New Insights into the Regulatory Non-Coding RNAs Mediating Rice–Brown Planthopper Interactions

Abstract

The brown planthopper (Nilaparvata lugens Stål, BPH) is a destructive pest of rice. Non-coding RNAs (ncRNAs) regulate the defense mechanisms in rice and the adaptive strategies of BPHs. In rice, ncRNAs modulate key resistance pathways such as jasmonic acid biosynthesis, flavonoid production, and phenylpropanoid metabolism, which increases BPH resistance. In BPHs, ncRNAs regulate processes such as reproduction, metabolism, and wing polyphenism, which facilitate adaptation and virulence. Cross-kingdom interactions between rice and BPHs reveal the dynamic molecular interplay that underpins this pest–host relationship. These new insights into ncRNA functions will help improve innovative pest management strategies and equip rice varieties with enhanced BPH resistance.

1. Introduction

Rice is an important grain crop that is threatened by several types of environmental stresses. The brown planthopper (BPH), Nilaparvata lugens Stål, is a major pest of rice. The BPH causes significant damage to rice through herbivory, egg laying, and the transmission of viral diseases. These activities can lead to substantial losses in yield and decreases in grain quality during BPH outbreaks [1]. The BPHs have evolved sophisticated strategies to overcome plant defenses, and clarifying the molecular mechanisms underlying these interactions is critically important for understanding the adaptations of BPHs to plant defenses [2,3]. The ability of rice to resist BPH infestation depends on major resistance genes [4,5], as well as on complex regulatory networks, including non-coding RNAs (ncRNAs), which have been identified to play key roles in modulating plant defense responses. The ncRNA-mediated mechanisms are receiving increased attention for their ability to enhance pest resistance, and they provide new directions for the development of more durable and sustainable pest control strategies [6].

The plant genome comprises both protein-coding and non-coding sequences. Over 90% of eukaryotic genomes are transcribed, yet only approximately 2% of these transcripts are translated into proteins. The remaining non-translated transcripts are classified as ncRNAs [7,8,9,10]. These ncRNAs target both DNA and RNA substrates and play key roles in regulating signaling pathways that control essential biological processes such as development, differentiation, and stress responses [11,12].

Eukaryotic ncRNAs include both housekeeping and regulatory ncRNAs. Housekeeping ncRNAs perform key cellular functions [13,14]. Regulatory ncRNAs include short ncRNAs (microRNAs [miRNAs], piwi-interacting RNAs [piRNAs] and small interfering RNAs [siRNAs]), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) [15]. miRNAs are 20–24 nt single-stranded non-coding RNAs that mediate post-transcriptional gene silencing by binding to mRNAs containing specific complementary base pairs [16]. piRNAs are insect sRNAs, which are small RNA molecules, approximately 26–31 nt in length, that bind to Piwi proteins that silence homeobox genes via PcG response elements; they play key roles in transposon silencing, genome stability, and germline development in animals, including insects and mites [17]. siRNAs, which are divided into small interfering RNAs (siRNAs) in plants and into endogenous-siRNAs (endo-siRNAs) in insects, are derived from long double-stranded RNA molecules (including RNAs arising from viral replication, transposon activity, or gene transcription), which can be cut by the Dicer enzyme into RNA fragments of 19–24 nt; the resulting RNA fragments exert their functions when they are loaded onto Argonaute (AGO) proteins and play important roles in gene silencing [15,16]. lncRNAs are another class of non-coding regulatory RNAs, typically longer than 200 nt, that regulate gene expression through mechanisms such as signaling, decoying, guiding, and scaffolding [15]. Unlike linear RNAs, circRNAs are a class of non-coding RNAs with a covalently closed loop structure; they are resistant to exonucleases and can serve as miRNA sponges and regulate gene expression by binding to and sequestering miRNAs [18]. Regulatory ncRNAs play key roles in plant development by regulating the expression of target mRNAs, which affects diverse processes in plants [19,20,21,22]. Moreover, regulatory ncRNAs mediate the stress responses of plants, including the response of rice to BPHs [16,23,24].

Here, we review the functions of regulatory ncRNAs (miRNAs, lncRNAs, and circRNAs) in interactions between rice and BPHs to clarify their potential applications in pest resistance management. We aimed to characterize the molecular mechanisms underlying ncRNA-mediated resistance to enhance our understanding of rice–planthopper interactions and aid the development of effective pest control strategies for this devastating agricultural pest [25].

2. Role of Non-Coding RNAs in Rice–BPH Interactions

ncRNAs regulate key physiological processes involved in both plant defenses and insect adaptation (Table 1) [26,27,28]. In rice, ncRNAs play roles in regulating the resistance to BPHs, while, in BPH, ncRNAs are involved in the adaptation of host plant defenses. (Figure 1). The roles of ncRNAs are often mediated by competing endogenous RNA (ceRNA) networks, in which lncRNAs and circRNAs sequester miRNAs to modulate the expression of the target genes that affect the BPH resistance of rice and the adaptation of BPHs to rice defenses [29]. Clarifying the biological roles of ncRNAs and their contribution to BPH resistance in rice is, thus, critically important for ensuring the sustainability of rice production.

2.1. Roles of ncRNAs in the BPH Resistance of Rice

In rice, ncRNAs regulate defense responses to BPH. Various ncRNAs involved in the response of rice to attack by pests, such as miRNAs, lncRNAs, and circRNAs, have been identified by high-throughput sequencing and genetic experimental studies [16,30]. These ncRNAs orchestrate complex molecular interactions that contribute to basal resistance and specific defense mechanisms against the BPH.

2.1.1. Rice miRNAs Involved in BPH Resistance

Recent small RNA sequencing studies have significantly contributed to our understanding of how miRNAs contribute to the resistance of rice to BPH infestation. A total of 158 differentially expressed miRNAs (DEmiRNAs) were identified before and after BPH feeding in resistant (BPH15 introgression line) and susceptible rice (9311) via small RNA sequencing, which reflects significant miRNA reprogramming [31]. Gene Ontology analysis revealed that their target genes were enriched in various pathways, such as stress response. Functional studies confirmed that miR160f-5p and miR167a-5p are negative regulators of ARF16 and NB-ARC, albeit their roles in resistance mechanisms remain unclear [31]. Additional insights have been provided by combined miRNA and transcriptome analyses of BPH6-transgenic plants (BPH6G) and Nipponbare (wild-type, WT) plants before and after BPH infestation [32]. This study has shown that miR160, miR166, miR169, miR1861, miR319, and miR390 family members play important roles in BPH6-mediated resistance to BPH [32]. Moreover, 34 miRNAs and their 42 corresponding target genes were identified as potential BPH resistance-associated miRNA–mRNA pairs [32]. The miRNA profiling of resistant IR56 rice (carrying BPH3) under virulent and avirulent BPH strains revealed that miRNAs play broader regulatory roles [33]. More miRNAs were downregulated during incompatible interactions, and several miRNAs were implicated to play a role in the responses of IR56 rice to BPH infestation. miR530-5p, miR812s, miR2118g, miR156l-5p, miR435, and two novel miRNAs (novel_16 and novel_52) were identified as potential negative regulators of IR56 rice defenses, which highlights the complex roles that miRNAs play in BPH resistance [33]. Comparative studies of two BPH-susceptible rice varieties (TN1 and Nipponbare) and four resistant varieties carrying different BPH-resistance genes highlight the diverse miRNA responses of miRNAs to BPH feeding [34]. This study revealed 45 DEmiRNAs between BPH-susceptible and BPH-resistant rice varieties, along with 144 miRNAs that responded to BPH feeding. Among 45 identified DEmiRNAs, some appeared to be involved in cross-kingdom RNAi, such as miR5795, which potentially regulates vitellogenin expression in BPHs. However, the precise mechanism of gene regulation by miR5795 requires further investigation [34]. Integrated miRNA and transcriptome analyses of the differential responses of YHY15 rice to both avirulent (biotype 1) and virulent (biotype Y) BPHs showed that biotype Y BPH infestation induced more intense transcriptional responses [35].

Genetic evidence also indicates that miRNAs play roles in mediating BPH resistance. miR156, a master ontogeny regulator, regulates JA/JA-Ile biosynthesis via two pathways: miR156-SPLs-MPK3/MPK6-WRKY70 and miR156-SPLs-OsHI-LOX, both of which negatively regulate BPH resistance [36]. Specifically, the silencing of miR156 in rice enhances resistance to BPH by suppressing jasmonic acid (JA) biosynthesis; the downregulation of miR156 increases the expression of its target SPL genes (e.g., SPL14), which represses JA synthesis by reducing OsHI-LOX expression and increasing Osr9-LOX1 and CYP94 activity, thereby lowering JA and JA-Ile levels [36]. MPK3 and MPK6 phosphorylate WRKY53/WRKY70, and miR156 silencing upregulates MAPKs, downregulates WRKY70, and suppresses OsHI-LOX expression, thereby lowering JA and JA-Ile levels [37]. These findings suggest that miR156 synergistically regulates resistance through multiple pathways. miR396 also negatively regulates BPH resistance via the “miR396-OsGRF8-OsF3H-flavonoid” module [38]. The silencing of miR396 or the overexpression of its target gene OsGRF8 enhances resistance and flavonoid levels, and OsF3H, a BPH-responsive flavonoid biosynthesis gene, is directly regulated by OsGRF8 [38]. The regulatory relationship among miR396, OsGRF8, and OsF3H has been confirmed through genetic modification. Furthermore, the role of flavonoids in the resistance of rice to BPH has been validated by analysis of the flavonoid content and BPH resistance of 39 natural rice varieties [38]. Another pathway mediated by miR159 was identified to enhance the BPH resistance of rice through the miR159-OsGAMYBL2-GS3 signaling pathway [39]. This study demonstrated that miR159 silencing or OsGAMYBL2 overexpression confers BPH resistance, and OsGAMYBL2 directly regulates GS3, which negatively regulates resistance [39]. The role of miR319 in the BPH resistance of rice was also elucidated. The overexpression of miR319 significantly decreased the BPH resistance of rice, and miR319-silenced plants showed reduced BPH susceptibility. The overexpression of the target gene OsPCF5 conferred BPH resistance. The downstream protein MYB30C was regulated by OsPCF5, which enhances BPH resistance via the phenylpropanoid pathway. In summary, miR319 regulates the BPH resistance of rice via the miR319-OsPCF5-OsMYB30C pathway [40]. However, some resistance pathways regulated by miRNAs require further investigation. For instance, R genes (such as BPH15 and BPH6) play a crucial role in the resistance of rice to BPHs. Although previous cytological studies have suggested that miRNAs can regulate the expression of these R genes, no studies have definitively identified the miRNAs that directly target the rice R genes involved in resistance to BPHs [31,32].

2.1.2. Rice lncRNAs and circRNAs Involved in BPH Resistance

lncRNAs and circRNAs participate in the regulatory networks underlying the BPH resistance of rice. The responses of lncRNAs to BPH feeding were examined in KW-BPH36-NIL and its parent line KW [41]. Differential expression analysis revealed 384 differentially expressed lncRNAs (DElncRNAs) affecting the expression patterns of coding genes. The most robust defense response was observed in the resistant line KW-BPH36-NIL 48 h after infestation, and the expression of growth- and metabolism-related genes was significantly downregulated; this is consistent with the metabolic balance theory [41]. Transcriptomic analyses in two BPH-resistant rice varieties (IR36 and R476) and one susceptible variety (TN1) revealed 649 DElncRNAs out of 2283 identified [42]. During BPH infestation, resistance-related lncRNAs targeted NBS-LRRs, RLKs, and stress-responsive miRNAs (e.g., miR2118, miR528, miR1320), which indicated that they play dual roles in basal defense and specific resistance mechanisms [42]. High-throughput sequencing was performed to characterize the response of circRNAs in rice to BPH [43]. A total of 186 circRNAs were identified in IR56 rice across three conditions: IR-IR56-BPH (infested by IR56-BPH), IR-TN1-BPH (infested by TN1-BPH), and IR-CK (uninfested control). A total of 39 circRNAs were upregulated and 43 circRNAs were downregulated in IR-IR56-BPH compared with IR-CK. Similarly, 42 circRNAs were upregulated and another 42 were downregulated in IR-TN1-BPH compared with IR-CK. These circRNAs may regulate mRNAs associated with defense responses, phytohormone pathways, and growth-regulating factors through the ceRNA network, which potentially affects BPH infestations in IR56 rice [43]. Sequencing analyses of lncRNAs and circRNAs in BPH6G and wild-type rice plants have clarified the roles of these ncRNAs in BPH resistance [29]. A total of 310 lncRNAs and 129 circRNAs were identified as differentially expressed, and these likely contributed to BPH resistance mechanisms [29]. The hypothesis that lncRNAs and circRNAs act as ceRNAs that regulate miRNAs, and their target genes were first proposed more than a decade ago [44]. Consistent with this model, a ceRNA network comprising 39 DElncRNAs, 21 differentially expressed circRNAs (DEcircRNAs), 133 DEmiRNAs, and 834 differentially expressed mRNAs (DEmRNAs) was constructed to explore their regulatory relationships [29]. Dual-luciferase reporter assays further revealed that miR1846c and miR530 are targeted by the lncRNAs XLOC_042442 and XLOC_028297, respectively, which provided support for the regulatory interactions within the network [29].

2.2. Roles of ncRNAs in the Adaptation of BPHs to Rice

ncRNAs regulate critical processes in BPHs, including adaptation, development, reproduction, and virulence [12,45,46,47,48,49]. Investigation of the molecular mechanisms of ncRNAs in BPHs and their interactions with rice targets can provide valuable insights for innovative pest management approaches.

2.2.1. BPH miRNAs Involved in Development, Adaptation, and Reproduction

miRNAs orchestrate complex regulatory networks that underlie the development of BPHs, enable adaptation to BPH-resistant rice varieties, and optimize reproductive strategies, thus making studies of miRNAs critically important for clarifying pest dynamics [12]. The knockdown of miRNA biogenesis genes resulted in high mortality rates and reduced fecundity [50]. Moreover, the expression profiles of miR-34-5p, miR-275-3p, miR-317-3p, miR-14, Let-7-1, and miR-2a-3p were significantly altered following the knockdown of core miRNA genes, indicating that the miRNA pathway is essential for BPH development and reproduction [50]. The roles of miRNAs in the adaptation of BPHs to rice were revealed through the high-throughput sequencing of two BPH populations, Biotype I and Biotype Y, which are adapted to the susceptible and moderately resistant rice varieties TN1 and YHY15, respectively [51]. Among 41 novel miRNAs identified, 26 were differentially expressed and related to metabolism pathways, including glycolysis and gluconeogenesis, which enhances our understanding of how miRNAs mediate the adaptation of BPHs to rice [51]. Molting, a key process in BPH development, is regulated by miRNAs that influence insect hormone 20-hydroxyecdysone (20E)-induced chitin biosynthesis pathways. miR-8-5p and miR-2a-3p were identified as key regulators of 20E-induced chitin biosynthesis by targeting Tre-2 and PAGM, respectively, which are essential components of the chitin biosynthesis pathway [52]. Both miRNAs are transcriptionally repressed by Broad-Complex (BR-C) in the 20E signaling pathway. miR-8-5p and miR-2a-3p overexpression disrupted molting, reduced chitin content, and induced molting defects, which highlights their roles in linking the 20E pathway to chitin biosynthesis [52]. Additionally, high-throughput sequencing identified 61 conserved and 326 novel miRNAs, including 36 differentially expressed miRNAs across developmental stages [53]. Nlu-miR-173 was shown to regulate molting by targeting the transcription factor NlFtz-F1 within the 20E pathway [53]. Additionally, its transcription was enhanced by BR-C, which indicates that it helps ensure proper molting. These findings indicate that miRNAs regulate the growth of BPHs and suggest that these miRNAs represent promising targets for pest control strategies [53]. Wing polyphenism in BPH, a critical adaptation for dispersal and reproduction, is regulated by miRNA [54]. Small RNA libraries from nymph instars of LW and SW BPH strains revealed an miRNA network that underlies differences in wing morphs by regulating gene and hormone expression. Key pathways were identified to play a role in wing morph variation. Nlu-miR-14-3p, Nlu-miR-9a-5p, and Nlu-miR-315-5p directly targeted insulin receptors, indicating that miRNAs play major roles in wing dimorphism and BPH adaptation [54]. Another study also showed that miR-9a is a regulator of the Hox gene Ultrabithorax (Ubx), which controls wing morphs in BPHs [55]. Host plant quality was shown to modulate this regulatory cascade: under low-nutritional conditions, increased NlInR1 and decreased NlInR2 expression elevated miR-9a levels, reducing NlUbx transcripts and leading to longer wings. This miRNA-mediated cascade highlights the significance of the interplay between environmental factors and genetic regulation in wing polyphenism [55]. Reproduction is essential for the maintenance of insect populations [56]. The mechanisms governing reproduction in insects have been extensively studied as they are crucial for refining pest control strategies. Key reproductive pathways, such as ecdysone, juvenile hormone, and insulin, are regulated by miRNAs [57,58,59,60,61]. Functional screening of miRNAs in Nilaparvata lugens revealed that miR-4868b is a key regulator of fecundity, and this miRNA targeted the fecundity-related gene NlGS (glutamine synthetase). The effects of the injection of miR-4868b mimicked the effects of reduced NlGS expression, which leads to decreased fecundity, the disruption of ovarian development, and the suppression of vitellogenin (Vg) expression; inhibitors had the opposite effect. These findings highlight the key role of miRNAs, specifically miR-4868b, in modulating the reproductive capacity of N. lugens, which enhances our understanding of miRNA-mediated regulation in BPH development and reproduction [62]. Furthermore, four miRNAs (miR-9a-5p, miR-34-5p, miR-275-3p, and miR-317-3p) were identified as critical regulators of reproduction in light of their effect on vitellogenin biosynthesis and reproductive processes across three developmental stages of short-winged morphs in female adults [63]. miR-34-5p was shown to be a key regulator of reproduction. miR-34-5p overexpression reduced fecundity and Vg expression. Additionally, the target genes of miR-34-5p were predicted to be involved in 20E signaling and apoptosis. These findings will help clarify how miRNAs regulate the reproductive development of BPHs [63].

2.2.2. lncRNAs Involved in the Adaptation, Fecundity, and Virulence of BPHs

lncRNAs regulate the adaptation, virulence, and fecundity of BPHs on diverse host plants, indicating that they have major implications for pest biology. Numerous studies have shown that lncRNAs mediate key biological processes, such as cell differentiation [64], transcription regulation [65], and dosage compensation [66,67]. Although the specific roles of lncRNAs have only been identified for a small subset of lncRNAs, the functions of most lncRNAs remain unknown [12]. Comparative lncRNA expression profiling between virulent BPH populations on susceptible (TN1) and resistant (YHY15) rice varieties identified 3112 high-confidence lncRNAs, including 157 DElncRNAs and 675 DEmRNAs. These RNAs were enriched in various GO terms, such as carbon metabolism, glutathione metabolism, and arginine and proline metabolism, indicating that they might significantly affect the adaptation of BPHs to different rice varieties [68]. A comprehensive analysis revealed 2439 lncRNA transcripts across multiple BPH populations, including high- and low-fecundity (HFP, LFP) strains and virulent Mudgo and TN1 strains. Some lncRNAs were expressed in fecundity- and virulence-related samples, and three lncRNAs in HFP and LFP populations were associated with reproduction-related genes. These findings indicate that lncRNAs mediate the regulation of reproductive and virulence-related traits, which has implications for the development of sustainable pest control strategies [69].

2.3. Cross-Kingdom Interactions Between Rice and BPHs Mediated by ncRNAs

Recent research has shown that ncRNAs can play bidirectional roles in regulating rice–BPH interactions, particularly via cross-kingdom RNAi [70,71]. Animals have been shown to acquire plant miRNAs through herbivory, and these plant miRNAs can regulate gene expression [72]. Therefore, rice miRNAs could be acquired by BPHs during feeding, which could regulate the expression of genes in BPHs [34]. BPH-derived miRNAs could also regulate plant physiology [73]. These interactions indicate that ncRNAs could serve as key effectors regulating the plant–insect dynamics, which has implications for both host immunity and pest adaptation.

2.3.1. Rice-Derived miRNAs Targeting BPH

Rice-derived miRNAs, such as miR162a and miR5795, play key roles in regulating defense against BPHs via cross-kingdom RNAi to disrupt important physiological processes in BPHs. For example, rice-derived miR162a targets the Target of rapamycin (NlTOR) gene in BPHs, which is essential for reproduction and nutrient sensing. The downregulation of NlTOR reduces vitellogenin expression, a key determinant of oviposition, which significantly impairs BPH fecundity. Transgenic rice plants expressing miR162a-m1 (a modified derivative of miR162a) effectively reduced BPH survival rates, and this did not have detrimental effects on plant development [74]. In commercial or experimental applications, this cross-kingdom RNA interference (RNAi) strategy has the potential to be harnessed for the development of BPH-resistant rice varieties. For instance, transgenic rice expressing optimized versions of miR162a, such as osa-miR162a-m1, shows high BPH resistance, and its growth and development are not inhibited. This strategy is not only effective in reducing pest populations and damage but also addresses the growing concerns over pesticide resistance and environmental sustainability. In addition, the inhibition of the α-linolenic acid metabolic pathway negatively affects the host choice of BPHs and suppresses the jasmonate-mediated defense response of rice; this potentially reflects a competitive mechanism that developed via long-term pest–host co-evolution [75]. Additionally, miR5795 targets the vitellogenin (NlVg) gene in BPH and results in decreased fecundity. This interference leads to a 16.07% reduction in egg production and a 16.45% decrease in hatching rates [34]. Both miR162a and miR5795 demonstrate the power of rice-derived miRNAs as natural insecticides and provide sustainable alternatives to chemical pesticides. Overall, these miRNAs indicate that cross-kingdom RNAi could be effective for the development of BPH-resistant rice varieties.

Table 1. Key ncRNAs involved in interactions between rice and BPH.

ncRNA	Species	Target(s)	Function in BPH Resistance	Method	Ref.
XLOC_042442	Oryza sativa	miR1846c	Function as ceRNAs by sponging miR1846c	Sequencing and experimental validation	[29]
XLOC_028297	Oryza sativa	miR530	Function as ceRNAs by sponging miR530	Sequencing and experimental validation	[29]
miR160f-5p	Oryza sativa	ARF16	Negatively regulates ARF16, influencing auxin signaling pathways	Sequencing	[31]
miR167a-5p	Oryza sativa	NB-ARC	Negatively regulates NB-ARC, involved in disease resistance	Sequencing	[31]
miR156b-3p	Oryza sativa	GDSL	Negatively regulates GDSL-like lipase	Sequencing	[32]
miR169i-5p.2	Oryza sativa	LRR	Negatively regulates leucine-rich repeat family protein	Sequencing	[32]
miR5795	Oryza sativa	NlVg	Mediates the fecundity of BPH by inhibiting vitellogenin (NlVg) expression in BPH	Sequencing	[34]
miR156	Oryza sativa	SPLs	Mediates JA/JA-Ile biosynthesis, negatively regulating BPH resistance	Transgenic validation	[36]
miR396	Oryza sativa	OsGRF8	Negatively regulates BPH resistance through flavonoid biosynthesis	Transgenic validation	[38]
miR159	Oryza sativa	OsGAMYBL2	Regulates OsGAMYBL2-GS3 pathway, enhancing BPH resistance	Transgenic validation	[39]
miR319	Oryza sativa	OsPCF5	Regulates miR319-OsPCF5-OsMYB30C pathway, mediating BPH resistance	Transgenic validation	[40]
miR162a	Oryza sativa	NlTOR	Mediates cross-kingdom RNAi, regulating BPH reproduction	Transgenic validation	[74]
miR-8-5p	Nilaparvata lugens	NlTre-2	Regulates chitin biosynthesis	Sequencing and experimental validation	[52]
miR-2a-3p	Nilaparvata lugens	NlPAGM	Regulates chitin biosynthesis	Sequencing and experimental validation	[52]
miR-173	Nilaparvata lugens	NlFtz-F1	Regulates molting by targeting the transcription factor NlFtz-F1 within the 20E pathway	Sequencing and experimental validation	[53]
miR-14-3p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-9a-5p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-315-5p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-9a	Nilaparvata lugens	NlUbx	Regulates wing length in BPHs	Experimental validation	[55]
miR-4868b	Nilaparvata lugens	NlGS	Modulates reproductive capacity in BPHs	Experimental validation	[62]
miR-34-5p	Nilaparvata lugens	NLHR4, NlCp-1, NlSPATA20	Is involved in reproductive regulation	Sequencing	[63]
miR-7-5P	Nilaparvata lugens	OsbZIP43	Weakens rice immune responses	Experimental validation	[73]

Notes: ARF16 (auxin response factor 16 gene), NB-ARC (NB-ARC domain-containing protein gene), GDSL (GDSL-like lipase gene), LRR (leucine-rich repeat family protein gene), NlVg (N. lugens vitellogenin gene), SPLs (squamosa promoter-binding protein-like gene), OsGRF8 (O. sativa growth regulating factor 8 gene), OsGAMYBL2 (O. sativa R2R3 MYB domain transcription factor gene), GS3 (G-protein γ subunit gene), OsPCF5 (O. sativa proliferating cell factor 5 gene), NlTOR (N. lugens target of rapamycin gene), NlTre-2 (N. lugens trehalase-2 gene), NlPAGM (N. lugens phosphoacetylglucosamine mutase gene), NlFtz-F1 (N. lugens Ftz-F1 transcription factor gene), NlInRs (N. lugens insulin receptors gene), NlUbx (N. lugens hox gene ultrabithorax), NlGS (N. lugens glutamine synthetase gene), NLHR4 (N. lugens hormone receptor 4 gene), NlCp-1 (N. lugens caspase-1 gene), NlSPATA20 (N. lugens spermatogenesis-associated protein 20 gene), OsbZIP43 (O. sativa bZIP transcription factor 43).

Table 1. Key ncRNAs involved in interactions between rice and BPH.

ncRNA	Species	Target(s)	Function in BPH Resistance	Method	Ref.
XLOC_042442	Oryza sativa	miR1846c	Function as ceRNAs by sponging miR1846c	Sequencing and experimental validation	[29]
XLOC_028297	Oryza sativa	miR530	Function as ceRNAs by sponging miR530	Sequencing and experimental validation	[29]
miR160f-5p	Oryza sativa	ARF16	Negatively regulates ARF16, influencing auxin signaling pathways	Sequencing	[31]
miR167a-5p	Oryza sativa	NB-ARC	Negatively regulates NB-ARC, involved in disease resistance	Sequencing	[31]
miR156b-3p	Oryza sativa	GDSL	Negatively regulates GDSL-like lipase	Sequencing	[32]
miR169i-5p.2	Oryza sativa	LRR	Negatively regulates leucine-rich repeat family protein	Sequencing	[32]
miR5795	Oryza sativa	NlVg	Mediates the fecundity of BPH by inhibiting vitellogenin (NlVg) expression in BPH	Sequencing	[34]
miR156	Oryza sativa	SPLs	Mediates JA/JA-Ile biosynthesis, negatively regulating BPH resistance	Transgenic validation	[36]
miR396	Oryza sativa	OsGRF8	Negatively regulates BPH resistance through flavonoid biosynthesis	Transgenic validation	[38]
miR159	Oryza sativa	OsGAMYBL2	Regulates OsGAMYBL2-GS3 pathway, enhancing BPH resistance	Transgenic validation	[39]
miR319	Oryza sativa	OsPCF5	Regulates miR319-OsPCF5-OsMYB30C pathway, mediating BPH resistance	Transgenic validation	[40]
miR162a	Oryza sativa	NlTOR	Mediates cross-kingdom RNAi, regulating BPH reproduction	Transgenic validation	[74]
miR-8-5p	Nilaparvata lugens	NlTre-2	Regulates chitin biosynthesis	Sequencing and experimental validation	[52]
miR-2a-3p	Nilaparvata lugens	NlPAGM	Regulates chitin biosynthesis	Sequencing and experimental validation	[52]
miR-173	Nilaparvata lugens	NlFtz-F1	Regulates molting by targeting the transcription factor NlFtz-F1 within the 20E pathway	Sequencing and experimental validation	[53]
miR-14-3p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-9a-5p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-315-5p	Nilaparvata lugens	NlInRs	Modulates the wing morph of BPHs	Sequencing	[54]
miR-9a	Nilaparvata lugens	NlUbx	Regulates wing length in BPHs	Experimental validation	[55]
miR-4868b	Nilaparvata lugens	NlGS	Modulates reproductive capacity in BPHs	Experimental validation	[62]
miR-34-5p	Nilaparvata lugens	NLHR4, NlCp-1, NlSPATA20	Is involved in reproductive regulation	Sequencing	[63]
miR-7-5P	Nilaparvata lugens	OsbZIP43	Weakens rice immune responses	Experimental validation	[73]

Notes: ARF16 (auxin response factor 16 gene), NB-ARC (NB-ARC domain-containing protein gene), GDSL (GDSL-like lipase gene), LRR (leucine-rich repeat family protein gene), NlVg (N. lugens vitellogenin gene), SPLs (squamosa promoter-binding protein-like gene), OsGRF8 (O. sativa growth regulating factor 8 gene), OsGAMYBL2 (O. sativa R2R3 MYB domain transcription factor gene), GS3 (G-protein γ subunit gene), OsPCF5 (O. sativa proliferating cell factor 5 gene), NlTOR (N. lugens target of rapamycin gene), NlTre-2 (N. lugens trehalase-2 gene), NlPAGM (N. lugens phosphoacetylglucosamine mutase gene), NlFtz-F1 (N. lugens Ftz-F1 transcription factor gene), NlInRs (N. lugens insulin receptors gene), NlUbx (N. lugens hox gene ultrabithorax), NlGS (N. lugens glutamine synthetase gene), NLHR4 (N. lugens hormone receptor 4 gene), NlCp-1 (N. lugens caspase-1 gene), NlSPATA20 (N. lugens spermatogenesis-associated protein 20 gene), OsbZIP43 (O. sativa bZIP transcription factor 43).

2.3.2. BPH-Derived miRNAs Targeting Rice

BPHs secrete salivary miRNAs into rice, which serve as salivary effectors that target multiple host genes and suppress plant immunity. Recent discoveries indicate that the BPHs secrete salivary miRNAs into rice to suppress plant immunity. miR-7-5P targets the rice immune-associated gene OsbZIP43, a bZIP transcription factor essential for defense signaling [73]. When OsbZIP43 expression is suppressed, miR-7-5P weakens rice immune responses, which enables sustained phloem sap extraction by the pest. The functional significance of miR-7-5P lies in its ability to enhance BPH feeding efficiency. miR-7-5P silencing significantly reduced honeydew excretion and offspring production, indicating that the feeding activity was impaired. The negative effects were only observed when BPHs fed on rice plants not when they were fed an artificial diet, indicating that miRNAs help overcome plant-specific defenses. This mechanism has implications for commercial and experimental applications. For example, researchers can develop transgenic rice varieties that express antagonistic factors to counteract the effects of miR-7-5P, thus enhancing the BPH resistance of rice. This approach is similar to that involving miR162a, but it specifically targets the expression of genes in the BPHs to suppress pest activity. Aside from miR-7-5P, other miRNAs, including miR-100-5P and miR-184-3P, are secreted into rice during BPH feeding, and they migrate systemically and may affect multiple host pathways [73]. These findings enhance our understanding of salivary miRNAs as key virulence factors and highlight their role as molecular targets in pest management strategies.

2.4. Integration of Multi-Omics Data for Clarifying Rice–BPH Interactions

Integrating multi-omics data, including transcriptomics, proteomics, and metabolomics data, can provide comprehensive insights into the molecular mechanisms underlying rice–BPH interactions. Transcriptomics analyses reveal gene expression changes, including those of non-coding RNAs such as miRNAs, lncRNAs, and circRNAs, which play a role in both rice defense and the adaptation of BPHs. The combined use of both transcriptomics and proteomics, which identifies protein expression patterns, allows researchers to link gene activity to protein function in key defense pathways [76]. Metabolomics can further complement these findings by identifying metabolic changes in rice in response to BPH feeding, which can provide new insights into plant resistance or susceptibility [77,78]. The integration of these datasets can provide comprehensive insights into the interactions between rice and BPHs at the molecular level. This approach can identify potential biomarkers for BPH resistance and uncover new targets for pest control strategies, thereby aiding the development of more effective pest management strategies and resistant rice varieties. Despite the challenges associated with data integration, advanced bioinformatics tools can help integrate the results of these different analytical approaches and enhance pest management strategies.

2.5. Practical Implications and Potential Technical or Economic Challenges

Non-coding RNAs (ncRNAs) offer promising prospects for sustainable pest control by targeting specific pest genes, thereby reducing the reliance on chemical pesticides [16]. However, the use of ncRNA-based pest control in integrated pest management strategies invariably involves practical, technical, and economic challenges that must be overcome for their large-scale implementation, especially in the management of pests such as BPHs in rice fields.

2.5.1. Practical Implications of ncRNA-Based Pest Control

The integration of ncRNAs into pest control strategies has profound implications for both pest management practices and ecological outcomes [79]. Given the complex interactions between rice and BPHs, successful applications must also account for the effects of environmental factors such as water stress, plant growth stage, and pest density on the efficacy of ncRNA-based control. The cost effectiveness and scalability of these methods must be evaluated; the challenges associated with applying these methods in the field, such as ensuring consistency across different environments and pest populations, also require consideration.

2.5.2. Technical Challenges in the Application of RNAi for Pest Control

The synthesis and delivery of dsRNA for pest control face significant technical challenges. The synthesis of dsRNA involves producing large quantities of high-purity dsRNA, ensuring optimal sequence design, and managing costly reagents [80]. Delivery systems, such as nanoparticles and liposomes, are still being refined to enhance their stability and efficacy under field conditions [81,82]. In rice ecosystems, environmental conditions such as high humidity, rainfall, and temperature fluctuations during the rice growing season may further complicate the effective delivery and persistence of dsRNA.

Another technical challenge associated with the use of RNAi in pest control is the off-target effects. Non-coding RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), can potentially silence genes in non-target organisms, which can have unintended ecological consequences [83]. In rice ecosystems, the risk of off-target effects can extend to beneficial insects or other arthropods that interact with rice plants, such as natural predators of BPHs. This may inadvertently disrupt pest control services in the field. In particular, unintended gene silencing in beneficial insects or other non-target organisms can disrupt local ecosystems and food webs.

2.5.3. Economic Challenges and Regulatory Considerations

The initial costs of RNAi-based pest control methods, including the production and delivery of dsRNA as mentioned above, pose barriers to their use [80,81,82]. Farmers may be hesitant to adopt these methods due to the potential for lower short-term returns compared with conventional chemical pesticides. Furthermore, the regulatory approval processes for RNAi-based technologies—along with the need for clear, standardized frameworks—must be addressed to facilitate their deployment [84]. For rice-based pest management, regulatory approval must also consider the potential ecological impacts on non-target organisms and the rice ecosystem as a whole, particularly when targeting pests such as BPHs, which are critical for maintaining the balance of the local food web. The development of cost-effective production and delivery methods and the establishment of regulatory guidelines will be essential for ensuring the economic feasibility of these technologies for their large-scale use in agriculture.

3. Conclusions and Perspectives

In this review, we summarized the latest advances in the ncRNA-mediated regulation of rice–BPH interactions. ncRNAs play a critical role in regulating rice–BPH interactions and influence both plant defense mechanisms and BPH adaptation strategies. Advances in high-throughput sequencing and genetic studies have revealed that miRNAs, lncRNAs, and circRNAs are key to the BPH resistance of rice and the ability of BPHs to adapt to host defenses (Table 1). These ncRNAs regulate key physiological processes, including stress responses, reproduction, and metabolism through complex molecular networks (Figure 1).

Future research should focus on further elucidating the regulatory pathways governing ncRNAs in both rice and BPHs, and there is a particularly urgent need to clarify how ncRNAs interact with specific resistance genes and environmental cues. Integrating genetic and multi-omics data (e.g., transcriptomics, proteomics, and metabolomics) will be crucial for constructing comprehensive models of rice–BPH interactions and for improving our understanding of these dynamic processes.

Moreover, cross-kingdom RNA interference (RNAi) is an area of growing interest, as both rice-derived and BPH-derived miRNAs have been shown to mutually modulate key biological pathways. Investigating these bidirectional interactions could lead to the development of innovative pest management strategies, in which ncRNAs are targeted to either enhance rice resistance or disrupt BPH development.

In conclusion, ncRNAs are central regulators in rice–BPH interactions, and continued research into their functions will provide valuable insights with implications for the development of sustainable pest control methods and improving rice productivity. Additionally, leveraging emerging technologies such as CRISPR/Cas to manipulate ncRNAs could enhance the BPH resistance of rice, which could promote the development of transgenic rice varieties and more effective RNAi-based pest management strategies.