Epigenetic Modifications, Immune Control Processes, and Plant Responses to Nematodes

Abstract

Plants adapt to biotic and abiotic stresses through physiological, morphological, and genetic changes. In recent years, the fundamental roles of epigenetic mechanisms as regulators of various immune–biological processes in nematode–plant interactions have been increasingly recognized. Epigenetic control mechanisms include non-coding RNAs (ncRNAs), DNA methylation, and histone modifications. Gene expression and gene silencing play crucial roles in activated induced resistance during pathogen attacks. DNA methylation and histone modifications are linked to defense priming or immune memory, such as systemic acquired resistance (SAR). In addition, epigenetic processes play important roles in long-term defense priming, contributing to the development of immunological memory under future stress conditions. Therefore, advances in understanding epigenetic mechanisms hold considerable potential for future research on plant–nematode interactions. However, further development in the basic understanding of interactions among various stresses, the expansion of markers for epigenetic changes, and the permanence of priming are necessary to optimize its utilization in crop protection programs. In this paper, we focus on the function of epigenetic mechanisms in plant defense responses to nematode infection, specifically root-knot nematodes (RKNs). Understanding the adaptive ability of RKNs is important for developing suitable control methods. Additionally, we explore the role of epigenetic mechanisms in plant interactions with biological control agents.

1. Introduction

Plants are consistently exposed to biotic stresses, including parasitic nematodes, which impair their growth and cause significant worldwide losses across diverse plant host ranges [1]. Therefore, in response to these stressful situations, plants exhibit a range of variable phenotypes (i.e., phenotypic plasticity), and these changes can transmit to the next generation, modulating the offspring phenotype through epigenetic mechanisms [2]. Preparing offspring to attack is important for plants with short life cycles, and in the long term, phenotypic plasticity can result in better-adapted populations to survive in unfavorable environments [3].

Plant parasitic nematode (PPN) attacks and feeding result in tissue damage, necrosis, and a weakened plant. In response, plants activate their constitutive or induced defense mechanisms against PPN parasitism. Understanding these plant defense mechanisms is crucial for developing effective, innovative, and sustainable strategies for PPN management.

Indeed, the interaction between plants and micro-organisms is one of the most considerable triggers in plant responses. When plants are exposed to pathogen attacks, they develop a complex defense system to identify the invading micro-organisms [4]. Plant immunity consists of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is correlated with a pathogen-associated molecular pattern (PAMP) or a damage-associated molecular pattern (DAMP). Plants detect PPNs before physical contact by perceiving PPN-secreted compounds and priming defense responses, similar to detecting PAMPs [5]. Some compounds released by PPNs, such as pheromone derivatives of dideoxysugar ascarylose (Ascarosides), have been expressed as nematode-associated molecular patterns (NAMPs) that can be detected by the host through surface-localized pattern recognition receptors (PPRs) [5]. One such NAMP, named ‘‘NemaWater’’ (a solution produced by incubating second-stage juveniles (J2s) in water for 24 h) involves a PTI response in the host plant [6]. Ascarosides are detected in NemaWater [6]. Indeed, pathogen-secreted effector molecules lead to specific defense responses [7].

In addition, contact with PPNs causes damage to the host tissues and results in the release of DAMPs, which can induce wounding-related plant defense responses [5]. Upon detecting DAMPs or NAMPs, hosts respond by triggering different biochemical changes with stress signaling, activating PTI as the inducible defense against invading nematodes. On the other hand, PPNs could neutralize PTI by producing effectors that dominate PTI responses [8].

Among PPNs, two groups of nematodes—root-knot and cyst nematodes—are important species to crops. RKNs, Meloidogyne spp., (the obligate sedentary endoparasites), cause worldwide losses to diverse host ranges of plants [9,10]. RKNs, due to their asexual reproduction, have various advantages for studying the mechanisms and processes involved in epigenetic phenomena. The genome sequencing of RKNs has identified many genes involved in adaptation to environmental stresses [11]. RKN–plant interactions are activated by forming feeding sites. The feeding regions derived by RKNs are named giant cells (GCs). The GCs are necessary for determining the feeding mechanisms in nematode life cycles. Indeed, these nematodes, by inducing GCs within galls, are distinguished by large-scale gene suppression at early stages [12]. Effector proteins released by the stylet directly or indirectly impress the interactions between nematodes and plants. These interactions between effectors and plant resistance proteins trigger susceptibility or resistance responses [13]. In these pathways, post-transcriptional and translational changes and epigenetic regulations play a definitive role [14].

Some plant species carry nematode resistance genes, including the Mi-1.2 gene that provides specific tomato cultivars resistance to RKNs like Meloidogyne incognita [15]. Resistance proteins detect nematode effectors, leading to the induction of ETI, which is typically systemic and crucial to acquiring a robust defense response [16]. Induced cellular defense mechanisms, like cell wall reinforcement, kinase-dependent signaling, reactive oxygen species (ROS) burst, pathogenesis-related (PR) protein synthesis, and transcription factor (TF) activation, are involved in PTI and ETI [17]. The interplay of these activities plays a vital role in strengthening immune responses, not only at the site of local infection but also in distant areas, thereby limiting the systemic spread of pathogens or pests [17].

Nevertheless, the plant immune system employs various strategies, demonstrating high plasticity in response to the invader lifestyle. These strategies involve gene regulation, signal molecules, small RNAs, and plant hormones [18]. Therefore, in plant–microbe interactions, genetic changes with adaptability advantages can be subject to natural selection and enhance the efficiency of biological systems [19]. Research indicates that epigenetic changes, which are heritable throughout an organism’s life cycles, play considerable roles in shaping plant–microbe relationships [20]. This review discusses the genetic and regulatory patterns of epigenetic mechanisms during plant–RKN interactions. Additionally, the role of epigenetic mechanisms during plant–biological control agents’ interactions is also investigated. Understanding the interplay between epigenetics modification and plant defense responses offers valuable insights into plant–nematode interactions.

2. Plant–Nematode Interaction

2.1. Environmental Factors in the Plant–Nematode Interaction

Environmental factors such as temperature, moisture, and soil quality influence plant defense mechanisms and nematode infection rates. Soil quality is evaluated based on chemical nutrient composition, physical structure, and biological indicators [21,22]. Soil nematodes, as biological indicators, are a key component of soil fauna, occupying various ecological niches [23,24]. The key factors influencing soil nematode community characteristics are, likely, the intensity of ecosystem disturbances and the level of resource input. Natural forest ecosystems typically sustain more diverse and abundant soil nematodes compared to agricultural ecosystems [25]. Additionally, in agricultural soils, nematode populations tend to be more abundant under no-tillage practices than under conventional tillage methods [22].

In addition, under diverse climatic conditions, PPNs cause significant economic damage to various agricultural and horticultural crops. Due to direct exposure to the surrounding environment, the physiology and biology of nematodes are heavily influenced by environmental factors such as temperature, humidity, precipitation, and extreme weather conditions. Changes in these environmental factors are expected to intensify PPN damage by promoting their distribution, abundance, and reproduction while reducing plant defenses. However, factors such as sex reversal, cryptobiosis, and decreased survival rates may mitigate some of these effects. Therefore, the bio-ecological changes in the PPNs will require tweaking their management strategies, such as integrated nematode management with reliance on host resistance and biocontrol [26].

2.2. Transcription Factors in the Plant–Nematode Interaction

Transcription factors (TFs) can play significant roles in plant resistance to biotic stresses by affecting the expression of defense-related genes. The TF families, including MYBs (R2R3-type MYB domain protein), WRKYs (WRKY domain protein), AP2/ERF (apetala 2/ethylene response factor protein), and bHLH (basic helix–loop–helix domain protein), have been identified as key regulators in plant responses to PPN infections [27,28].

These TF genes facilitate the development of genetically engineered plants with enhanced performance to PPN infections. Therefore, identifying the interaction between TFs and effectors could lead to the development of strategies for disrupting these interactions and preventing nematode infections [29]. Some studies indicate that TFs act as transcriptional reprogramming during plant responses to PPN parasitism. For example, differential expression of WRKY and MYB TFs was observed in eggplant roots in reaction to RKNs [30]. Also, about 93 differentially expressed TFs, including WRKY, ERF, and MYB, were identified in response to RKN infection [31]. Furthermore, the upregulation of SlWRKY45 reduced resistance to RKNs and suppressed jasmonic acid (JA) biosynthesis in tomato [32].

However, the expression of the transcription factor genes ERF115 and PHYTOCHROME A TRANSDUCTION1 (PAT1), induced by M. incognita, plays a crucial role in maintaining gall functionality, thereby positively influencing nematode reproduction [33]. Similarly, the TF PUCHI gene in Arabidopsis exhibited overexpression after RKN infection, facilitating the development of giant cells through regulating fatty acid biosynthesis [34].

Even among the members of the same family of TFs, various functions have been observed. For example, the upregulation of SlWRKY31 and SlWRKY16 led to increased M. javanica infection in tomato [35]. Furthermore, the inoculation of M. incognita resulted in the upregulation of SlWRKY80 in the resistant tomato roots that possess the Mi-1 gene, indicating that SlWRKY80 is important to the Mi-1-mediated disease resistance mechanism [36]. Similarly, the upregulation of SlWRKY3 in tomato roots led to a reduction in M. javanica infection, which was associated with the activation of defense signaling pathways mediated by lipids, salicylic acid, and indole-3-butyric acid [37].

Notably, these stimuli successfully activate the innate immune system of plants, thereby inhibiting PPN infections in various plant species. Consequently, farmers can incorporate them into PPN management strategies [38].

2.3. Epigenetics in Plant–Nematode Interaction

Epigenetics involves processes that result in stable changes in gene expression throughout cell divisions without changing the DNA sequence [39]. Epigenetic mechanisms comprise DNA methylation, histone modifications, and the regulation of gene expression by non-coding RNAs (ncRNAs). This mechanism plays an important role in determining chromatin structure, which significantly influences the cell transcriptome under normal and stressful conditions [40]. Hence, the relationship between epigenetic and plant defense responses has attracted particular attention in plant–pathogen interaction research. Notably, PPNs, which depend on syncytia or giant cells for survival, use epigenetic mechanisms in their pathogenic interactions. In establishing these specialized nematode feeding sites, huge changes in chromatin structure and gene expression are required [40].

There is evidence of epigenetic mechanisms in the biological interaction between pathogens and hosts. In addition, the modulation of epigenetic plasticity and epigenetic inheritance mechanisms to experimental studies and evolutionary models of pathogen–host interactions could offer new insights into evolution and coevolution [41]. Studies have shown noticeable alterations in the combination of plant-associated micro-organisms when epigenetic mechanisms in plants are either activated or suppressed [42]. Microorganisms utilize specific epigenetic mechanisms to interact with plants. These mechanisms influence the timing of plant defense systems after pathogen infection and also the utilization of beneficial environmental microorganisms to combat biotic and abiotic stresses [43]. Some of these mechanisms cause prime responses for forecasting the next robust responses to similar situations in the future. Moreover, these mechanisms can be passed on to subsequent generations through the inheritance of modification patterns [43].

In addition, studies reveal that these epigenetic mechanisms play basic roles in regulating various immune–biological processes in nematode–plant interactions [11]. However, the nematode attack can induce histone modification, smRNA synthesis, and DNA methylation [44]. These epigenetic modifications cause plant defense response against pathogen infection [45]. The RKN M. incognita is a suitable model for studying mechanisms of asexual multiplication in plants. Despite research on the genetic variation level of M. incognita, the function of epigenetic variation is less known. Indeed, the RKN Meloidogyne spp. can adapt rapidly to undesirable conditions. Understanding the adaptive ability of RKNs is important for developing suitable control methods. However, the mechanisms of this plasticity and their possible effect on gene expression remain unknown [46].

2.3.1. DNA Methylation

Epigenetic mechanisms, especially DNA methylation, play important regulatory roles in plant–nematode interactions. This process causes susceptible and resistant responses during interactions. However, the transcriptional activity of genes mediating DNA methylation in the nematode feeding sites remains largely unknown [47,48].

DNA methylation in CG, CHH, and CHG sequences (H representing A, T, or C) is determined by different enzymes during nematode parasitism. Methylation of CG and CHG is maintained by Methyltransferase 1 (MET1) and Chromomethylase (CMT2 and CMT3), respectively. Meanwhile, de novo DNA methylation is conducted by the RNA-directed DNA methylation (RdDM) pathway [49]. In this process, transcripts of RNA polymerase IV are copied to long non-coding double-stranded RNAs, which are then processed by DICER-LIKE 3 (DCL3) to produce small interfering RNAs (siRNAs). These siRNAs are conducted ARGONAUTE proteins (AGO4 and AGO6) to complementary genome sequences. This pathway illustrates the link between various epigenetic mechanisms, specifically DNA methylation and ncRNAs [50].

Indeed, DNA methylation proposes involvement in the plant’s immune response to pathogens [51]. Several studies demonstrate that DNA methylation plays a noticeable role in plant–nematode interactions. For example, changes in DNA methylation were reported in soybean–cyst nematode interactions and in galls caused by Meloidogyne javanica in Arabidopsis [12,52]. Furthermore, increased resistance to RKN infection was reported in RdDM mutants. In Arabidopsis, the dcl2/dcl3/dcl4 triple and rdr2/rdr6 double mutants exhibited lower susceptibility to M. javanica [53]. Also, it has been reported that impaired mutants in non-GC DNA methylation reduced susceptibility to RKNs [53,54]. DNA methylation in M. javanica-induced galls in Arabidopsis was studied at early infection stages. Results showed that early galls were hypermethylated, and the giant cells were the main contributors to hypermethylation. DNA methylation devastated gall/giant cell development and nematode reproduction. Indeed, DNA hypermethylation patterns in the CHG context were seen in early-developing galls induced by the RKNs, M. javanica in Arabidopsis [12]. Additionally, researchers have demonstrated insights into the regulatory role of DNA methylation in forming interactions between host plants and cyst nematodes (Heterodera schachtii) [55]. In another study, the activation of intergenerational acquired resistance in the offspring of rice plants (Oryza sativa) treated with dehydroascorbate demonstrated that cooperation of DNA demethylation and remethylation causes intergenerational acquired resistance phenotypes and induced resistance at dehydroascorbate-treated plants against Meloidogyne graminicola [2].

In general, the modulation of defense-responsive genes in hyper- and hypomethylated mutants displayed various responses to different phytopathogens [56]. During the early stages of infection, the promoters of different DNA demethylases are more active in galls compared to syncytia. The expression of CG-context methyltransferases is restricted to developmental stages and feeding site formation. Methyltransferase (DRM2 and DRM3) and chromomethylase (CMT1, CMT2, and CMT3) mediate non-CG methylation, illustrating distinct and similar expression patterns in the galls and syncytia at different time points [47]. In another study, in the RKN-infected roots, methyl-transferase genes were upregulated, and total DNA was hypermethylated. Also, DNA hypomethylation, as an upstream mechanism, triggered gene over-expression in plant resistance. Nematode-induced gene silencing can occur through the activation of methyl-transferase genes and DNA hypermethylation [57]. Generally, RNA-directed DNA methylation (RdDM; DRM2/1), methyltransferases (MET1/CMT3), and demethylation (ROS1) are key epigenetic mechanisms during RKN infection [12].

Considering that PPNs are important parasites of plants, it is crucial to determine whether the demethylation is a consequence of nematode pathogenicity or plant defense responses. During the tomato-compatible interaction, the methyltransferases were upregulated, and DNA was hypermethylated [57]. In addition, the rice plants inoculated with azacytidine (a chemical DNA demethylating agent) exhibited resistance to M. graminicola infection [55], and giant cells (seven-day-old) showed increased expression of the RdDM pathway [58]. These reports suggest that DNA hypomethylation is important in plant defense responses, whereas PPNs can hijack this system to their advantage [38].

2.3.2. Non-Coding RNAs

Non-coding RNAs (ncRNAs) are generally categorized into two groups: long non-coding RNAs, lncRNAs, (about 200 nucleotides), and small RNAs, smRNAs, (less than 40 nucleotides) [38]. Based on their origin and roles, smRNAs can be categorized into two main classes: small interfering RNAs (siRNAs) and microRNAs (miRNAs) [59].

Regulatory lncRNAs have been noticed in different plants, which regulate gene expression through epigenetic mechanisms, as well as at the transcriptional and post-transcriptional stages [60]. Also, these lncRNAs have significant regulatory processes in different defense responses and developmental programs [61,62,63,64]. Currently, at least four widely recognized mechanisms of lncRNA regulation are recognized: transcriptional regulation, miRNA target mimicking, histone/chromatin modification, and post-transcriptional alterations [65].

There are limited studies on the accumulation of lncRNAs in response to plant–nematode interaction. However, advancements in sequencing techniques have facilitated the extensive detection and characterization of lncRNAs associated with RKNs in various plants, including soybean [66], tomato [67], and peanut [68]. Previous research has shown that the lncRNA48734-miR156-SPL plays a noticeable role in managing the tomato plant’s response to RKN infection [16]. Overall, lncRNAs likely serve a significant function in regulating plant resistance to RKNs [69]. Indeed, they have considerable regulatory potential and have been associated with defense against pathogens [38]. For example, in the tobacco–M. incognita interactions, 565 lncRNAs were identified [70]. Similarly, in Nicotiana tabacum RKNs and soybean–H. glycines interaction, about 565 and 384 lncRNAs were identified, respectively [66,70,71]. These lncRNAs were related to different nematode stress responses through cis or trans interactions [66]. In the rice–M. graminicola interaction, these lncRNAs were related to the regulation of signaling proteins, demonstrating the broad regulatory ability of lncRNAs. In addition, 44% of those demonstrated overlap with hypomethylated regions, showing that lncRNAs can be significant in DNA methylation reprogramming of the surrounding genes [38].

In addition, some epigenetic effectors such as smRNAs are affected in transcriptomic, epigenomic indexes, memory, and communication in other species [72]. smRNAs are achieved from double-stranded RNAs (dsRNAs) via the action of Dicer-like proteins [73,74]. These smRNAs can be categorized into two main classes based on their origin and biological roles: microRNAs (miRNAs) and small interfering RNAs (siRNAs) [59].

The DICER-like (dcl) mutants exhibited reduced susceptibility to infection by the RKN, M. javanica [53]. Additionally, the assessment of ARGONAUTE mutants, ago2–1, ago1–25, ago1–27, ago1–27/ago2–1, displayed decreased susceptibility to the RKN M. incognita. These findings suggest that the disruption of smRNA biosynthesis plays a significant role in the parasitic function of RKNs [75].

siRNAs are short dsRNAs (20–25 nucleotides) that play a key function in the RNA interference (RNAi) pathway. They are organized by the cleavage of longer dsRNAs by the Dicer enzyme. One of the strands is conducted to an RNA-induced silencing complex (RISC), which directs the siRNAs to the complementary mRNA sequence. Then, RISC accelerates the mRNA cleavage, resulting in its degradation and gene silencing [76].

siRNAs constitute an important investigation in understanding the molecular mechanisms of plant responses to PPNs [75]. These RNAs contribute to gene silencing by the RdDM pathway and originate from transposable elements (TE). siRNAs explain how TEs influence gene expression [77]. Since TEs are predominantly demethylated and activated under stress conditions, this would likely lead to an increase in siRNA production [78]. Indeed, in Arabidopsis–M. javanica, and –M. incognita interactions, 23–24 nt siRNAs were shown as the largest responsive ncRNAs to nematode infection and were upregulated in galls [53,75]. PPNs stimulate siRNAs to repress plant defense responses and promote the reprogramming of feeding sites. In addition, transposon hypomethylation and siRNA production are plant responses to increase a directed immune response against PPNs [38].

According to studies, high-throughput sequencing displayed that smRNA isolated from galls of Arabidopsis (caused by M. incognita) led to the identification of expressed siRNA clusters at 7–14 days post-infection [75]. In other studies on galls induced by M. javanica in Arabidopsis, siRNAs were assisted in early galls at differentially methylated regions [12]. The higher abundance of siRNA clusters within galls, compared with non-infected roots, expresses the importance of the silencing process and nematode-mediated siRNA biosynthesis [75]. A survey of siRNAs associated with transposons in the induced galls of M. javanica in Arabidopsis roots found that 22–24 nucleotide siRNAs were dominant and associated with retrotransposon (Gypsy and Copia). These siRNAs decreased the transcript levels of retrotransposons [53]. The abundance of siRNA clusters, along with gene expression analysis, suggests that these clusters play a role in the regulation of gall formation through the RdDM pathway.

Therefore, researchers determined the importance of epigenetic modifications through DNA methylation and accumulation of siRNAs in regulating the proliferation and mobility of transposons. This process is performed to maintain genome stability and integrity during genome-wide programming in plant–nematode interactions [79].

Also, miRNAs are small non-coding RNAs (about 20–21 nucleotides) that involve the regulation of post-transcriptional genes. These miRNAs are transcribed from primary miRNAs (pri-miRNAs), which are processed into precursor miRNAs (pre-miRNAs). Then, pre-miRNAs are transferred to the cytoplasm, where they are further processed into mature miRNAs by the Dicer enzyme. The mature miRNAs are interconnected into the RISC, attach to the 3′ untranslated region (UTR) of mRNAs, and lead to mRNA degradation or translational inhibition [76].

In addition, the number of miRNA genes in nematode-infected plants seems to play a role in post-transcriptional reprogramming [48]. These miRNAs consist of non-coding RNA nucleotides, regulating post-transcriptional gene silencing. These act as pioneers of mir genes catalyzed by Dicer proteins that play a key role in plant–nematode interactions [71]. Dicer proteins are RNAase-III like enzymes that split RNAs into small RNAs. These proteins have other important roles, such as modifying chromatin structures and processing miRNAs and siRNAs [80].

Previous studies have shown that miRNAs play a significant role in responding to nematode infections. Various molecular regulatory modules, including miR319/TCP, miR156/SPLs, miR390/ARFs, miR396/GRFs, and miR482/NBS-LRR, have been identified as potential contributors to the processes of induction and resistance. In this study, lncRNA47258 was detected to affect miR319b, regulating the levels of jasmonic acid (JA) in tomatoes and prohibiting the impact of M. incognita [81]. The miR159 and miR319 families are closely related [82]. These two families have various targets (miR319 guiding the cleavage of TCP TF and miR159 regulating MYB TF). However, some of those are likely targeted by both families. For example, MYB65 and MYB33 are targeted by miR319 [82,83]. The miR159abc mutant exhibited strong resistance to RKNs, highlighting the role of the miR159 family in gall formation induced by RKNs in Arabidopsis [84].

Previous studies reported that about 60 soybean cyst nematode-responsive miRNA genes were involved in miRNA regulation during plant–cyst nematode associations [85]. Similarly, differential mediation of miRNAs in response to RKN infections has been reported. For example, the differential expression of 61 miRNA genes in early-forming galls of M. javanica showed that 11 genes were overexpressed, while 51 genes were repressed [79]. However, these up/downregulations remain unclear. Numerous miRNA genes were also identified from infected tomato roots to M. incognita across various stages of development [86]. In addition, infection of Arabidopsis with M. incognita resulted in the differential expression of 24 miRNA genes. This study suggested miRNA temporospatial expression in galls via the promoter–reporter fusion process [84]. These findings confirmed that miRNAs have a noticeable role in regulating gene networks involved in gall formation and feeding structures. Therefore, these miRNAs are identified for reaction to various genera of plant parasitic nematodes, particularly RKNs, inducing defense pathways and regulating genetic patterns after infection [71,87].

Functions of miRNAs in plant–RKN interactions: Sequencing studies have assessed the functional role of miRNA in plants. There are various miRNAs classified in infected plants with RKNs. Jasmonic acid (JA), a systemic signaling molecule, has important roles in plant–RKN interactions [88,89]. miR319, as a JA-responsive miRNA, regulates host susceptibility to M. incognita via target TCP4 (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 4) [83]. Upregulation of miR319 increases plant susceptibility, whereas overexpression of TCP4 reduces susceptibility. Analysis of endogenous JA levels in plants displayed the TCP4 role in JA biosynthesis [90].

In a study, the role of four miRNAs (miR319, miR159, miR408, and miR398) in the interaction of Arabidopsis and M. incognita was investigated. In this study, only miR159 changed plant susceptibility to M. incognita. This phenotype corresponded to mature miR159 in the giant cells. The abundance of miR159 in giant cells was associated with a reduction in the expression of the MYB33 transcription factor. Nevertheless, the downregulation of MYB33 during nematode parasitism remains unclear [84]. Another important miRNA, miR390, was strongly induced in galls triggered by M. javanica in Arabidopsis [79]. miR390 controls the biogenesis of trans-acting, small interfering RNAs (TAS3-derived tasiRNAs). These bind the transcripts of 3-auxin response factors (ARF3–5) and regulate their degradation [91]. miR390 and TAS3 are extremely induced in galls and giant cells during the early stages of infection. Therefore, mutant lines of miR390 and TAS3 demonstrated a high reduction in the gall numbers.

In addition, miR172, a highly conserved miRNA in plants, was activated in the giant cells and galls formed by M. javanica in pea, tomato, and Arabidopsis [92]. In the Arabidopsis–M. javanica interaction, miR172 triggers the negative regulation of the AP2-like transcription factor target TOE1 [92]. Inactivation of miR172 and overexpression of TOE1 showed a significant reduction in the number of galls and the size of giant cells in plants [93]. Also, the regulatory functions of miR319-TCP4 and miR390-TAS3-ARF3 during RKN infection associated with miR172 responsiveness to auxin demonstrated the role of these miRNAs in auxin–JA signaling pathways of giant cells [48].

2.3.3. Histone Modifications

Histone modification is the process of removing or adding chemical groups to the histone proteins [94]. While extensive research has explored the relationship between histone modifications and plant defense mechanisms, the wide range of modification types and their complex interactions cause histone modifications to be less understood in comparison to DNA methylation [95].

This mechanism affects the gene expression and chromatin structure [96]. Histone modifications contain different types of methylation, acetylation, ubiquitination, and phosphorylation. The process of methylation and acetylation affect the plant epigenome during stress and development responses [44]. Histone acetylation involves gene expression activation, while histone deacetylation involves gene expression suppression [97]. For example, histone acetylation of lysine on histone H3 is associated with gene activation. In contrast, methylation of H3 may be correlated with transcriptional activation of lysine 36 and 4 or suppression of lysine 27 and 9 [98]. Therefore, methylation of H3K4me (lysine 4 of histone H3) activates gene expression, while the methylation of H3K9me (lysine 9 of histone H3) involves gene silencing [99].

It has been reported that in M. incognita, H3K9me3 exhibits lower expression levels compared to other histone modifications. Additionally, most H3K9me3 modifications were identified on annotated TEs, implying that H3K9me3 plays a role in repressing the mobile elements within the genome and suggesting that its function is preserved in M. incognita [46]. In addition, it has been demonstrated that the equilibrium between H3K27 acetylation and H3K27 trimethylation plays a crucial role in gene expression regulation [100].

H3K27me3 is a widely recognized repressive histone modification that causes gene expression downregulation [101,102]. In contrast, H3K27ac makes a histone modification active and is widely distributed [103]. In M. incognita, H3K27ac and H3K27me3 exhibited a widespread distribution across the genome, notwithstanding their dual effects [46]. H3K27ac is typically located on enhancers and is used as a marker to differentiate between poised and active enhancers [46].

Nevertheless, histone acetyltransferases and histone deacetylases balance histone acetylation levels [104]. Lack of the H3K4 methyltransferase ARABIDOPSIS TRITHORAX1 (ATX1) triggers the downregulation of WRKY70 and PR1 in JA- or SA-mediated defense pathways [105]. It has also been reported that the induction of systemic resistance in treated rice plants is correlated with the activation of the SA pathway and the production of ROS. SA signaling triggers the induction of WRKY45 and then leads to the reduction of rice susceptibility to M. graminicola [106]. Another histone modification, H4K20me1, typically results in chromatin modifications [107]. In M. incognita, H4K20me1 demonstrated a profile of this type across the entire genome and was linked to higher elevated expression levels compared to the repressive histone modifications. Furthermore, H4K20me1 levels have been shown to change throughout the cell cycle [108].

Chromatin immunoprecipitation sequencing (ChIP) and related techniques are technologies for the studying of histone modifications in plants [109]. Extensive epigenetic research, such as histone modifications, have been performed in Caenorhabditis elegans in response to the environmental changes [110]. Studies have displayed that M. incognita has no 5-methylcytosine (5mC) and cytosine-DNA (cytosine-5)-methyltransferase (DNMT1 and DNMT3) [11]. Generally, the effects of histone modifications on gene transcription are crucial parameters in biological processes, containing parasitic success in RKNs [46]. As a result, histone marks are significantly influenced by the plant–nematode interaction. However, considerable assays are still required to unravel these processes [38].

2.4. Emerging Technologies in the Plant–Nematode Interaction

Epigenetic mechanisms are responsible for the generation of phenotypic diversity that causes the ability for rapid adaptation. Therefore, the understanding of the molecular basis of epigenetic modulations and the heritability of these changes has led to the flourishing of evolutionary epigenetics [41].

The plant epigenome affects plant phenotypes and their interactions with biotic stresses. However, PPNs, such as RKNs, can trigger epigenetic changes that redirect plant metabolism to create optimal conditions for their growth and development. Genetic resistance prevents RKNs from destroying plant immune response by producing pathogenesis-related (PR) proteins and reactive oxygen species (ROS), which are toxic to the invading J2 [57]. Significant advancements have been reported in developing RNA interference (RNAi)-based transgenic crops to provide resistance against nematodes. However, the approach of host-induced gene silencing that targets nematode effectors (interacting with plant R genes) can lead to the emergence of nematode phenotypes capable of overcoming plant resistance [111]. Nevertheless, augmented DNA hypomethylation has been identified as an upstream mechanism that induces the widespread gene overexpression associated with plant resistance. Gene silencing triggered by nematodes can also occur through DNA hypermethylation and activation of methyltransferase genes. Plant resistance is marked by suppression of the antioxidant enzyme system and the stimulation of the defense enzyme chitinase. In contrast, nematode-attacked roots demonstrate the opposite response, with the activation of the antioxidant system and the suppression of the defense enzyme glucanase [57].

In addition, CRISPR/Cas9 is a highly effective gene editing tool. This system has been deployed to host resistance against pathogens. Using CRISPR/Cas9 technology to knock out susceptibility (S) genes or genes that facilitate nematode parasitism in plants appears to be a promising strategy for managing PPNs. Triggered mutations in the S genes are often long-lasting, influencing their expression within the host system. As a result, they may offer a certain level of resistance against the feeding nematode. Therefore, the CRISPR/Cas9 system is employed to investigate the molecular mechanisms of plant–nematode interactions, aiming to enhance tolerance in plants [111].

Accordingly, the overall mechanism of plant priming against biotic and abiotic stresses likely involves similar epigenetic modifications. These modifications can either inhibit or activate the transcription of critical regulators within the immune system. Environment-induced epigenetic changes can be passed on to future generations, aiding plants’ adaptation to evolving environmental conditions. Therefore, understanding these mechanisms could lead to the development of eco-friendly strategies to ensure sustainable protection against biotic stress based on the long-lasting immune memory in host plants [57].

2.5. Endophytic Micro-Organisms in the Plant–Nematode Interaction

Endophytic micro-organisms can limit the development of plant pathogens. Changes in phytohormone accumulation, protein regulation, and transcription occur during plant-beneficial micro-organism interactions [112]. These micro-organisms as biofertilizers can affect long-term soil sustainability and fertility, which are essential for the safety of soils and food in future generations [113,114]. Moreover, epigenetic plasticity triggers permanent changes in the plant’s transcriptional capacity in plant–microbe interactions, with a role in priming and memory [112]. Post-transcriptional and epigenetic modifications promote host resistance to pathogens and facilitate symbiotic relationships. Thus, it is necessary to evaluate the function of these modifications in the plant adaptation to environmental stress, such as the plant resistance to pathogens, the creation of symbiotic relationships, and plant growth promotion [115]. It has been demonstrated that some endophytic bacteria induced resistance to the RKN M. incognita in kiwifruit. In this study, resistance induction against M. incognita was observed using Bacillus altitudinis. The treated plants with this bacterial isolate demonstrated higher expression of pathogenesis-related genes (PR-1 and PR-5). Therefore, B. altitudinis primes host plants against RKN by triggering pathogenesis-related genes [9]. Induced resistance, a phenotypic status triggered by an exogenous agent and characterized by enhanced resistance to future biotic challenges, is important for plant immunity [116]. Additionally, endophytic micro-organisms induce SAR by producing plant hormones [117]. The integrated pest management of RKNs with biological control agents creates an economical and safe method to control RKNs that can be applied in breeding programs [9].

Also, in secondary metabolite production, epigenetics is used as an important mechanism to alter the expression of genes encoding secondary metabolites [118]. Therefore, endophytic micro-organisms such as fungi and bacteria can modify plants’ physical composition and gene expression by epigenetic changes in the host [119]. The import and travel of smRNA between host and bacteria is an active process [72]. The application of beneficial microbes enhances the defense enzyme levels in plants. The production of these enzymes and metabolites and the induction of resistance indirectly affect nematodes [120,121]. Epigenetic modifiers can induce the silencing of genes encoding biosynthetic pathways that limit their ability for the production of bioactive secondary metabolites. Also, the epigenetic modifications can induce endophytic microbe-derived bioactive metabolites. The chemical epigenetic methods, such as histone deacetylase inhibitors and DNA methyltransferase inhibitors, trigger the biosynthetic pathways of metabolites. In addition, epigenetic modifiers can improve plant efficiency under varying stress conditions [119].

In addition, secreted effector proteins by PPNs are affected in plant immune responses [52]. High-throughput sequencing has a significant role in the identification of gene candidates of nematode effectors in parasitic relationships [122]. These proteins have no similar sequence to public domain proteins; therefore, the functions of these effectors in nematode parasitism are largely unknown. Nevertheless, a few effectors displayed sequence homology with epigenetic modulations [123]. Horizontal gene transfer (HGT) in bacteria has been demonstrated as an evolutionary factor for eukaryotic lineages. Nematode effector proteins are produced in esophageal gland cells and are secreted into plant hosts. In M. incognita, two genes encode putative invertase. The studies of invertase in PPNs have characterized that these genes are acquired in PPNs via horizontal gene transfer from bacteria. For example, the nematode GLAND1-effector displayed sequence homology with GCN5-related N-acetyltransferases, GNATs, from Streptomyces sp. According to phylogenetic analysis, GLAND1 can be obtained with horizontal gene transfer from bacterial species. In addition, there are homologs in the nematode species Rotylenchulus reniformis, Globodera rostochiensis, and Heterodera avenae [123]. The GNAT effector of Mycobacterium tuberculosis involves defense expression [124]. These nematode GNATs simulate histone acetyltransferase in plants and modulate acetylation, resulting in gene expression and plant susceptibility [48]. Generally, identification of plant–nematode GNAT protein interaction displayed a mechanism of histone acetylation for transcriptional reprogramming and gene expression in infected plants to nematode.

2.6. Plant Memory in the Plant–Nematode Interaction

Epigenetic information can be inherited during a plant’s lifecycle (somatic inheritance), such as in priming. This transmission also occurs through vegetative propagation via mitosis in the stem cells of meristems [125]. Additionally, epigenetic information can be inherited through meiosis [126], resulting in intergenerational (permanent in the first generation) and transgenerational inheritance (permanent to at least two generations) [112,127,128]. Somatic stress memory, triggered during the early stages of plant development, can be categorized as either short-term or long-term memory. Short-term memory enables plants to maintain resistance to specific stressors for several days or weeks. This phenomenon is primarily attributed to temporary shifts in metabolite levels. Once the stressful condition subsides, the plants revert to their original growth state, effectively “forgetting” the stress event [126]. In contrast, long-term stress memory, regulated by epigenetic mechanisms, can remain throughout the life of the stressed plant [127,129].

The significance of the mechanisms driving priming may differ depending on the type and time of stress, but priming represents a form of plant stress memory. This memory enables plants to respond more effectively to recurring stress events, potentially enhancing their survival and performance at both the individual and community levels in variable environments [130]. Although substantial advancements have been made in understanding stress memory, many aspects of its mechanisms remain unclear. Ongoing research continues to investigate the duration and underlying processes of stress memory, offering promising approaches for progressing crop resilience [129].

Plants under stress conditions create changes in gene expression levels [131]. Encountering plants to environmental stresses can increase their resistance to pathogens attacks. PTI-responsive genes are associated with transcriptional activation [132]. Epigenetic memory induces plant resistance to pathogens using priming agents, consisting of chemical compounds (β-aminobutyric acid, β-homoserine, and benzothiadiazole), hormones (JA, SA, MeJA), beneficial micro-organisms Trichoderma spp., arbuscular mycorrhizal fungi, plant-growth-promoting rhizobacteria, Pseudomonas, Bacillus, and abiotic stress [120,133,134,135]. Some priming is short-term, while others are long-term and can be transmitted between plant generations. There are limited studies on epigenetic mechanisms, immune memory, and plant defense priming to nematode pathogens. Therefore, in this review, we focused on epigenetic mechanisms of increasing plant resistance to nematode infections.

Research on the interaction between rice and M. graminicola has revealed that parent plants infected by RKNs can transmit stress memory to their offspring. This results in the next generation being more resistant to M. graminicola and Pratylenchus zeae. In offspring that were not infected, this memory response was characterized as a decrease in the expression of immunity-related genes. However, after infection, plants exhibited a robust response by triggering these memory genes. This process led to a resistance phenotype (spring-loading of genes), inducing more relative changes in gene expression in the offspring, thereby eliciting a more intense immune response. The critical ET and JA pathways were spring-loaded, resulting in increased resistance [38]. Three basic mechanisms are underlying the transmission of epigenetic information among generations: chromatin modifications, DNA methylation, and smRNAs. Both siRNAs and DNA methylation play vital roles in the development of phenotype. The huge expression burst in siRNAs during the initial stages of nematode infection may play a key role in establishing intergenerational and transgenerational memory [38,75,136]. In another study, intergenerational acquired resistance (IAR) was triggered in the offspring of rice plants that were treated with dehydroascorbate (DHA). The progeny of plants treated with DHA (DHA-IAR) exhibited less susceptibility to the RKN M. graminicola. They also inherited the responses of DHA-induced transcriptional observed in their parent plants [2].

Nevertheless, comprehending epigenetic mechanisms is important. Methylation can affect defense genes by targeting regulatory genes in stress responses [137]. The genomes of tomato plants treated with β-aminobutyric acid displayed a noticeable reduction in cytosine methylation, particularly in the CHH sequence. The CHH contexts in the differentially methylated region were hypomethylated. Therefore, treating plants with β-aminobutyric acid causes changes in genome-wide DNA methylation [137,138]. Pretreated plants with strains of non-pathogenic memorize the hypomethylation patterns and afterward react more effectively against pathogen infection [139].

3. Conclusions

Plant parasitic nematodes impact various types of plants, causing significant economic losses by reducing yield and quality. In response to PPN invasion, plants trigger complex defense strategies. Epigenetic regulations are key components of these mechanisms. Environmental signals can trigger epigenetic modifications that modulate the plant–micro-organism interactions or trigger defense responses. Plants under the pressure of variable environmental conditions require adaptive mechanisms and effective defense strategies. They can develop a stress memory that transmits to the next generation. Intergenerational and transgenerational acquired resistance support these epigenetic changes. Research on transgenerational inheritance and phenotypic plasticity demonstrates that epigenetic modulation is transferred between generations, and that the environment affects epigenetic processes. Recent studies exhibited the significant role of epigenetic modulation in plant–nematode interactions. This mechanism is important in inducing suitable plant response to nematode infections. In this review, we exhibited how plants apply epigenetic mechanisms against nematode infection. These mechanisms are activated in plants during pathogenic infection. Epigenetic mechanisms are effective in plant priming and the formation of epigenetic memory in environmental stress situations. This review provides comprehensive information on host–nematode interactions for future studies. Future research could show how microbiome engineering helps plant growth and resistance against infectious nematodes.