1 Introduction

Rice (Oryza sativa L.) is a staple food for more than half of the world's population, making its cultivation critical for global food security. However, rice production is increasingly threatened by a variety of viral and mycoviral pathogens. Viral diseases, often transmitted by insect vectors such as leafhoppers and planthoppers, have caused significant yield losses in rice-producing regions, particularly in Asia (Wei and Li, 2016). Notable viruses include the southern rice black-streaked dwarf virus (SRBSDV), rice black-streaked dwarf virus (RBSDV), and rice yellow mottle virus (RYMV), which have led to devastating epidemics.

In addition to viral threats, mycoviruses—viruses that infect fungi—pose a significant risk to rice cultivation by affecting fungal pathogens that cause diseases such as rice blast, rice false smut, and rice sheath blight (Umer et al., 2023). Mycoviruses have been identified in major fungal pathogens like Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, which are responsible for substantial yield reductions. These mycoviruses can influence the pathogenicity and virulence of their fungal hosts, thereby indirectly impacting rice health and productivity.

The emergence of rice viruses has been documented since the late 19th century, with 19 species recorded globally, each causing varying degrees of damage to rice crops (Wang et al., 2022). The spread of these viruses has often been linked to agricultural practices, such as crop intensification and the movement of infected plant material. For instance, RYMV emerged in East Africa in the 19th century following the intensification of rice cultivation along the Indian Ocean coast and later spread inland with the introduction of rice (Pinel-Galzi et al., 2015).

Mycoviruses, on the other hand, have been studied for several decades, with significant discoveries made in recent years. The diversity of mycoviruses in rice pathogens has been revealed through advanced metatranscriptomic analyses, identifying numerous novel mycoviruses and highlighting their widespread presence in fungal pathogens. These studies have shown that mycoviruses are not only common but also highly diverse, with many new species being discovered in recent years (Jiang et al., 2015; He et al., 2022).

This study provides a comprehensive overview of emerging viral and fungal viral threats in rice cultivation. It summarizes the current knowledge on the diversity, transmission, and impact of rice viruses and fungal viruses, explores the historical context and factors contributing to the emergence and spread of these pathogens, and discusses the implications of these threats for rice production and global food security. The study highlights recent scientific advances and identifies knowledge gaps that require further research.

2 Common Rice Viruses and Their Impacts

2.1 Identification of major viral pathogens affecting rice

Rice cultivation is significantly threatened by various viral pathogens, which have been identified across different regions globally. Among the most notable are the southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America. These viruses have been recorded since the late 19th century and continue to cause substantial damage to rice production. The rice gall dwarf virus (RGDV) and the recently discovered rice tiller inhibition virus (RTIV) also pose significant threats, with RTIV emerging from native wild rice habitats and causing low-tillering disease in cultivated rice (Yan et al., 2022; Yang, 2024).

2.2 Transmission pathways and vectors for rice viruses

The transmission of rice viruses is predominantly facilitated by insect vectors, particularly planthoppers and leafhoppers. For instance, SRBSDV and RBSDV are transmitted by the white-backed planthopper (Sogatella furcifera), while RYMV is spread by various species of beetles (Figure 1) (Wang et al., 2022; Wu et al., 2022). The rice reoviruses, including SRBSDV, are transmitted in a persistent propagative manner by leafhoppers or planthoppers, which means the virus replicates within the vector and is transmitted throughout the vector's life. RTIV is transmitted by specific aphid vectors, highlighting the diverse range of insect vectors involved in the spread of rice viruses. The complex interactions between these viruses and their vectors involve evolutionary trade-offs that balance the fitness cost of viral infection in insects with the need for persistent transmission (Wei et al., 2018).

The transmission of rice viruses is closely related to their hijacking of host factors through viral proteins. Viruses are able to finely regulate processes, not only suppressing the host's defenses but also utilizing the host's resources for their own reproduction. Meanwhile, the host employs mechanisms such as RNA silencing to defend against viral infections, but viruses have their own strategies to overcome these defenses. This complex virus-host interaction mechanism is at the core of rice virus transmission and pathogenicity.

2.3 Economic and agricultural impact of viral infections

The economic and agricultural impacts of rice viral infections are profound, leading to significant yield losses and threatening food security. For example, SRBSDV has been shown to cause widespread vulnerability in rice cultivars, with high susceptibility observed in both conventional and hybrid varieties, leading to characteristic disease symptoms and substantial yield reductions. The presence of rice reoviruses in insect vectors further exacerbates the threat to rice production stability in Asia (Wei and Li, 2016). The emergence of new viral pathogens like RTIV from native plants underscores the ongoing risk of viral spillover into cultivated rice, potentially leading to new disease outbreaks and further economic losses. The global dimensions of plant virus diseases highlight the need for integrated, smart, and eco-friendly strategies to manage these threats and ensure sustainable rice production (Jones and Naidu, 2019).

3 Emerging Viral Threats

3.1 New rice viruses identified in recent years

Recent advancements in metagenomic and metatranscriptomic sequencing have led to the identification of several new rice viruses. For instance, the rice tiller inhibition virus (RTIV), a novel RNA virus, was discovered in colonies of Asian wild rice (O. rufipogon) and has been shown to cause low-tillering disease in cultivated rice varieties (Figure 2) (Yan et al., 2022). High-throughput sequencing has revealed the presence of eight novel virus species in rice plants, transmitted by the brown planthopper, which significantly impacts rice yield by causing sterile characteristics in infected plants (Chao et al., 2021). These discoveries underscore the importance of continuous surveillance and advanced diagnostic tools to detect and manage emerging viral threats to rice cultivation.

The discovery of the RTIV virus, along with its detailed genomic, structural, and functional analyses, has provided a new perspective for rice virus research. By using molecular biology techniques to validate its infection status and phylogenetic relationships, researchers can better understand the pathogenic mechanisms of this virus in rice. Future research will need to explore effective control measures against the RTIV virus and its impact on rice production, while further harnessing the potential of metagenomics and metatranscriptomics sequencing technologies to uncover more potential plant viruses.

3.2 Genomic evolution and mutation rates of emerging viruses

The genomic evolution and mutation rates of rice viruses are critical factors that influence their emergence and pathogenicity. For example, the evolutionary analysis of the 2019-nCoV, a coronavirus, demonstrated significant clustering with bat SARS-like coronaviruses, highlighting the role of mutations in the spike glycoprotein and nucleocapsid proteins in its ability to infect humans (Benvenuto et al., 2020). Similarly, the genetic diversity of begomoviruses, as revealed by high-throughput sequencing, indicates that these viruses undergo rapid evolution, which can lead to the emergence of new strains capable of infecting a wide range of plant species (Rodríguez-Negrete et al., 2019). Understanding these evolutionary dynamics is essential for developing effective strategies to mitigate the impact of emerging rice viruses.

3.3 Regional outbreaks and their global significance

Regional outbreaks of rice viruses have significant implications for global food security. For instance, the southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) have caused devastating epidemics in Asian countries, posing a major threat to rice production (Wang et al., 2022; Wu et al., 2022). These viruses are transmitted by insect vectors, and their outbreaks are often exacerbated by climate change and globalization, which facilitate the spread of viral pathogens across regions (Kreuze et al., 2023). The emergence of rice yellow mottle virus (RYMV) in Africa and rice stripe necrosis virus (RSNV) in America further illustrates the global significance of regional viral outbreaks. Effective management of these outbreaks requires international collaboration and the implementation of advanced surveillance and diagnostic technologies to prevent the spread of these viral threats.

4 Mycoviruses in Rice-Associated Fungi

4.1 Overview of mycoviruses and their hosts

Mycoviruses, or fungal viruses, are widespread across all major fungal taxa and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV) (Hough et al., 2023). These viruses are characterized by the absence of an extracellular phase and rely on intracellular transmission mechanisms such as cell division, sporogenesis, and hyphal anastomosis. Mycoviruses have been identified in a variety of fungal hosts, including plant pathogenic fungi, endophytic fungi, and fungi involved in human and animal diseases (Kotta-Loizou, 2021). Recent advances in nucleic acid sequencing technologies have significantly increased the number of identified mycoviruses, with a notable diversity in genome types, including dsRNA, ssRNA, and ssDNA.

4.2 Transmission dynamics between fungi and plants

The transmission of mycoviruses occurs primarily through intracellular routes, such as hyphal anastomosis and vertical transmission via conidia (García-Pedrajas et al., 2019; Tonka et al., 2022). This mode of transmission limits the spread of mycoviruses to individuals within the same or closely related vegetative compatibility groups (Ghabrial et al., 2015). However, artificial transfection methods have shown promise in expanding the host range of mycoviruses, potentially allowing them to infect a variety of fungal species. This expanded host range could be leveraged to control a broader spectrum of fungal pathogens in agricultural settings.

4.3 Influence of mycoviruses on fungal pathogenicity in rice

Mycoviruses can significantly influence the pathogenicity of their fungal hosts, often inducing hypovirulence, which reduces the virulence of the fungus and its ability to cause disease. For instance, mycoviruses have been shown to alter the pathogenicity of Rhizoctonia solani, a major pathogen responsible for rice sheath blight, by inducing hypovirulence (Abdoulaye et al., 2019; Umer et al., 2023). This hypovirulence is associated with changes in the expression of key pathogenicity factor genes in the fungal host, thereby reducing its ability to infect and damage rice plants (Zhang et al., 2020).

4.4 Role of mycoviruses in controlling fungal infections

The potential of mycoviruses as biocontrol agents has garnered significant interest due to their ability to reduce the virulence of plant pathogenic fungi. Mycoviruses that induce hypovirulence in their fungal hosts can be used to manage fungal diseases in crops, including rice. For example, the application of hypovirulent mycovirus-infected fungal strains has been shown to reduce the severity of diseases such as rice sheath blight and improve crop yields. The diversity of mycoviruses identified in major rice pathogens, such as Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, highlights the potential for developing targeted biocontrol strategies using specific mycoviruses (He et al., 2022).

5 Mechanisms of Virus and Mycovirus-Plant Interactions

5.1 Molecular and cellular mechanisms of rice-virus interactions

Rice plants have evolved sophisticated mechanisms to counteract viral infections. These mechanisms include the activation of resistance (R) genes, RNA silencing, and autophagy. R genes play a crucial role in recognizing specific viral proteins and triggering defense responses. RNA silencing, mediated by virus-derived small interfering RNAs (vsiRNAs), targets viral RNA for degradation, thereby limiting viral replication. Autophagy, a cellular degradation process, also contributes to antiviral defense by degrading viral components and enhancing immune responses (Jin et al., 2020).

5.2 Host immune responses to viral infection

5.2.1 Activation of pattern recognition receptors (PRRs)

Pattern recognition receptors (PRRs) are essential components of the plant immune system that detect pathogen-associated molecular patterns (PAMPs) and initiate immune responses. In rice, PRRs such as receptor-like kinases (RLKs) and receptor-like proteins (RLPs) recognize viral PAMPs and activate downstream signaling pathways, leading to the expression of antiviral genes. This process is crucial for the early detection and response to viral infections (Saijo et al., 2018; Carty et al., 2020).

5.2.2 RNA silencing mechanism in rice

RNA silencing is a primary antiviral defense mechanism in rice. It involves the production of vsiRNAs that guide the RNA-induced silencing complex (RISC) to degrade viral RNA. Viruses, in turn, have evolved viral suppressors of RNA silencing (VSRs) to counteract this defense. For instance, members of the Closteroviridae family encode VSRs that inhibit RNA silencing, allowing the virus to replicate and spread. The interplay between RNA silencing and VSRs represents a dynamic arms race between the host and the virus (Hussain et al., 2021).

5.2.3 Hormonal regulation in virus defense

Phytohormones such as jasmonates (JAs) play a significant role in regulating antiviral defenses in rice. JA signaling can enhance RNA silencing by upregulating key components such as Argonaute 18 (AGO18). This upregulation is mediated by the JA-responsive transcription factor JAMYB, which binds to the AGO18 promoter. The interaction between JA signaling and RNA silencing pathways exemplifies the complex regulatory networks that rice plants employ to defend against viral infections (Calil and Fontes, 2016; Yang et al., 2020).

5.3 Symbiotic or antagonistic roles of mycoviruses in rice cultivation

Mycoviruses, which infect fungi, can have both symbiotic and antagonistic effects on rice cultivation. Symbiotic mycoviruses can enhance the fitness of their fungal hosts, potentially benefiting rice plants by improving nutrient uptake or stress tolerance. Conversely, antagonistic mycoviruses can weaken pathogenic fungi, reducing their virulence and thereby protecting rice plants from fungal diseases. Understanding the dual roles of mycoviruses in rice cultivation could lead to novel strategies for managing rice diseases and improving crop resilience.

6 Current and Emerging Control Strategies

6.1 Traditional control methods: cultural practices and chemical treatments

Traditional control methods for managing viral and mycoviral threats in rice cultivation include cultural practices and chemical treatments. Cultural practices such as crop rotation, proper field sanitation, and the use of resistant varieties have been employed to reduce the incidence of diseases. Chemical treatments, including the application of fungicides and insecticides, have also been widely used to control the spread of pathogens. However, these methods have limitations, including the development of resistance in pathogens and environmental concerns associated with chemical use.

6.2 Breeding for virus-resistant rice varieties

Breeding for virus-resistant rice varieties is a sustainable and effective approach to managing viral threats. Traditional breeding methods, along with molecular marker-based breeding approaches, have been instrumental in developing resistant cultivars. The identification and utilization of resistance (R) genes and quantitative trait loci (QTL) have significantly contributed to the development of broad-spectrum disease-resistant rice varieties (Nizolli et al., 2021). Marker-assisted selection (MAS) and marker-assisted backcross breeding (MABB) have accelerated the breeding process, enabling the development of durable resistance against various pathogens.

6.3 Biotechnological approaches: gene editing and RNA interference

Biotechnological approaches, including gene editing and RNA interference (RNAi), have revolutionized the development of disease-resistant rice varieties. The CRISPR/Cas9 system has emerged as a powerful tool for precise genome editing, allowing for the modification of specific genes associated with disease resistance (Figure 3) (Cao et al., 2020; Mishra et al., 2021). RNAi technology has been used to silence viral genes, providing an effective strategy for controlling viral infections in rice. These advanced techniques offer the potential to develop transgene-free, virus-resistant rice varieties with enhanced resistance to a wide range of pathogens (Zhao et al., 2019).

The CRISPR/Cas system plays an important role in plant antiviral defense and control. When plant viruses invade plant cells, they rely on host factors for uncoating, transcription, or translation, and they replicate their genomes in the cytoplasm or nucleus. The CRISPR/Cas9 system inhibits viral infection by targeting viral DNA or RNA, disrupting or interfering with the viral genome within the cell. For RNA viruses, Cas13 or FnCas9 can target viral RNA, while DNA viruses are primarily targeted by Cas9 through their DNA.

6.4 Application of microbial biocontrol agents in managing viral and mycoviral threats

The application of microbial biocontrol agents is an emerging strategy for managing viral and mycoviral threats in rice cultivation. Beneficial microorganisms, such as certain bacteria and fungi, can suppress the growth of pathogens and enhance the plant's immune response. These biocontrol agents offer an environmentally friendly alternative to chemical treatments and can be integrated into sustainable disease management programs. Research is ongoing to identify and develop effective microbial biocontrol agents that can be used to protect rice crops from viral and mycoviral infections (Liu et al., 2021; Sahu et al., 2022).

7 Global Monitoring and Surveillance of Rice Viruses and Mycoviruses

7.1 Importance of early detection and real-time monitoring

Early detection and real-time monitoring of rice viruses and mycoviruses are crucial for mitigating the impact of these pathogens on global rice production. The rapid spread of viral diseases, exacerbated by globalization and climate change, poses a significant threat to food security. High-throughput sequencing and nucleic acid amplification methods have revolutionized the ability to detect and monitor these pathogens in real-time, providing plant health specialists with the tools needed to respond swiftly to emerging threats. For instance, the use of metatranscriptomic analysis has revealed a rich diversity of mycoviruses in major fungal pathogens of rice, highlighting the importance of continuous surveillance to understand and manage these threats effectively (He et al., 2022).

7.2 International collaboration in virus surveillance

International collaboration plays a pivotal role in the surveillance of rice viruses and mycoviruses. Collaborative efforts have enabled the development and deployment of advanced diagnostic tools and surveillance systems across different regions, particularly in low- and middle-income countries. The CGIAR, for example, has been instrumental in supporting these initiatives by building local capacities and facilitating the sharing of knowledge and resources. Such collaborations are essential for addressing the transboundary nature of viral threats and ensuring a coordinated global response. The prevalence and diversity of mycoviruses in different geographical regions, such as those infecting Ustilaginoidea virens in China, underscore the need for a unified approach to monitoring and managing these pathogens (Jiang et al., 2015).

7.3 Technologies and tools for virus detection in rice fields

The detection of rice viruses and mycoviruses in the field has been greatly enhanced by advancements in genome sequencing, metatranscriptomics, and epidemiological modeling. High-throughput sequencing technologies allow for the comprehensive analysis of viral genomes, facilitating the identification of novel viruses and the monitoring of known pathogens (Kreuze et al., 2023). Metatranscriptomic approaches have been particularly effective in uncovering the diversity of mycoviruses in various fungal pathogens, providing insights into their potential impact on rice health and productivity (Marzano et al., 2016). The use of real-time PCR and other nucleic acid amplification techniques enables the rapid and accurate detection of viral infections in rice fields, allowing for timely interventions to prevent the spread of disease. These technologies, combined with field-based diagnostic tools, form a robust framework for the effective surveillance and management of rice viral diseases.

8 Challenges and Future Directions

8.1 Limitations of current control methods for rice viruses and mycoviruses

Current control methods for rice viruses and mycoviruses face several limitations. Traditional breeding for resistance often struggles with the rapid evolution of viral pathogens, which can quickly overcome resistance genes. For instance, the emergence of hypervirulent pathotypes of Rice yellow mottle virus (RYMV) that can bypass known resistance alleles poses a significant challenge to sustainable resistance breeding. Similarly, the dynamic and quickly evolving populations of the rice blast pathogen, Magnaporthe oryzae, complicate the deployment of resistant varieties, as new virulent isolates can emerge and render previously effective resistance genes obsolete (Sahu et al., 2022). Genetic engineering approaches, such as RNA silencing, have shown variable success, with some constructs failing to confer stable resistance. The high genetic variability and broad host range of pathogens like Rhizoctonia solani, which causes sheath blight, further complicate the development of effective control strategies (Molla et al., 2019).

8.2 Importance of early detection and monitoring systems

Early detection and monitoring systems are crucial for managing viral and mycoviral threats to rice cultivation. Continuous surveillance of pathogen dynamics is essential to identify emerging virulent isolates and adapt resistance breeding strategies accordingly. For example, the surveillance of rice blast resistance genes and the monitoring of Magnaporthe oryzae populations in Taiwan have been instrumental in identifying shifts in pathogen virulence and guiding the deployment of effective resistance genes (Syauqi et al., 2022). Similarly, the development of resistance-breaking risk maps for RYMV in Africa helps optimize the deployment of resistant rice lines and mitigate the impact of hypervirulent pathotypes (Hébrard et al., 2018). Advanced molecular techniques, such as metatranscriptomic analysis, can also reveal the diversity and evolution of mycoviruses in major fungal pathogens, providing valuable insights for developing targeted control measures.

8.3 Future research on viral evolution and resistance breeding

Future research should focus on understanding the mechanisms of viral evolution and developing durable resistance breeding strategies. Investigating the molecular determinants of resistance breakdown, as seen in the case of RYMV, can provide insights into how viruses adapt to host immunity and inform the design of more robust resistance genes (Bonnamy et al., 2022). Exploring the cooperative antiviral activities of different Argonaute proteins, such as AGO18 and AGO1, can uncover new strategies for enhancing broad-spectrum virus resistance in rice. Advances in biotechnological tools, including CRISPR/Cas9 and other genome editing techniques, offer promising avenues for precise genetic modifications to improve resistance against both viral and fungal pathogens. Integrating traditional breeding methods with modern biotechnological approaches will be key to developing rice cultivars with durable and broad-spectrum resistance to emerging viral and mycoviral threats.

Acknowledgments

I appreciate Dr Huang from the Hainan Institution of Biotechnology for her assistance in references collection and discussion for this work completion.

Conflict of Interest Disclosure

The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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