport under compacted or flooded soils. These morphological traits collectively endow rice root with high plasticity and adaptability to adverse soil conditions [12,13,14]. Recent studies have shown that ethylene plays a key role in rice roots response to mechanical stress [13,14]. Increased soil impedance promotes ethylene production and decreased soil aeration limits ethylene diffusion, which further triggers a complex hormone interaction network to modulate root architecture to cope with compacted soils [13,15,16]. Notably, disruption of ethylene transduction improves root penetration in compacted soils [13], providing a potential strategy for breeding rice varieties with better resistance to soil compaction. Further dissecting the genetic network involved in root adaptation in rice would contribute to stress-resilient rice breeding and provide guidance for the genetic improvement of other crops.
In this review, we summarize the recent progress on the interaction between ethylene and other plant hormones in regulating rice root system architecture (RSA) under soil compaction, and highlight the central role of ethylene in root response to soil compaction. This will improve our understanding of the molecular mechanisms involved in root adaptation and offer new strategies for breeding rice varieties with improved performance under compacted soil conditions.

2. Soil Compaction Reduces Crop Yield by Restricting Root Growth

Soil compaction refers to the phenomenon that soil particles are closely arranged under external pressure, resulting in reduced soil porosity and increased bulk density [17]. Poor soil management, such as excessive irrigation without proper drainage, can exacerbate soil compaction, especially in the topsoil [18,19]. As one of the key symbols of soil degradation, soil compaction is becoming more severe with frequency droughts and flooding events caused by climate change [20,21]. These extreme weather change the soil water balance and increase mechanical pressure on the soil, resulting in a destruction in soil structure, reduced air exchange, and slower water infiltration [10,17]. Changes in soil bio-physico-chemical properties limit the elongation and expansion of root system, thereby reducing the respiration of root system and the uptake of water and nutrients, leading to lower biomass and crop yield [17,22,23]. Soil bulk density is a typical indicator to assess soil compaction [24]. In farmland where heavy machinery is frequently used, soil bulk density can reach up to 1.6 g/cm3 [5]. This change significantly restricts the root growth space, thereby impacting the uptake of water and nutrients by plants [25]. Many studies have confirmed that inadequate rooting caused by compaction severely reduces crop yield by up to 30% [1,26,27,28]. Therefore, improving root penetration in compacted soils may reduce yield penalties under such conditions.
Optimizing RSA is an effective strategy to help plants acquire soil resources. A deeper root system with well-developed branches and a high root-to-shoot ratio is often associated with enhanced tolerance to environmental stress [29,30,31]. RSA is regulated by both internal signals and external environmental factors [32,33]. Plants attain environmental adaptive reconfiguration by dynamically modifying root spatial distribution, including factors such as root elongation rate, adventitious and lateral roots density and angle. Root mechanosensation plays a key role in root responses to compacted soils. During the process of plant root development, mechanical stimuli such as obstacles and physical trauma activate mechanosensitive ion channels. These channels control the movement of ions like Ca2+, K+, and Na+ across the cell membrane, and subsequently triggers mechanical responses through intricate signaling cascades [34,35]. In Arabidopsis thaliana, loss-of-function mutants of the ion channel gene MID1-COMPLEMENTING ACTIVITY 1 (MCA1) exhibit a complete inability to root penetration, highlighting the critical role of MCA1 in mediating the mechanical response required for soil penetration [36]. In rice, soil compaction hinders the elongation of rice root epidermal cells and promotes the expansion of cortical cells, causing short and swollen roots [13,16]. Soil compaction can also increase the crown root number by facilitating the differentiation of crown root primordia [14], leading to a dense and shallow root structure. In many cases, soil compaction induces an increase in root hair density. This morphological change enhances root penetration ability in compacted soil and reflects the plant’s environmental adaptability [37,38]. Using mutants, numerous genes involved in root responses to soil compaction have been identified (Table 1). These genes provide valuable targets and avenues for breeding rice varieties with improved resistance to mechanical stress and better adaptability to different soil conditions.

3. Ethylene Functions as a Key Signal for Root Adaption to Compacted Soils

Ethylene, a fundamental gaseous plant hormone, diffuses rapidly throughout plant tissues and plays crucial roles in root development. It inhibits root elongation, promotes root radial swelling, induces crown roots formation, and triggers the growth of ectopic root hairs. These effects resemble the morphological changes caused by soil compaction [13,14,16,48]. Ethylene is recognized by a family of receptors localized in the endoplasmic reticulum (ER). Upon ethylene binding, these receptors subsequently deactivate the Ser/Thr kinase CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1), which leads to the dephosphorylation and C-terminal cleavage of ETHYLENE INSENSITIVE2 (EIN2). The cleaved C terminus (CEND) of EIN2 then enters two cellular compartments: it migrates to the P-body to suppress the translation of the F-box proteins EIN3-BINDING F BOX PROTEIN1 (EBF1) and EBF2, and it also moves to the nucleus to activate key transcription factors EIN3/EIN3-LIKE1 (EIL1)-dependent transcription [49]. Soil compaction increases mechanical resistance and reduces soil aeration. Increased soil impedance enhances ethylene biosynthesis by upregulating the expression of ethylene biosynthesis genes, and poor aeration restricts ethylene diffusion, leading to the accumulation of ethylene in root tissues and inhibiting root growth [13,15]. Mutants of the core components of rice ethylene signaling, osein2 and oseil1, exhibit improved penetration ability in compacted soil. These results indicate that ethylene is the primary phytohormone involved in root response to soil compaction [13].
Root growth relies on the coordination of cell proliferation in the meristematic zone and cell elongation in the elongation zone [50]. Environmental stresses commonly disturb this balance by triggering adaptive remodeling, including premature cellular differentiation or a reduction in cell division activity. Ethylene functions as a central regulator in root response to soil compaction, by influencing cell division and elongation. Studies indicate that ethylene inhibits root elongation in rice by promoting auxin biosynthesis [51]. Furthermore, mutants with impaired ethylene signaling and auxin biosynthesis showed enhanced root penetration in compacted soils, suggesting that ethylene acts upstream of auxin in regulating root adaptation to compacted soil [16]. How does ethylene inhibit root elongation at the cellular level? Recent evidence suggests that ethylene directly restricts the axial extension of epidermal cells by regulating gene clusters responsible for cell wall synthesis in rice. Specially, ethylene activates OsCSLCs (1/2/7/9/10) and OsCESAs (3/4/7/9), which facilitate the deposition of xyloglucan and restrict the loosening of cellulose microfibrils, to reduce cell wall extensibility, ultimately forming a more rigid root tip structure [52]. Mechanical stress from compacted soil induces similar effects, not only mimicking the ethylene-induced inhibition of cell elongation [13], but also intensifying growth inhibition by reducing cell division activity in the apical meristematic zone. This process involves a cascade of hormonal networks including auxin, gibberellin, and ABA [16,51,53,54].
To mitigate root growth restriction caused by soil compaction, the number of crown roots increased under compacted conditions, and this process is also mediated by ethylene [14]. Under compacted conditions, ethylene biosynthesis is enhanced, while limited gas diffusion results in ethylene accumulation in root tissues. This leads to localized accumulation of OsEIL1, a central transcription factor in the ethylene signaling pathway. In turn, OsEIL1 directly upregulates the expression of WUSCHEL-RELATED HOMEOBOX 11 (OsWOX11), a positive regulator of crown root development, to stimulate the emergence of crown root primordium, thereby increasing rice crown root number [13,14,15]. Increased crown root number improves the plant’s ability to anchor itself and enhances soil exploration under compacted conditions. Ethylene-induced expression of OsWOX11 at the stem base to promote crown root emergence may be explained by two potential mechanisms: (i) OsWOX11 itself could relocate directly to the crown root primordia at the stem base, or (ii) ethylene produced in roots might diffuse to the initiation region of crown root primordia. These hypotheses need further investigation and provide a promising direction for future research on the causal mechanisms underlying ethylene–WOX11 interactions in compacted soil.
To enhance root penetration in compacted layers, plants develop specialized cell types localized in the outer cortex of nodal roots, forming a cluster of cells known as multiseriate cortical sclerenchyma (MCS). MCS cells enhance the tensile strength of roots and improve the resilience of root tip [55]. Experimental evidence showed that maize genotypes with MCS had root systems with 22% greater depth under compaction than genotypes lacking MSC. Moreover, exogenous ethylene treatment promotes MCS formation in non-MCS maize genotypes [55]. In addition to strengthening the cortical structure, ethylene also contributes to root circumnutation, the helical movement of the root tip enables roots to bypass physical obstacles. This ethylene-mediated movement is particularly important for roots to navigate compacted or rocky soil layers [56,57].
Together, these findings reveal that ethylene promotes crown root formation and enhances mechanical properties and spatial flexibility of root to compensate for the reduction in root elongation caused by soil compaction. These adaptive changes enable plants to maintain root function under challenging soil conditions and provide useful targets for breeding crops with enhanced performance in compacted soils. Despite ethylene playing a crucial role in root adaptation to soil compaction, considering it as the sole regulator may oversimplify the complex network of hormonal interactions. Future studies should investigate how these hormonal networks interact under real environmental conditions.

4. Ethylene Interacts with Other Hormones to Modulate Root Architecture Under Soil Compaction

Accumulating studies have demonstrated that ethylene orchestrates with other hormones to modulate rice root plasticity under soil compaction. These interactions form a complicated regulatory network that precisely coordinates root response to soil compaction. (Figure 1).
Soil compaction enhances ethylene biosynthesis and restricts its diffusion, leading to its accumulation in root tissues. Acting as a primary signal, ethylene mediates root responses to mechanical stress by coordinating downstream phytohormones, including abscisic acid (ABA), auxin, gibberellins (GA), and cytokinins (CK). These hormonal interactions collectively orchestrate root elongation, radial expansion of cortical cells, crown root formation and root hair development.

4.1. Interaction of Ethylene and Auxin in Response to Soil Compaction

Auxin is generally recognized as an omnipotent regulator of plant root growth and development [56,58,59,60]. In most cases, plants synthesize auxin through the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway. Within this pathway, TAA aminotransferases convert tryptophan (Trp) to indole-3-pyruvate (IPA), and YUC flavin monooxygenases subsequently convert IPA into indole-3-acetic acid (IAA) [61]. In rice, loss of OsTAA1 function leads to abnormal root development, including agravitropic roots, longer seminal roots, fewer crown roots, and insufficient lateral roots [61]. Suppressing the expression of OsYUC1 impairs root generation and proliferation. In contrast, overexpression of TAA1 or YUC genes increases IAA content, resulting in shorter seminal roots, increased crown roots, and excessive root hairs [62]. These findings demonstrate the essential role of the TAA/YUC pathway in auxin biosynthesis, with proper auxin production being critical for shaping rice root architecture.
Extensive studies have indicated that ethylene employs auxin as a downstream signal to regulate root growth in response to soil compaction (Figure 1). In rice, the ethylene signaling component OsEIL1 directly stimulates the transcription of auxin biosynthesis genes OsYUC8 and OsTAA1. This results in increased IAA content in root, which subsequently suppresses root elongation [51]. Mutants of OsYUC8 or OsTAA1 exhibited reduced sensitivity to ethylene and showed improved root penetration ability in compacted soil [16]. In contrast, exogenous application of NAA restored root growth in osein2 and oseil1 mutants under compaction conditions, suggesting that ethylene regulates root growth in response to soil compaction depends on auxin produced by the TAA/YUC pathway [16]. Auxin transport is also critical for root growth in compacted soil. Auxin produced in rapidly cell proliferation tissues must be delivered to the elongation zone. This transport is mediated by specific membrane proteins that control auxin influx and efflux [63]. Although OsEIL1, OsTAA1, and OsYUC8 are predominantly expressed in the internal tissues of the root tip, roots growing in excessively compacted soil demonstrate an enhanced auxin response in the epidermis [51,54]. This raises the question: how does auxin derived by OsTAA1/OsYUC8 transport to the epidermal cell layer? Recent findings indicate that OsAUX1, the homologue of the Arabidopsis auxin influx carrier AtAUX1, is responsible for the transport of auxin from the root tip to the elongation zone. Disruption of OsAUX1 reduces root sensitivity to ethylene and enhances root capability to penetrate compacted soil [16]. Furthermore, OsIAA1/9 and OsIAA21/31, the repressor proteins of auxin signaling, interact with OsEIL1 to modulate its transcriptional activation toward its target gene OsTAA1. This regulatory circuit reveals a feedback mechanism in which auxin biosynthesis positively regulates ethylene signaling [54].
In addition to inhibiting root elongation, compacted soil stimulates crown root initiation and development, a process regulated by both ethylene and auxin. Recent studies have shown that compacted soil promotes the accumulation of OsEIL1 in root tissues, which subsequently activates OsWOX11 expression to accelerate the emergence and development of crown root primordia. Mutation of OsWOX11 impairs the plant’s response to ethylene and soil compaction, resulting in delayed crown root development [14]. Moreover, the expression of OsWOX11 is elevated in the OsYUC overexpression plants, and TAA1/YUC-mediated auxin synthesis modulates crown root development dependent on the participation of OsWOX11. This suggests that ethylene and auxin may cooperate to regulate OsWOX11 to control the formation of crown root under compacted soil conditions [42]. ADVENTITIOUS ROOTLESS 1/CROWN ROOTLESS1 (ARL1/CRL1), a member of the plant-specific ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (LOB) protein family [64], directly interacts with OsWOX11 to enhance its transcriptional activity toward its target gene during crown root emergence and elongation [43]. Exogenous auxin treatment increases the transcription of OsCRL1, and this induction requires the degradation of AUX/IAA proteins [65]. Together, these findings reveal the regulatory module of ethylene-auxin-OsWOX11/OsCRL1 involved in crown root formation in response to compacted soil: Ethylene promotes the transcription of OsWOX11 and simultaneously enhances auxin biosynthesis by upregulating the expression of auxin biosynthesis genes. In turn, auxin promotes the transcription of OsCRL1 by inducing the degradation of the AUX/IAA1 protein. OsCRL1 interacts with OsWOX11 to strengthen its transcriptional activity on crown root development-related genes.
Another key adaptation to soil compaction is root circumnutation, which refers to the helical movement of growing root tips that allows them to successfully penetrate heterogeneous or compacted layers [56]. In rice, the histidine kinase OsHK1 promotes circumnutation by influencing auxin transport and response. Additionally, OsHK1 also acts downstream of ethylene receptors and positively regulates ethylene signaling, suggesting that OsHK1 may serve as a crosstalk node between ethylene and auxin pathways in regulating circumnutation under compaction conditions [57]. These findings support the view that auxin functions downstream of ethylene in the root’s response to soil compaction. The presence of a feedback loop between these two hormones may help fine-tune root behavior. Further understanding the regulatory relationship of key genes involved in the ethylene and auxin pathways could facilitate plants’ adaptation to compacted soil environments.

4.2. Coordination of Ethylene and ABA in Response to Soil Compaction

Abscisic acid (ABA) is a principal plant hormone involved in the response to abiotic stress and plays an important role in root development [66,67]. Studies have shown that mutations in AtABI4 and AtABI1, two core components of the ABA signaling pathway, lead to abnormal root architecture [68,69]. In rice, exogenous application of ABA promotes crown root formation and root hair elongation [70,71], highlighting its essential role in root development. The effect of ABA on root development is influenced by its concentration, environmental conditions, and plant species. In general, low concentrations of ABA promote root growth, while high concentrations tend to suppress it [72]. This dose-dependent effect reflects the complex role of ABA in balancing growth and stress responses within the root system.
Increasing studies have shown that ABA functions downstream of ethylene in regulating rice root development in response to soil compaction (Figure 1). Two rice mutants, mhz4 and mhz5, were identified through screening for altered ethylene response in roots. MHZ4 encodes a homolog of Arabidopsis AtABA4 and is localized on the chloroplast membrane, responsible for a branch of ABA biosynthesis [46]. MHZ5 encodes a carotenoid isomerase and functions in the carotenoid biosynthesis pathway, which provides precursors for ABA synthesis [47]. Both mhz4 and mhz5 mutants showed reduced ABA levels and diminished ethylene response in roots [46,47]. Genetic analysis suggest that the MHZ4/5-mediated ABA pathway acts downstream of ethylene signaling to inhibit root growth [47]. Soil compaction promotes ABA biosynthesis in roots, and this induction is weakened in oseil1 and osein2 mutants. Furthermore, ABA-deficient mutants, such as mhz4, mhz5, aba1, and aba2, showed reduced sensitivity to ethylene and enhanced root penetration in compacted soil [16]. These results indicate that ethylene functions upstream of ABA in regulating root development under compacted soil conditions.
Soil compaction induces the radial expansion of cortical cells in rice roots. However, this response is blocked in oseil1, osein2, and ABA-deficient mutants. ABA treatment rescued radial expansion of cortical cells in oseil1 and osein2 mutant roots, mimicking the response observed in wild-type roots under compacted soil and ethylene treatment. These results suggest that ABA acts downstream of ethylene to facilitate cortical cell expansion during compaction stress [16]. In addition, auxin functions as another downstream signal of ethylene to regulate root growth in compacted soil. In compacted soil, exogenous application of 1-naphthaleneacetic acid (NAA), a synthetic auxin, partially rescued root elongation in oseil1 and osein2 mutants. However, NAA treatment did not restore radial swelling of cortical cells in these mutants [16]. These results indicate that ethylene regulates both auxin and ABA to coordinate root growth response under soil compaction. Specifically, ethylene uses auxin to suppress root elongation and ABA to promote radial expansion of root cortical cells.
The interaction between auxin and ABA within root growth and development under soil compaction has also been investigated. Recent studies have shown that ABA suppresses cell division in root meristem and inhibits cell elongation in maturation zones, thereby restricting root extension. This limitation is facilitated through its interaction with auxin [45]. Disruption of auxin biosynthesis decreased root sensitivity to ABA, resulting in longer roots with larger root meristem size and longer cell length in maturation zones. These findings suggest that auxin is required for ABA-mediated inhibition of root growth. Further investigations showed that OsbZIP46 functions as a key regulator between ABA and auxin during root development. In compacted soil, both auxin-deficient and osbzip46 mutants exhibit improved root penetration ability, suggesting that ABA utilizes auxin as a downstream signal to modulate root elongation in compacted soils [45]. Together, these results indicate that both ABA and auxin act downstream of ethylene signaling to regulate root responses to soil compaction. Although they share some regulatory functions, each hormone also plays distinct roles in balancing root elongation and radial expansion during adaptation to compacted soil.

4.3. Crosstalk of Ethylene and Cytokinin in Response to Soil Compaction

Cytokinin acts in opposition to auxin within the root apical meristem (RAM). Plants with defective cytokinin signaling or biosynthesis typically exhibit larger RAMs and accelerated root growth [73]. In rice, OsCKX4, a member of cytokinin oxidase/dehydrogenase (CKX) family, promotes crown root growth and development. Overexpression of OsCKX4 reduces cytokinin levels in roots and increases crown root number [43]. In contrast, knockdown of cytokinin A-type responsive regulator 2 (OsRR2), leads to reduced number of crown roots [41]. Exogenous application of ethylene inhibits OsRR2 expression and induces OsCKX4 expression, this tendency is abolished in the oswox11 mutant [14]. Further studies have shown that OsWOX11 directly binds to the promoters of OsRR2 and OsCKX4, regulating their expression during crown root emergence and elongation. Mutation of OsWOX11 abolishes the promoting effect of soil compaction on crown root development [14]. These results suggest that ethylene may modulate cytokinin signal or cytokinin content through the OsWOX11-OsRR2/OsCKX4 transcription module, and this regulation plays an essential role in crown root growth and development under soil compaction condition (Figure 1).
Accumulating studies have shown that multiple regulators function corporately with OsWOX11 to control crown root development in rice. One example is OsERF3, an AP2/ERF family transcription factor whose expression is induced by ethylene. OsERF3 directly interacts with OsWOX11 to enhance its inhibition on OsRR2, thereby modulating rice crown root emergence [41]. In addition, OsCRL1, a pivotal regulator of crown root formation, directly interacts with OsWOX11 and enhances its activation on OsCKX4 to control crown root emergence and elongation [43].
Furthermore, OsWOX11 also regulates crown root development through epigenetic mechanisms. It promotes gene expression within root-specific locus by recruiting the histone acetyltransferase module of ALTERATION/DEFICIENCY IN ACTIVATION 2 (ADA2)-GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5). This recruitment activates cell division programs in the crown root primordium [74]. In addition, WOX11 increases the transcription of lateral organ boundaries domain (LBD) transcription factor LBD16 to stimulate crown root growth. This activation depends on the recruitment of histone demethylase Jumonji domain-containing protein 706 (JMJ706) to demethylate histone H3 lysine 9 (H3K9me2) on LBD16 promoter [75]. These findings highlight that OsWOX11 is a central regulator of crown root growth and development. Collectively, these studies suggest that OsWOX11 acts as a crucial pivot to modulate crown root growth and development. Given that OsWOX11 functions downstream of ethylene signaling to regulate crown root formation during soil compaction [14], it is likely that ethylene influences crown root formation by modulating the OsWOX11-centered regulatory network. Moreover, OsWOX11 may act as a crosstalk node between ethylene and cytokinin signals, coordinating hormonal pathways that control root development under soil compaction.

4.4. Integration of Ethylene and GA in Response to Soil Compaction

Gibberellins (GAs) are a category of crucial hormones that regulate various physiological and developmental processes in plants [76]. For normal growth and development, plants must synthesize and maintain appropriate levels of bioactive GAs. In flowering plants, these bioactive GAs include GA1, GA3, GA4, and GA7, which are inactivated by gibberellin-2-oxidases (GA2oxs) [77]. In rice, exogenous application of GAs promotes primary root elongation. In contrast, blocking GA biosynthesis inhibits root growth [53,76], suggesting that maintaining an appropriate level of bioactive GAs is essential for proper root development. Blocking the biosynthesis of GA via paclobutrazol (inhibitor of GA production), or mutations in genes involved in GA biosynthesis significantly decrease the cell division rate in root meristem. This highlights the key role of GA in promoting root cell proliferation during root development [53].
The interaction between ethylene and GA has been investigated during various developmental processes. In rice seedlings, ethylene signaling center transcription factor OsEIL1 directly activates SD1, a key gene involved in GA biosynthesis, to promote mesocotyl elongation and emergence [78]. A similar regulatory mechanism operates under submergence, where OsEIL1 induces SD1 expression to promote GA biosynthesis and enhance internode elongation, thereby facilitating rice plant survival in flooded conditions [79]. In roots, however, ethylene appears to function differently. Our recent study in rice root found that OsEIL1 activates the expression of OsGAox1, OsGAox2, OsGAox3, and OsGAox5, which encode GA-inactivating enzymes. This activation leads to reduced levels of bioactive GAs in the root meristem and suppressed cell division, ultimately inhibiting root elongation under compacted soil conditions [53]. These findings suggest that ethylene regulates GA homeostasis in a tissue-specific manner. Namely, ethylene promotes GA synthesis in shoots to support elongation under submergence, while it reduces GA levels in roots to restrict root growth during compacted conditions. Therefore, GA-mediated cell proliferation plays a crucial role in ethylene-regulated root growth in response to soil compaction (Figure 1). It remains to explore whether ethylene’s regulation on gibberellin biosynthesis genes and related metabolic pathways may influence rice crown root development. This could provide a valuable perspective on how ethylene-GA interactions mediate rice RSA adaptation to soil compaction.
Although cytokinin and gibberellins are known to influence root growth under various stress conditions, their role in soil compaction-induced root adaptation has not been explored. Current research often overlooks the interactions between these hormones and other key regulators such as ethylene, auxin and ABA. More comprehensive studies are needed to understand how these hormones synergistically regulate RSA under compaction.

5. Conclusions and Perspectives

5.1. Bio-Based Practices: Effective Strategy for Soil Compaction Management

Rice is a staple food for more than half of the global population, contributing approximately 20% of global caloric intake, with a cultivated area exceeding 160 million hectares, predominantly in Asia [80]. In irrigated systems, rice is traditionally grown in flooded fields, where waterlogging significantly exacerbates soil compaction, particularly under mechanized farming conditions. These conditions impair root development, reduce water and nutrient uptake, and ultimately limit crop yield. Therefore, understanding the delicate balance between water management and soil structure is crucial for optimizing rice productivity under changing climatic and agronomic conditions [81]. Integrating effective soil management practices that address both waterlogging and soil compaction is essential for enhancing the sustainability and productivity of rice cultivation.
Although practices such as subsoil management and reduced tillage can alleviate compaction, they are costly, provide only short-term benefits, and susceptibility to secondary compaction [17]. In contrast, Bio-tillage has emerged as a promising strategy for alleviating soil compaction. This method uses cover crops with strong and deep roots to loosen compacted soil. As the roots grow, they create channels, which remain as macropores when the roots die and decompose. These macropores improve air flow and water flow in the soil and also facilitate root growth for subsequent crops [82]. Moreover, root decomposition adds organic matter to the soil, and provides a vital nutrient source for soil microorganisms, thereby enhancing biological activity and ecological functions [83]. Thus, bio-tillage offers an effective way to mitigate the negative effects of compaction on root development. Selecting cover crops with strong root penetration capacity is the key to maximizing the benefits of bio-tillage under compacted conditions.
In addition to feedback between plants and soil, it is essential to elucidate the interactions between beneficial microorganisms and plant roots [84]. For instance, the use of rhizosphere microorganisms to modulate ethylene biosynthesis has been shown to influence the root system’s ability to adapt to compacted soil. Studies indicate that certain bacteria produce ACC deaminase to degrade ACC, a key precursor in ethylene biosynthesis [85]. Inoculating these bacteria into the soil can reduce ethylene production in the root system, thereby alleviating the inhibitory effects of soil compaction on root elongation [86,87]. Developing microbial inoculants with broad environmental adaptability offers a potential approach to alleviate the negative effects of soil compaction on root growth. By enhancing the positive regulatory roles of biological interactions, such strategies may contribute to maintaining crop productivity under stress conditions. Despite bio-tillage and microbial inoculants have shown promise in alleviating soil compaction, their effectiveness is often limited by factors such as soil type, climate variability, and agricultural practices. Future research should systematically evaluate the long-term benefits of these strategies, particularly their role in different soil types and environmental conditions.

5.2. Ethylene: A Central Signal in Root Adaptation to Soil Compaction

Comprehending the mechanisms of soil compaction adaption, from the molecular to the plant scale, may facilitate the breeding of crops adapted to compacted soil. In rice, ethylene plays a key role in root growth under compaction. Mechanical impedance promotes ethylene production and restricts its diffusion, leading to root architectural changes such as reduced elongation, increased crown root formation, cortical cell expansion, and root hair development—all of which contribute to enhanced soil exploration under stress [14,15,16,38].
Manipulating ethylene signaling components has shown promise in breeding programs. As mentioned, suppressing ethylene biosynthesis in roots through rhizosphere microorganisms can alleviate the inhibition of root elongation by soil compaction [86,87]. Genetic studies also support this idea. Mutations in OsEIL1 and OsEIN2, which are key components of the ethylene signaling pathway, showed improved root penetration in compacted soil [13]. Moreover, loss-of-function mutants osein2 and oseil1 exhibit increased resistance to salinity and chilling, and show decreased size of grain and total grain weight per plant [39,40,88]. Ethylene has multiple roles in plant growth and stress response, and balancing its diverse functions remains a challenge that requires further investigation. It has been reported that overexpressing the genes associated with phytohormone response enhance plant stress resistance without negatively impacting on growth and development [89]. This means that targeting downstream response genes in the ethylene signaling pathway may help increase root growth in compacted soils without yield penalties. In the future, identifying advantageous alleles in ethylene-related genes can enhance crop breeding by minimizing the unwanted side effects caused by gene pleiotropy. This may help breeders develop superior rice varieties with optimal growth and increased grain yield in both normal and compacted soil conditions.
Importantly, the OsEIL1–OsWOX11 transcription module has emerged as a key regulatory node. Compacted soil promotes ethylene production, leading to the accumulation of OsEIL1. Subsequently, OsEIL1 directly activates the expression of OsWOX11, which promotes crown root emergence and elongation [14]. This regulation helps maintain plant anchorage and soil exploration under mechanical constraints. Manipulating this module through genome editing or molecular-assisted selection could accelerate the breeding of compaction-tolerant cultivars with stable agronomic performance.

5.3. From Lab to Field: Relevant Phenotyping and Functional Validation

Studying how roots grow and respond to compacted soil under real field conditions remains a major challenge. This is because soil physico-chemical and biological properties vary in both time and space, and they interact with each other. In contrast, most laboratory systems use simplified models such as agar plates or uniformly compacted soil, which do not reflect the heterogeneous structure of natural soil, where nutrients and abiotic stress factors are distributed heterogeneously. As a result, there is often a gap between the molecular mechanisms found in the lab and the actual root traits seen in the field. To bridge this gap, researchers need tools that can observe root growth in situ without disturbing the soil. Techniques such as 2D imaging, root cross-section analysis, X-ray computed tomography (CT), and electrical impedance tomography (ERT) provide viable options. These techniques allow the observation of root structure under real-world conditions, including deformation zones, mechanical impedance hotspots, and branching behavior in response to compaction [90,91].
Integrating these imaging methods with high-throughput molecular technologies, such as genome-wide association studies (GWAS), single-cell transcriptomics, proteomics, and spatial omics, provides a comprehensive framework to identify functional traits and regulatory genes. This can help identify key genes that control root growth in compacted soil. For example, researchers constructed a high-resolution cell atlas of rice roots grown in both compacted and non-compacted soils through single-cell transcriptomic profiling. The results reveal that over half of the compaction-responsive genes were enriched in outer root tissues, particularly the cortex and epidermis, indicating that rice roots prioritize peripheral tissue responses to enhance nutrient uptake and stress adaptation in compacted soils. Furthermore, the exodermis and endodermis showed increased expression of lignin and suberin biosynthesis genes, reinforcing cell walls to provide mechanical protection under high soil impedance [92,93].
In addition, gene editing technologies, particularly CRISPR, have advanced from single-base modifications to targeted chromatin rearrangements [94,95]. This progress enables the precise stacking of multiple favorable alleles involved in root responses to soil compaction. As a result, developing new crop varieties with enhanced compaction resistance may become more efficient and targeted. In the long run, these findings may guide new strategies to improve crop yield and reduce the harmful effects of soil compaction. Although most current studies focus on laboratory-based research, soil compaction is influenced by multiple dynamic factors in the field, such as soil texture, water content, and environmental stressors. Therefore, future research should prioritize field-based experiments to validate the laboratory findings and identify practical solutions that can be directly applied in agricultural practices.

5.4. Towards Precision Breeding: Multi-Hormonal Networks and Trait Integration

Root adaptation to compacted soils is not governed by a single hormone but relies on a complex network of interacting hormonal pathways. Ethylene functions as the primary signal, coordinating the actions of auxin, abscisic acid (ABA), gibberellins (GA), and cytokinins [14,43,46,51,53,54]. Ethylene accumulates in compacted soil due to restricted gas diffusion and increased mechanical resistance [13], and acts upstream of several hormonal cascades that shape root architecture. Therefore, future breeding strategies should focus on ethylene-centered regulatory modules as primary targets for enhancing root performance in compacted environments.
The combination of bio-based practices, molecular breeding, and in situ technologies to address root adaptation to soil compaction is emerging as a major trend. In particular, uncovering the molecular mechanisms centered on ethylene signaling and identifying elite alleles will be critical. These strategies not only improve root growth but also help maintain grain yield under mechanical stress. Future research must focus on integrating these multi-hormonal signaling pathways to deepen our understanding of root system adaptation under compaction. Furthermore, there is an urgent need to translate laboratory-based research into field applications to enhance crop performance under real agricultural conditions. Moving forward, interdisciplinary efforts linking soil science, plant biology, and technology will be critical for improving crop performance in compacted soils and securing global food production.

Author Contributions

Writing—original draft preparation, Y.L. and B.G.; writing—review and editing, Y.L., C.Y., Z.Q., R.H. and H.Q.; funding acquisition, H.Q. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China, grant number 32472037; the Youth innovation of Chinese Academy of Agricultural Sciences, grant number Y2024QC14; Basic Research Center, Innovation Program of Chinese Academy of Agricultural Sciences, grant number CAAS-BRC-AL-2025-02, and the Central Public-interest Scientific Institution Basal Research Fund, grant number 1610392023004.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

No new data were created in this study.

Acknowledgments

We acknowledge the use of BioRender.com for creating Figure 1 in this manuscript. During the preparation of this manuscript, we used deepseek.com for refining the language. The authors have reviewed and edited the output and take full responsibility for the content of this publication.

Conflicts of Interest

The authors declare no conflicts of interest.

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Agriculture 15 02071 g001
Figure 1. Hormonal regulatory network mediated by ethylene in rice root adaptation to soil compaction. (A) Root phenotype of rice grown in compacted soil. (B) Three developmental stages of crown root primordia: initiation, emergence, and elongation. (C) Longitudinal section of the root tip. (D) Regulatory network of ethylene integrates downstream phytohormones to regulate root adaption under soil compaction. The green panel highlights regulatory modules associated with crown root development (corresponding to panel (B)), while the gray panel indicates regulatory pathways involved in root elongation and root hair formation (corresponding to panel (C)). Arrows denote positive regulation, while lines terminating in a flat head signify negative regulation. The solid lines represent direct contacts, while the dashed lines denote indirect interactions.
Figure 1. Hormonal regulatory network mediated by ethylene in rice root adaptation to soil compaction. (A) Root phenotype of rice grown in compacted soil. (B) Three developmental stages of crown root primordia: initiation, emergence, and elongation. (C) Longitudinal section of the root tip. (D) Regulatory network of ethylene integrates downstream phytohormones to regulate root adaption under soil compaction. The green panel highlights regulatory modules associated with crown root development (corresponding to panel (B)), while the gray panel indicates regulatory pathways involved in root elongation and root hair formation (corresponding to panel (C)). Arrows denote positive regulation, while lines terminating in a flat head signify negative regulation. The solid lines represent direct contacts, while the dashed lines denote indirect interactions.
Agriculture 15 02071 g001
Table 1. Genes involved in root development in response to soil compaction.
Table 1. Genes involved in root development in response to soil compaction.
Gene Name Gene FunctionReference
MHZ7/OsEIN2
(Os07g0155600)		Key component of ethylene signaling pathway, roots of mutants display enhanced ability to penetrate compacted soil.[13,39]
MHZ6/OsEIL1
(Os03g0324300)		Key component of ethylene signaling pathway, roots of mutants display enhanced ability to penetrate compacted soil.[13,40]
OsWOX11
(Os07g0684900)		Key regulator of crown root development, positively regulates ethylene and soil compaction-promoted crown root development[14,41,42,43]
OsAUX1
(Os01g0856500)		Involved in auxin influx, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16,44]
OsYUC8
(Os03g0162000)		Involved in auxin biosynthesis, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16,44,45]
OsbZIP46
(Os06g0211200)		Positively regulates ABA-induced root inhibition and radial expansion; roots of mutant display enhanced ability to penetrate compacted soil.[45]
MHZ4
(Os01g0128300)		Involved in ABA biosynthesis, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16,46]
MHZ5
(Os11g0572700)		Involved in ABA biosynthesis, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16,47]
OsABA1
(Os04g0448900)		Involved in ABA biosynthesis, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16]
OsABA2
(Os03g0810800)		Involved in ABA biosynthesis, roots of mutant display reduced response to ethylene and enhanced ability to penetrate compacted soil[16]
OsRHL1
(Os06g0184000)		Acts downstream of auxin and mediates root hair elongation;
roots of mutant display reduced ability to penetrate compacted soil.		[44]
OsCSLD1
(Os10g0578200)		Acts downstream of auxin and mediates root hair elongation;
roots of mutant display reduced ability to penetrate compacted soil.		[44]
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Li, Y.; Ge, B.; Yan, C.; Qi, Z.; Huang, R.; Qin, H. Ethylene-Triggered Rice Root System Architecture Adaptation Response to Soil Compaction. Agriculture 2025, 15, 2071. https://doi.org/10.3390/agriculture15192071

AMA Style

Li Y, Ge B, Yan C, Qi Z, Huang R, Qin H. Ethylene-Triggered Rice Root System Architecture Adaptation Response to Soil Compaction. Agriculture. 2025; 15(19):2071. https://doi.org/10.3390/agriculture15192071

Chicago/Turabian Style

Li, Yuxiang, Bingkun Ge, Chunxia Yan, Zhi Qi, Rongfeng Huang, and Hua Qin. 2025. "Ethylene-Triggered Rice Root System Architecture Adaptation Response to Soil Compaction" Agriculture 15, no. 19: 2071. https://doi.org/10.3390/agriculture15192071

APA Style

Li, Y., Ge, B., Yan, C., Qi, Z., Huang, R., & Qin, H. (2025). Ethylene-Triggered Rice Root System Architecture Adaptation Response to Soil Compaction. Agriculture, 15(19), 2071. https://doi.org/10.3390/agriculture15192071

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