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Review

Plant Long Non-Coding RNAs: Multilevel Regulators of Development, Stress Adaptation, and Crop Improvement

by
Xiyue Bao
1,
Xiaofeng Dai
1,2,
Jieyin Chen
1,2 and
Ran Li
1,2,*
1
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
2
Xinjiang Key Laboratory for Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS, Changji 831100, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(8), 1950; https://doi.org/10.3390/agronomy15081950
Submission received: 16 June 2025 / Revised: 24 July 2025 / Accepted: 5 August 2025 / Published: 13 August 2025
(This article belongs to the Section Crop Breeding and Genetics)
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Abstract

Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of various biological processes in plants, including development, stress responses, and pathogen defense. Advances in multi-omics sequencing analysis and molecular biology methods have significantly expanded our understanding of the plant lncRNA landscape, revealing novel lncRNAs across diverse species. In this review, we provided an overview of the essential roles of lncRNAs in multilevel regulatory functions in plant growth, development, and stress responses. Moreover, we bridged the module network among these different conditions. One of the most important functions of lncRNA is gene expression regulation. Thus, we summarized the plant lncRNAs acting in cis/trans and as endogenous target mimics (eTMs) to influence the expression of target genes in transcription and post-transcription regulation. This review also sheds light on several application values in agricultural production and development of plant-specific databases and bioinformatic tools. These datasets facilitated the exploration of lncRNA function, enabling the identification of their expression patterns, phylogenetic relationships, and molecular interactions. As research progresses, multi-omics approaches will provide deeper insights into the regulatory mechanisms of lncRNAs, offering promising strategies for enhancing crop resilience and productivity in response to climate change.

1. Introduction

The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein [1]. The initial draft of the human genome revealed several unexpected findings, one of the most notable being that exonic regions of protein-coding genes comprise less than 2% of the genome, while the remainder was largely composed of what was once referred to as “junk” DNA [2,3]. With research development, this “junk” DNA was defined as non-coding RNAs (ncRNAs). These ncRNAs are extensively transcribed in many organisms, accounting for over 90% of the eukaryotic genomes. NcRNAs can be categorized into two major types based on their functions: housekeeping ncRNAs and regulatory ncRNAs [4]. Housekeeping ncRNAs usually have no regulatory function, including ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA). Meanwhile, regulatory ncRNAs are regulators in diverse biological processes, further classified into short non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The first eukaryotic lncRNA-H19 was identified in mouse in 1984, and the first plant lncRNA was discovered in Medicago named Enod40 in 1993, which triggered changes in subcellular localization of the nuclear RNA-binding protein MtRBP1 [4]. LncRNAs are mainly transcribed by RNA polymerase II (Pol II), featuring a 5′ cap structure and 3′ polyadenylated tails. They are characterized by shorter open reading frames (ORFs), lower abundance, reduced conservation, tissue-specific expression, and minimal protein-coding potential [5]. LncRNAs represent a diverse class of molecules, including long intergenic non-coding RNAs (lincRNAs), long intronic non-coding RNAs (incRNAs), natural antisense transcripts (lncNATs), and bidirectional lncRNAs, categorized based on their transcriptional direction and genomic location [6].
Growing evidence suggests that lncRNAs are key modulators of a wide range of biological processes, functioning through diverse mechanisms. LncRNAs can regulate mRNA expression via cis- and/or trans-acting mechanisms, serve as signals and decoys for microRNAs (miRNAs) or RNA-binding proteins, control alternative splicing, and act as scaffolds, bringing together large molecular complexes. The discovery of plant lncRNA biology has provided many functional and mechanistic insights that have increased our understanding of this gene class. In plants, lncRNAs have been implicated in regulating developmental processes, biotic and abiotic stress responses, and in modulating essential cellular functions. Comparative analyses across multiple plant species have enhanced our understanding of the conservation and evolutionary dynamics of lncRNAs [7]. These evidences suggest that lncRNAs are pivotal regulators in plants, offering significant potential for agricultural innovation, such as crop improvement, molecular breeding, and plant protection [8]. Thus, we summarized the plant lncRNAs acting in cis/trans and as endogenous target mimics (eTMs) to influence target gene expression in plant growth, development, and stress responses, also showing several application values in agricultural production.

2. Multilevel Regulatory Rules of LncRNAs in Plant Growth and Stress Response

The significant role of lncRNAs in plants has been extensively described in numerous reviews. In this review we primarily encompass plant lncRNAs’ roles in growth, development, and response to diverse stress conditions, systematically summarizing the multilevel regulatory network of lncRNAs (Figure 1).

2.1. Growth and Development Regulation

Flowering time is an important process in plants, controlled via internal signals such as plant hormones and environmental cues. Several lncRNAs have been discovered to regulate flowering time, such as in Arabidopsis [9,10,11,12], chickpea [59], trifoliate orange [60], apricot [61], rape [62], rice [63], and rose [64]. The well-known lncRNAs COLD-INDUCED LONG ANTISENSE INTRAGENIC RNA (COOLAIR) and COLD-ASSISTED INTRONIC NON-CODING RNA (COLDAIR) downregulated the expression of the major flowering repressor FLOWERING LOCUS C (FLC) during vernalization to promote flowering [13]. Obstructed flowering may result in abnormal pollen development. The failure to produce functional pollen leads to male plant sterility. In wheat, several lncRNAs have been identified as candidates influencing male sterility through alternative splicing [65,66]. However, 94 lncRNAs are predicted precursors of 49 miRNAs in cotton cytoplasmic male sterility [67].
Yield is a crucial agronomic trait for cereal crops’ genetic improvement. In rice, a leucine-rich repeat receptor kinase (LRK) gene cluster from a quantitative trait locus (QTL) is linked to yield improvement. The lncNAT LAIR is transcribed in the opposite direction of this cluster and can increase grain yield [14,15]. Furthermore, lncRNA SUPPRESSOR OF FEMINIZATION (SUF), specifically transcribed antisense of FEMALE GAMETOPHYTE MYB (FGMYB) in male plants, is required for controlling sex differentiation in liverwort [16]. Yield improvement in economic crops is mainly related to their fruits. In recent years, numerous lncRNAs have been identified to participate in the ripening process across various fruits [68]. In tomato, many lncRNAs have been demonstrated at different stages of fruit ripening [17,69,70]. A large number of lncRNAs were also identified, which were differentially expressed during fruit ripening in sea buckthorn [18], baogua melon [71], and sweet cherry [72].
In addition, lncRNAs have been shown to participate in other diverse processes of plant growth and development, such as leaf development, seed development, root development, trichome formation, fiber initiation and elongation, and floral thermogenesis. Thousands of novel lncRNAs have been identified in peanut derived from seed development [73]; in tomato, lncRNAs participate in the pollen development [74]; in cotton, lincRNAs and lncNATs, which show low conservation, high methylation, and repetitive sequence enrichment, play key roles in fiber initiation and elongation [75]; in Norway spruce, lincRNAs involved in somatic embryogenesis development [76]; in kiwifruit, the antisense transcript lncNAT function with MADS-box gene AcFLCL promoting budbreak in growth activation [77]; and in jasmine, many lncRNAs may be involved in the terpenoid and phenylpropanoid/benzenoid biosynthesis pathways, which potentially contribute to the production of jasmine floral scents [78].

2.2. Abiotic Stress Adaptation

Drought is a major global ecological challenge that severely impacts plant growth by disrupting physiological processes, including growth, photosynthesis, hormone metabolism, and enzyme activity, leading to reduced cell water potential, wilting, leaf drop, poor fruiting, and even plant death [79]. Recent studies have identified specific genes and lncRNAs involved in plant drought responses, highlighting their functional roles in species such as cotton [80], cassava [81], rice [82], sorghum [83], and leaf mustard [84]. Under varying water stress conditions, numerous lncRNAs were identified acting as target mimics for miRNAs or regulating stress-responsive pathways. For instance, in C. songorica, 52 lncRNAs were predicted to target miRNAs like miR397 and miR166 [85], while in cassava, 682 lncRNAs were linked to hormone signaling, secondary metabolism, and sucrose metabolism [86], and in cotton, lncRNAs regulated DNA methylation and fiber quality during drought stress [87,88].
Salt stress is a major abiotic stress that negatively impacts plant growth and reproduction through complex physiological and biochemical reactions. It causes ionic toxicity, osmotic stress, and oxidative stress, leading to nutrient imbalances, inhibited growth, increased energy consumption, and reduced yield and quality, potentially resulting in plant death. Salt stress also affects photosynthesis, ionic homeostasis, seed germination, and membrane permeability [89]. Several salt stress-related lncRNAs have been investigated, such as in soybean [90], sugar beet [91], cotton [92], alfalfa [93], tea plant [19], and Limonium bicolor [94]. Several lncRNAs were found to be differentially expressed in two different poplars, speculating target plant growth and stress response-related genes [95]. Moreover, 1183 lncRNAs differentially expressed responses to salt in Populus trichocarpa [20].
In addition, several lncRNAs have been identified to play a role in other abiotic stress conditions to maintain homeostasis. For example, a large number of lncRNAs were identified in response to excess micronutrients boron [96]; macronutrients phosphorus [97,98] and nitrogen [99]; toxic chemicals cadmium [100,101] and aluminum [102]; gibberellin [103]; and UV-B treatment [104]. Previous studies also found that some lncRNAs can not only respond to one abiotic stress but can also respond to various stress conditions. For example, DROUGHT-INDUCED lncRNA (DRIR) is a novel positive regulator of the plant response to drought and salt stress in Arabidopsis. Expression of DRIR can be significantly activated by salt stress, drought, and ABA treatment, resulting in a series of abiotic stress response-related genes differentially expressed [21]. In addition, polyadenylated and non-polyadenylated lncRNAs in Arabidopsis under ABA, drought, and cold treatments were identified by high-depth ssRNA-seq [22].

2.3. Biotic Stress Defense

Plants are also continuously exposed to a wide range of biotic interactions. It is important for plants to evolve a resistance mechanism for defense adaptation. The defense response instigated in plants is regulated by a number of regulators, including lncRNAs.
Previous studies have proved that lncRNAs are important for plant–bacteria pathogen interactions. Differentially expressed lncRNAs were identified playing a role in tomato defense against Pseudomonas syringae pv. tomato (Pst) [105]; novel lncRNAs were identified in walnut fruits defense against Colletotrichum gloeosporioides [106]; putative lncRNAs were identified in kiwifruits linked to immune response and signal transduction with Pseudomonas syringae pv. actinidiae (Psa) [107]; and long intergenic non-coding RNAs (lincRNAs) in potato were identified responding to Pectobacterium carotovorum subsp. brasiliense and Candidatus Liberibacter solanacearum (CLso) challenge [108,109]. Additionally, the lncRNA ALTERNATIVE SPLICING COMPETITOR (ASCO) binds the spliceosome components PRP8a and SmD1b to regulate the transcription of genes involved in the response to flagellin [23]. UNA1 is a 5′ snoRNA-capped and 3′ polyadenylated lncRNA, enhancing Arabidopsis resistance to Pst DC3000 induced by infection in an NPR1-dependent manner [24]. LncRNA ALEX1 was identified in rice in response to Xanthomonas oryzae pv. oryzae (Xoo) infection activates jasmonic acid (JA) signaling, and enhances the endogenous levels of JA and JA-Ile to improve resistance to bacterial blight [25]. LncRNA MuLnc1 was found to be cleaved by mul-miR3954, generating secondary siRNAs in a 21-nt phase in mulberry [26].
LncRNAs also play vital roles in fungal pathogen defense regulation. While research on lncRNAs in plant resistance lags behind other areas, this review also focuses on recent advances in their role in fungal responses and the regulatory mechanisms underlying these functions, such as lncRNA resistance to Fusarium oxysporum [110,111], Hyaloperonospora brassicae [112], Puccinia striiformis f. sp. tritici [113], Plasmodiophora brassicae [114], Erysiphe necator [115], Alternaria alternata [116], Fusarium circinatum [117], Sclerotinia sclerotiorum [27], and Magnaporthe oryzae [118,119,120]. In cotton, several lncRNAs are resistant to Verticillium dahiae. GhlncLOX3 positively regulates resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis [28]; lncRNA2 interacting with Polygalacturonase 12 (GbPG12) negatively regulate cotton resistance to V. dahliae, while lncRNA7 interacting with pectin methylesterase inhibitor 13 (GbPMEI13) positively regulate it by promoting IAA accumulation and activating itself to increase pectin methylation [29].
Tomato lncRNAs play crucial roles in enhancing resistance to viruses by modulating viral replication and transcription. Tomato yellow leaf curl virus (TYLCV) is one of the most damaging viruses threatening tomato production. A set of lncRNAs responds to TYLCV infection [30,121]. SlLNR1, a novel lincRNA in tomato, targets viral small-interfering RNA (vsRNA) from TYLCV IR sequence, which can mediate viral DNA replication and transcription in hosts to suppress the TYLCV infection and enhance tomato antiviral resistance [31]. In addition, potato virus Y (PVY) is one of the most important pathogens of potato, significantly reducing potato crop yield and quality. A range of PVY-response lncRNAs were identified under heat stress [122]. In addition, plant lncRNAs respond to other biotic stress conditions, such as oomycete [115,123], herbivore attack [124], pyrethroid resistance [125], Meloidogyne incognita parasitism [126], and mowing [127].

2.4. Functional Module Network: Bridging Stress and Development

Plant lncRNAs are always specifically expressed in different tissues and respond to diverse stress conditions to play various biological functions. Many investigations on plant lncRNAs revealed that they can participate in multiple biological processes simultaneously, playing roles in the module network. For example, Arabidopsis lncRNA ELF18-INDUCED LONG-NON-CODING RNA1 (ELENA1) can be induced by both pathogen-associated molecular patterns of bacterial flagellin flg22 and translation elongation factor Tu elf18 to enhance resistance against Pseudomonas syringe pv tomato DC3000 [32,33]. Meanwhile, further research identified that ELENA1 is nitrogen inducible and attenuates nitrogen-induced leaf senescence in Arabidopsis [99].
In addition, some lncRNAs can be induced by stress conditions to perform regulatory functions in growth and development. Arabidopsis FLINC downregulated at higher ambient temperature can affect ambient temperature-mediated flowering [10]. Hybrid rice exhibits photoperiod-sensitive male sterility (PSMS), allowing fertility control based on day length. The lncRNA long-day-specific male-fertility-associated RNA (LDMAR) is crucial for maintaining male fertility under long-day conditions [34]. LncRNAs also play key roles in salt tolerance to induce flowering, which can enhance chickpea yield [59,128], and in drought stress to increase rice yield [129].

3. Functional Mechanism of Plant lncRNAs in Regulating Gene Expression Involved in Growth and Stress Response

LncRNAs have a regulatory mechanism to regulate gene expression, performed in cis- or trans- action. In this review, we elaborate on the role of lncRNAs acting in cis or trans on target genes and acting as endogenous target mimics (eTMs) on target microRNAs in regulating gene expression involved in plant growth and stress response (Figure 2).

3.1. Act in Cis on Target Genes

Gene expression can be controlled by regulatory elements located in their surrounding genomic regions. This function in the regulation of gene expression is defined as cis-action. One of the most important roles of lncRNAs is to function in such cis-regulatory domains, spatially interacting with their neighboring mRNA genes [132]. One of the mechanisms is regulating chromatin remodeling. The most typical lncRNA function in cis-action is COLD-INDUCED LONG ANTISENSE INTRAGENIC RNA (COOLAIR). FLOWERING LOCUS C (FLC) is the vital regulator to promote flowering in Arabidopsis vernalization. COOLAIR, transcribed from the antisense of the FLC locus, can specifically bind and recruit Polycomb Repressive Complex 2 (PRC2) to FLC to regulate flowering during vernalization [13]. This regulatory mechanism is COOLAIR, which prevents H3K36 methylation at the intragenic FLC site [13]. LncNAT-MAS, transcribed from the antisense strand of MADS AFFECTING FLOWERING4 (MAF4), is induced by cold and enhances MAF4 transcription by recruiting WDR5a, promoting histone H3K4 trimethylation to suppress flowering during vernalization [22]. In addition, tomato lncRNA16397 is transcribed from antisense of glutaredoxin SlGRX22, which induces SlGRX22 and SlGRX21 transcription, resulting in reducing ROS accumulation and cell membrane injury [35]; lncNAT-TWISTED LEAF (TL) in rice regulates leaf development by acting as a cis-regulator of the transcription factor OsMYB60, mediating its expression through chromatin modifications [130]; cis-NATZmNAC48 in maize negatively regulates ZmNAC48, leading to increased water loss and stomatal opening through chromatin modifications [36]; populus tlinc-NAC72 is strongly induced by long-term salt stress and upregulates PtNAC72.A/B expression by targeting tandem GAAAAA elements in the PtNAC72.A/B promoter [20]; lncRNA LAL in Medicago truncatula regulates LIGHT-HARVESTING CHLOROPHYLL A/B BINDING (MtLHCB1)’s expression to induce salinity tolerance [37]. These lncRNAs are only analyzed for their function in cis-action to regulate their neighbor genes’ expression, but the further regulatory mechanism needs to be deeply discovered.

3.2. Act in Trans on Target Genes

Compared with cis-action, the trans-action of lncRNAs has been little reported. The trans-action of lncRNAs has been reported to regulate the expression of genes related to several biological pathways by RNA sequencing and bioinformatics analysis [132]. Most of them found that modifying a cluster of genes’ expression related to specific biological pathways, such as MSTRG.8888.1 [38] and MSTRG.139242.1 [19]. Few studies revealed that lncRNA can interact with a specific protein to bind the target gene locus to regulate the target gene expression through trans-action. For example, Arabidopsis thaliana lncRNA ELENA1 directly interacts with mediator subunit 19a (MED19a) to elevate MED19a enrichment on pathogenesis-related gene1 (PR1) promoter, enhancing the expression of PR1, and thereby the innate immune response in Arabidopsis [33]. Meanwhile, FIBRILLARIN 2 (FIB2) directly interacts with MED19a, forming the FIB2/MED19a complex, which is a negative regulator for PR1 transcription. ELENA1 can also directly interact with FIB2, resulting in dissociation of the FIB2/MED19a complex and promoting MED19a binding to the PR1 promoter by displacing the repressor FIB2 [32]. Flowering-associated intergenic lncRNA (FLAIL) acts in trans in repression of Arabidopsis flowering time. RNA-seq and ChIRP-seq showed that FLAIL binds genes circadian (CIR1) and laccase 8 (LAC8) connected to flowering, directly mediating their transcriptional level in affecting Arabidopsis flowering [11].

3.3. Act as Endogenous Target Mimics (eTMs)

MicroRNAs (miRNAs) can recognize specific mRNA sequences based on sequence complementarity, resulting in mRNA degradation [133]. LncRNAs function as endogenous target mimics (eTMs) to regulate gene expression in plants by acting as molecular decoys for miRNAs, thereby modulating miRNA activity and downstream target gene expression. LncRNA INDUCED BY PHOSPHATE STARVATION1 (IPS1) includes a motif with sequence complementarity to the phosphate starvation-induced miRNA miR-399. However, IPS1 cannot be cleaved by miR-399 due to a mismatched loop at the cleavage site. miR-399 can guide the cleavage of PHO2, which encodes an E2 ubiquitin conjugase-related protein that negatively affects shoot phosphate content and remobilization. Thus, IPS1 functions as a target mimicry to abolish miR-399 cleavage activity on PHO2, resulting in enhancing the transcription of PHO2 [97]. LncRNA67 was highly expressed in flower buds of the plasmic male sterility cotton line 2074B, and the expression of lncRNA67 was significantly correlated with GhVYP724B, a member of the cytochrome P450 (CYP450) protein family catalyzing the hydroxylation/oxidation reaction during BR biosynthesis. LncRNA67 paired with miR3367 and inhibited the miR3367-mediated cleavage of GhVYP724B to positively regulate male sterility in upland cotton [39]. The function of miRNAs was mainly related to stress response. ABA treatment induces lncRNA35557 to act as an eTM of miR6206, preventing tae-miR6206 from cleaving the NAC transcription factor gene TaNAC018 to enhance drought-stress tolerance [131]. LncRNA354 is identified in salt-treated cotton and functions as an eTM of miR160b, thereby enhancing ARF transcription factors GhARF17/18 in response to salt stress in upland cotton [40]. LncR9A, lncR117, and lncR616 act as eTMs to modulate miR398 target Cu-Zn superoxide dismutase 1 (CSD1) expression under wheat response to cold stress [41]. In tomato, several lncRNAs identified function as eTM to decoy target miRNAs and then regulate resistance-related genes defense against P. infestans [42,43,44,45,46].

4. Applications and Future Directions

Extensive research has revealed their diverse applications in regulating gene expression, influencing plant growth and development, and enhancing stress tolerance. However, current studies also highlight several limitations in understanding their regulatory mechanisms and full potential. Looking ahead, plant lncRNAs hold great promise for revolutionizing agricultural production, offering opportunities to improve crop yield and quality, enhance stress resistance, and optimize agricultural management strategies.

4.1. Bioinformatics Database of Plant-Specific lncRNA for Function Investigation

The expanding repertoire of lncRNAs across plant species underscores their critical roles in development, growth, and stress adaptation, necessitating comprehensive studies of their functions. Dedicated databases archiving plant lncRNA information have emerged over recent years. While these databases greatly facilitate lncRNA research, they suffer from inconsistent annotation standards and lack critical features like expression profiles, target predictions, and epigenetic data (Table 1).
CANTATAdb was an online database that collected 45,117 lncRNAs in 10 plant species, and then CANTATAdb 2.0 was created, encompassing 239,631 lncRNAs in 39 plant and algae species. These two databases took advantage of publicly available sets of RNA-Seq data and provided annotation for the identified lncRNAs with expression values, coding potential, and sequence alignments [134,135]. Subsequently, CANTATAdb 3.0 was updated to include 571,688 lncRNAs from 108 species, offering extended search capabilities and downloadable data in standard formats [136]. PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs, including genomic information, a genome browser, integration of transcriptome datasets, epigenetic modification datasets, and small RNA datasets [137]. Upgraded PLncDB V2.0 currently contains 1,246,372 lncRNAs for 80 plant species with visual expression patterns and epigenetic signals, and targets and regulatory networks for lncRNA function exploration [138]. LncRNAdb documents biological functions of 287 eukaryotic lncRNAs, curating sequences, structural data, genomic context, expression profiles, subcellular localization, conservation patterns, and functional evidence. It further provides a platform for collating literature on lncRNA interactions with genomic elements [139]. LncRNAdb v2.0 significantly expanded its functional lncRNA reference database by integrating Illumina Body Atlas expression profiles, nucleotide sequences, a BLAST search tool, and streamlined data export via direct download or REST API [140]. PLNlncRbase serves as a curated platform hosting 1187 experimentally identified plant lncRNAs from 43 species. Each entry documents species, lncRNA identifier, classification, sequence, inferred biological functions, expression profiles (tissue-, stage-, and condition-specific), experimental validation methods, predicted targets, and primary literature sources [141]. GreeNC established an lncRNA annotation pipeline applied to 37 plant and 6 algal species, annotating more than 120,000 lncRNAs [142].

4.2. Application Values in Agricultural Production

Improving crop yield and quality: Through in-depth research on lncRNAs that regulate crop flowering time, fruit ripening, and yield-related traits, and by precisely regulating the expression of these lncRNAs using gene-editing techniques, it is possible to optimize the flowering time of crops, avoid yield reduction caused by abnormal flowering time, promote better fruit ripening, improve fruit quality, and increase key yield traits such as the number of ears, grains, and grain weight, thereby enhancing crop yield.
Enhancing crop stress resistance: Based on the research on the action mechanisms of lncRNAs in stress responses such as drought, salt stress, diseases, and insect pests, crop varieties with stronger stress resistance can be cultivated. For example, lncRNAs related to drought and salt resistance can be introduced into crops to enhance their survival ability in harsh environments. lncRNAs involved in plant disease and pest defense can be utilized to improve the resistance of crops to diseases and pests, reduce the use of pesticides, and achieve green agricultural production.
Optimizing agricultural production management: Understanding the functions of lncRNAs in plant growth, development, and stress responses is helpful for formulating more scientific and reasonable agricultural production management strategies. According to the response characteristics of lncRNAs to environmental signals, the growth environment of crops can be precisely regulated. For example, before the onset of drought, specific measures can be taken to induce the expression of lncRNAs related to drought resistance, improving the drought resistance of crops. During the critical growth periods of crops, lncRNAs that regulate flowering time can be used to artificially control the flowering time of crops, facilitating unified management and harvesting.

4.3. Limitations and Perspectives of Plant lncRNA Exploration

The discovery and functional analysis of lncRNAs in plants have advanced significantly over the past few decades, particularly with the aid of high-throughput sequencing technologies. Advanced sequencing techniques like strand-specific RNA-seq, isoform-seq, and PacBio SMRT-seq have provided a comprehensive view of lncRNA landscapes across different plant species, leading to the identification of thousands of novel lncRNAs. A growing body of research highlights their critical roles in regulating a wide array of biological processes, with many plant lncRNAs remaining to be fully characterized. These studies underscore the versatility of lncRNAs in mediating plant adaptation to abiotic or biotic stresses and maintaining normal growth and development. As mentioned in this review, lncRNAs were not only associated with a single biology process, but an intricate regulatory network. The most frequent phenomenon is that expression of several lncRNAs responds to different stresses to perform specific biological functions. LncRNA can be used as a molecular marker for breeding and synthetic biology for crop improvement. However, the utilization in production practice still has some limitations due to the operation conditions being highly demanding.
This review synthesizes evidence indicating that lncRNAs coordinate gene expression in response to diverse environmental stressors adversely affecting plants. Although several mechanistic roles for lncRNAs have been identified, current research predominantly emphasizes lncRNA discovery over functional validation. Computational predictions frequently substitute empirical characterization, while biochemical verification of these mechanisms remains challenging. Consequently, rigorous functional studies are imperative. Emerging models position lncRNAs as master regulators of gene expression, primarily through interactions with DNA, miRNAs, and proteins. The protocol to detect lncRNA interactions is different from that for protein-coding genes. To detect lncRNA-protein interaction, tRSA RNA pull-down can be used in vitro [143], yeast three-hybrid assay can detect interaction in vivo [144], and trimolecular fluorescence complementation (TriFC) assay can be used for visualization of RNA-protein interaction [145]. For lncRNA-DNA interaction, chromatin isolation by RNA purification (ChIRP)-seq/qPCR is an executable protocol for identification of DNA sequences interacting with lncRNA [146]. In addition, several plant-specific comprehensive databases have been established and updated for plant lncRNAs annotation, expression pattern, and functional mechanism analysis.

4.4. Conclusions

There are a huge number of lncRNAs in plants; they far outnumber protein-coding genes. Thus, revealing the function of lncRNAs is significant for botanical development. This review overviewed and highlighted the essential roles of lncRNAs in mediating plant responses to abiotic and biotic stresses through complex regulatory networks involving epigenetic regulation, alternative splicing, microRNA precursor formation, and the regulation of gene transcription and translation, providing deeper insights into the regulatory mechanisms of lncRNAs and offering promising strategies for enhancing crop resilience and productivity in response to climate change.

Author Contributions

Writing—original draft preparation, X.B. and R.L.; writing—review and editing, J.C.; supervision, X.D. and J.C.; funding acquisition, X.D. and J.C. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key Research and Development Program of China (2022YFE0111300), the Beijing Natural Science Foundation (6242025), National Natural Science Foundation of China (32270212), the “Tianshan Innovation team” project (2024D14007), the Key R&D Task Special Project of Xinjiang Uygur Autonomous Region (2022B02052-2), and the first batch of “2  +  5” key talent plan in Xinjiang Uygur Autonomous Region.

Data Availability Statements

No new data were created or analyzed in this study. Data sharing is not applicable to this article.

Acknowledgments

During the preparation of this manuscript, we used Doubao (V1.0) for the purposes of modification and beautifying Figure 1. 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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Agronomy 15 01950 g001
Figure 1. Multilevel regulatory rules of lncRNAs in plant growth and stress response [9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58].
Figure 1. Multilevel regulatory rules of lncRNAs in plant growth and stress response [9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58].
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Figure 2. Functional mechanism of plant lncRNAs in regulating gene expression involved in growth and stress response [11,13,20,22,32,33,35,36,37,39,40,41,97,130,131].
Figure 2. Functional mechanism of plant lncRNAs in regulating gene expression involved in growth and stress response [11,13,20,22,32,33,35,36,37,39,40,41,97,130,131].
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Table 1. An overall of plant-specific lncRNA datasets.
Table 1. An overall of plant-specific lncRNA datasets.
NameNo. of lncRNAsPlant SpeciesLinkReference
CANTATAdb45,11710http://yeti.amu.edu.pl/CANATA/,
URL (accessed on 10 August 2025)		[134]
CANTATAdb 2.0239,63139http://yeti.amu.edu.pl/CANTATA/
URL (accessed on 10 August 2025)		[135]
CANTATAdb 3.0571,688108http://yeti.amu.edu.pl/CANTATA/
http://cantata.amu.edu.pl
URL (accessed on 10 August 2025)		[136]
PLncDB16,227Arabidopsis-[137]
PLncDB V2.0246,37280http://plncdb.tobaccodb.org/
URL (accessed on 10 August 2025)		[138]
lncRNAdb28760http://www.lncrnadb.org/
URL (accessed on 10 August 2025)		[139]
lncRNAdb v2.028371https://rnacentral.org/
URL (accessed on 10 August 2025)		[140]
PLNlncRbase118743http://bioinformatics.ahau.edu.cn/PLNlncRbase
URL (accessed on 10 August 2025)		[141]
GreeNC120,00037-[142]
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Bao, X.; Dai, X.; Chen, J.; Li, R. Plant Long Non-Coding RNAs: Multilevel Regulators of Development, Stress Adaptation, and Crop Improvement. Agronomy 2025, 15, 1950. https://doi.org/10.3390/agronomy15081950

AMA Style

Bao X, Dai X, Chen J, Li R. Plant Long Non-Coding RNAs: Multilevel Regulators of Development, Stress Adaptation, and Crop Improvement. Agronomy. 2025; 15(8):1950. https://doi.org/10.3390/agronomy15081950

Chicago/Turabian Style

Bao, Xiyue, Xiaofeng Dai, Jieyin Chen, and Ran Li. 2025. "Plant Long Non-Coding RNAs: Multilevel Regulators of Development, Stress Adaptation, and Crop Improvement" Agronomy 15, no. 8: 1950. https://doi.org/10.3390/agronomy15081950

APA Style

Bao, X., Dai, X., Chen, J., & Li, R. (2025). Plant Long Non-Coding RNAs: Multilevel Regulators of Development, Stress Adaptation, and Crop Improvement. Agronomy, 15(8), 1950. https://doi.org/10.3390/agronomy15081950

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