New Threats to Rice Production: Emerging Pathogens and their Impact

2.1 Virus

Rice hoja blanca virus (RHBV) is a member of the species Tenuivirus oryzalbae, in the genus Tenuivirus, family Phenuiviridae, closely related tenuiviruses include Echinocloa hoja blanca virus and Urochloa hoja blanca virus, assigned to the species Tenuivirus echinochloae and Tenuivirus urochloae, respectively [14, 15]. Like other tenuiviruses, RHBV has a tetrapartite, single stranded, RNA genome. RHBV virions are nonenveloped, spiral, filamentous particles measuring approximately 3 nm in diameter and have varied lengths [16, 17].

RNA1 is approximately 9 kilobases (kb) in size and encodes the RNA-dependent RNA polymerase, with negative polarity. Conversely, RNAs 2–4 utilize ambisense strategy, wherein each RNA component encodes two open reading frames (ORF), one with positive polarity (viral sense) on the 5’ proximal region, and one with negative polarity (complementary sense) at the 3’ proximal region with a noncoding region spanning the two ORFs. RNA2 is approximately 3.6 kb. The viral sense ORF encodes a membrane glycoprotein, and the complementary sense ORF encodes a nonstructural protein (NS2) [18]. RNA3, approximately 2.3 kb, encodes a nonstructural protein (NS3) at the proximal 5’ end and a nucleocapsid protein (NCP) at the 3’ proximal end. NS3 serves as a viral suppressor of RNA silencing (VSR) by binding to double-stranded RNA (dsRNA) and small-interfering RNA (siRNA) and blocking its incorporation into the RNA induced silencing complex (RISC), ultimately halting host immunity responses and allowing for infection [19, 20]. The NCP provides stability to the genome and offers some resistance to degradation by host RNase activity [21]. Finally, RNA4, 2 kb in size, encodes a major nonstructural protein in the viral sense which accumulates in infected plants, and a nonstructural protein (NS4) in the complementary sense [22, 23, 24].

There is little evidence of significant diversity and virulence among RHBV isolates. A study comparing isolates from Colombia and Costa Rica found 98.9 and 98.6% sequence identity of the coding and noncoding regions of RNA3, respectively. Similarly, further comparison of the isolates revealed 96.9 and 91.5% sequence identity in the coding and non-coding regions of RNA4, respectively [25].

2.2 Hoja Blanca disease

RHBV is the causal agent of hoja blanca disease (HBD). As indicated by the name, hoja blanca (white leaf), infected rice plants exhibit chlorotic stripes or complete bleaching (Figure 1a). Beyond foliar symptoms, infected plants are often stunted with reduced root formation, potentially leading to plant death. Panicles exhibit partial or total sterility, while tillers are stunted, discolored, and malformed. Eventually, necrosis of leaf blades begins at the apical portion of leaves and extends to the base of young plants. Mature plants are less likely to exhibit severe symptoms compared to younger plants. In susceptible cultivars, yield losses ranged from 25 to 75% but have been observed to be 100% [26, 27, 28, 29]. These losses included plant death and increased panicle sterility [30, 31].

HBD was first identified in Cauca Valley, Colombia, in 1935 [28]. High incidence of HBD was not seen again until 1952 in Panama, though little yield loss was observed. In 1956, outbreaks in Cuba and Venezuela recorded crop losses of 25 and 50%, respectively. In Venezuela, all 75,000 acres of rice production exhibited disease symptoms only 90 days after initial disease onset [30]. Ongoing outbreaks were observed throughout Central and Southern America and the Caribbean from 1957 to 1967. Epidemic levels were reported in Latin American countries from 1980 to 1985 [32], with an additional outbreak in Colombia occurring in 1996–1999 [29].

HBD was first observed in the United States in 1957 in Florida, though this outbreak was several hundred miles away from large production areas. Similarly, in 1958, RHB was observed in Mississippi and close to small-scale commercial rice production. Growers and researchers became concerned in 1959 when HBD was found in commercial rice production in the Louisiana “rice belt”. The virus was only found in mature plants and losses were minimal as these plants were destroyed before further spread could occur [26, 30]. After a 65-year hiatus, RHBV reemerged in the United States. Surveys conducted in Texas in 2024 revealed over 800 hectares of infected rice plantings, though this is likely an underestimate of the area impacted [33].

To date, HBD, and subsequently RHBV, is distributed across the western hemisphere in tropical and subtropical America, including Brazil, Belize, Colombia, Costa Rica, Cuba, Dominican Republic, El Salvador, Ecuador, Guatemala, Guyana, Honduras, Mexico, Nicaragua, Panama, Peru, Puerto Rio, Surinam, United States, and Venezuela [29].

2.3 HBD epidemiology

RHBV is not mechanically, or seed transmitted [30, 34]. Rather, the spread of RHBV is largely attributed to the planthopper, Tagosodes orizicolus (Muir) (Hemiptera; Delphacidae), formerly Sogata orizicola (Figure 1b). Within this species, females (Figure 1c) are typically larger than the males (Figure 1d) and lighter in color. Both alate (winged) and brachypterous (wingless) individuals exist in populations, with females more commonly wingless compared to males. Females deposit egg clusters in the midrib of the rice leaf blade. Eggs are typically white, 0.7 mm in length, and sensitive to desiccation. The incubation period prior to nymphal emergence is 1–2 weeks, dependent on temperature. First instars emerge and begin feeding within 24 hours. Each of the five nymphal stages takes 3–7 days. Adults can mate 2 days upon maturation, after which females will lay approximately 160 eggs throughout their lifetime. The time required to complete their lifecycle is temperature dependent, requiring relatively high temperatures (27°C) and high humidity (>80%) [35]. This sap sucking insect typically feeds lower on the plant. In high numbers, this feeding causes yellowing or reddening on young leaves, and results in significant yield losses, referred to as hopper burn.

Tagosodes orizicolus adults and nymphs transmit RHBV in a circulative, propagative manner [36, 37]. When feeding on an infected plant, virions entering the stylet travel to the midgut and perforate the mid-gut barrier to the hemolymph. This acquisition process can take up to 12 hours. Following an incubation period of 20-25 days, the virus reaches the salivary glands of the insect and transmission can occur after 3–7 hours of feeding with a transmission efficiency of 90% following 5 hours of feeding. Viruliferous insect feeding for 24 hours or more on healthy tissue resulted in transmission rates of 100% [36, 37].

While circulating through the insect body, RHBV replicates and infects insect tissues, particularly those of the digestive and respiratory systems [17]. RHBV replication in insects is not ubiquitous but rather driven by recessive gene inheritance [38]. This results in reduced fecundity, nymphal viability, and longevity. Indeed, viruliferous insects deposited one-third as many eggs as healthy individuals. The number of resultant nymphs was similarly decreased. It was noted that overall fertility was reduced for both infected males and females [39, 40]. Transovarial transmission is observed in up to 100% of progeny when the maternal parent is infected with RHBV, and symptoms of infection are exacerbated when the male parent is similarly infected [40]. These nymphs can transmit RHBV shortly after emergence. Following acquisition, whether maternally or by feeding on infected material, insects retain RHBV throughout their lifetime [39]. In natural populations, 5–15% of T. orizicolus are infected and capable of transmitting RHBV. This value is likely influenced by the deleterious impacts of RHBV infection [39].

In the United States, the presence of T. orizicolus corresponded with RHBV presence in the late 1950s [26, 30]. It was not until 2015 that the vector was seen again in the country. Rice fields in Texas exhibited symptoms of hopper burn corresponding to high T. orizicolus populations [41]. Insects from this outbreak and one in 2018 were negative for RHBV following testing via polymerase chain reaction (PCR) [42]. The cyclical nature of T. orizicolus infestations corresponds to RHBV epidemics, indicating vector populations and the environmental conditions supporting them are the driving force of RHBV outbreaks [29].

2.4 RHBV detection

Several lab-based methods have been developed to determine the presence of RHBV in plant and insect tissues. Antibodies targeting the coat protein of the RHBV virion were initially developed when establishing the causal relationship between the filamentous RHBV particles and RHB symptoms in double immunodiffusion tests [16]. Further advancements allow for RHBV detection in both the plant and insect on a microplate for larger scale detection with increased sensitivity via double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) [38, 43].

A PCR assay has been developed to determine the presence of RHBV via amplicons of regions of the NS3 and NS4 ORFs [44]. These primer pairs have been used to detect Peruvian and Colombian isolates of RHBV in plant and insect samples [44], while they were similarly used in Texas, no vector samples tested positive for the virus [42].

2.5 HBD management

Management of HBD targets both RHBV and its vector, T. orizicolus. Insecticidal control is a widely adopted method with limited success. Small-plot studies showed pyrethroids were not effective compared to dinotefuran in Texas [41]. The use of broad-spectrum organo-phosphates and pyrethroids was shown to be deleterious to parasitoids used to control T. orizicolus populations. These biocontrol agents remain a viable option for countries in which the use or importation of chemical pesticides is highly regulated [29].

In addition to rice, the virus and vector have been observed in several weed species. Vector reproductive success has been documented in wild grasses, including Panicum and Echinochloa species, barnyard grass, and jungle rice [36], though deposited eggs are more exposed compared to deposition in Oryza species, leaving them vulnerable to the environment and degradation [45]. Furthermore, E. colona, while prevalent in rice fields and shown to be a host of the virus, does not appear to be an inoculum reservoir for subsequent transmission, but rather a dead end in the transmission cycle [29]. Despite being susceptible to RHBV via natural and experimental settings, wheat, barley, oats, and rye do not appear to be contributors to HBD incidence due to different growing environments compared to rice [29, 30].

The best management practice is to implement varieties resistant to both RHBV and the feeding of T. orizicolus. While this venture has been successful, particularly in cultivar Fedearroz 2000, monocultural practices run the risk of resistance breaking, especially considering complete resistance to RHBV has not been observed in any cultivar [29, 46]. Nevertheless, the South American varieties Fedearroz 2000, Linea 34, and Altamira 1 N show promising resistance to vector feeding and should be a consideration for breeding programs in Central America and the United States [47].

Breeding for resistance to RHBV proves more challenging. Cultivars derived from O. sativa japonica with the QTL, qHBV4.1, showed reduced HBD symptoms upon infection. Within this region, a gene encoding argonaute 4 (AGO4), a key protein in RNA silencing and viral defense in plants, has been implicated in RHBV resistance [46, 48]. Ordinarily, AGO4 binds to dsRNA and siRNA, which is then incorporated into RISC and targeted for degradation. In wildtype Fedearroz 2000, AGO4 expression increased upon insect feeding, and overexpression was maintained in the presence of RHBV; in susceptible varieties or in AGO4 knockout mutants, AGO4 gene expression decreased in the presence of RHBV [48]. The role of the VSR, NS3, in this process warrants further attention. While the presence or absence of this quantitative trait locus (QTL) greatly impacted HBD incidence and severity, complete resistance was not observed, indicating resistance to RHBV is controlled by multiple genes [46]. Additional QTLs of interest different than those of O. sativa japonica have been found in O. sativa indica and provide a promising outlook for future breeding programs.

To assess the potential for resistance, the Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) successfully optimized unmanned aerial vehicles (drones) for in-field detection of HBV breeding lines. This tool has allowed for earlier and time-efficient HBV detection when compared to more subjective human observation [49]. Furthermore, the group has developed a reliable, standardized method of insect-mediated transmission assays to determine a breeding line’s susceptibility to RHBV in controlled settings [29].

3.1 Global distribution and pathogen characterization

Pantoea ananatis has emerged as a globally distributed bacterial species. Initially isolated in tropical regions in association with pineapple (Ananas comosus), P. ananatis has since emerged as a notable pathogen across multiple cropping systems, especially rice (O. sativa), a globally important staple food [50, 51, 52]. Its subsequent isolation from economically important crops across multiple continents has expanded our understanding of its ecological breadth and significance [53].

In rice, the pathogen has been linked to both outbreaks and sporadic infections from Asia to the Americas, positioning it as a globally relevant emerging threat [54]. Its occurrence has been documented in several Asian countries (e.g., Japan, China, Philippines, Malaysia, Thailand), African nations (notably Togo), Latin America (Brazil, Argentina), and even in Europe (primarily on other monocots rather than rice), as well as in North America, particularly in the southern United States, including Arkansas and Louisiana [55, 56, 57, 58, 59, 60, 61, 62, 63] field surveys, phytosanitary reports, and active surveillance.

Pantoea ananatis is a bacterial species of growing significance in food production, primarily due to its broad host range, emerging virulence in key crops, and complex ecological behavior. First described in 1989, the genus Pantoea belongs to the Enterobacteriaceae family [64]. The genus name derives from the Greek word Pantoios, meaning “of all sorts or sources,” reflecting its diverse global distribution [65]. Species within this genus are considered highly versatile and ubiquitous, inhabiting a variety of ecological niches and hosts, and some exhibit the ability to interact with both plants and animals [66, 67].

Morphologically, P. ananatis is a Gram-negative, rod-shaped, facultatively anaerobic bacterium, typically measuring 0.5–1.0 μm in diameter and 1.5–2.5 μm in length. It is motile due to the presence of peritrichous flagella and forms distinctive round, yellow-pigmented colonies on nutrient agar, aiding in preliminary identification [68]. The yellow pigmentation results from carotenoid production, which is believed to confer protection against oxidative stress and ultraviolet radiation. Biochemically, P. ananatis exhibits broad metabolic capabilities, utilizing a wide array of carbon sources. Its facultative anaerobic nature allows it to thrive in both oxygen-rich and low-oxygen environments, including plant tissues, soil, and aquatic habitats [69].

For molecular identification, multilocus sequence analysis (MLSA) represents the most robust method for species-level classification [70]. Studies employing sequences of four housekeeping genes have demonstrated that MLSA enables clear differentiation among Pantoea species [67]. Comparative analyses of the gyrB (DNA gyrase subunit B) and rpoB (RNA polymerase beta subunit) gene sequences offer reliable identification of P. ananatis strains, with strong concordance between gyrB sequences and DNA–DNA hybridization values. Advances in genome sequencing have further elucidated the organism’s genetic architecture, uncovering genes linked to plant colonization, virulence, and environmental adaptability [71, 72, 73, 74].

Pantoea ananatis displays pronounced ecological plasticity, largely attributed to its extensive genomic flexibility [75]. While strains share a conserved core genome, they also possess a highly variable accessory genome enriched with genes specific to colonization of diverse hosts, including plants, animals, and insects [76, 77]. This accessory genome, shaped in part by integrated prophages and mobile genetic elements, encodes proteins involved in carbohydrate and amino acid metabolism, host tissue adherence, immune evasion, and potential pathogenicity [69]. Key mobile genetic elements include the large plasmid LPP-1, which harbors genes associated with metabolic diversity, nutrient acquisition (e.g., iron and nitrogen), resistance to antimicrobials and heavy metals, and host interactions [78, 79].

Another major contributor is the Integrative and Conjugative Element (ICE), found in some P. ananatis strains, which encodes proteins involved in antibiosis and stress responses. These elements may confer competitive advantages by producing bacteriocins and putative antibiotics [80]. Such genetic features, particularly mobile elements and accessory proteins are central to the organism’s ability to shift between pathogenic, commensal, and mutualistic lifestyles [80]. The ecological diversity of P. ananatis is further evidenced by its isolation as a pathogen, endophyte, epiphyte, and even from human clinical samples, complicating its detection and management [75].

In addition to its pathogenic potential, P. ananatis has been reported to produce indole-3-acetic acid (IAA), a plant hormone involved in cell elongation and tissue differentiation [81]. IAA acts as a potent growth regulator, exerting physiological effects even at low concentrations and promoting plant cell wall loosening during expansion [82]. Although the complete suite of virulence factors in P. ananatis remains largely undefined, recent genomic studies have begun to shed light on its potential mechanisms of pathogenicity. The genome of a virulent P. ananatis strain isolated from eucalyptus, as well as the type of strain derived from pineapple, have been sequenced using 454 pyrosequencing and Solexa technology, respectively [74]. Preliminary comparative analyses have revealed a lack of the classical Type II, Type III, and Type IV secretion systems, which are typically associated with virulence and often found on pathogenicity islands in both plant- and animal-associated bacteria [69]. Interestingly, P. ananatis possesses a gene cluster showing high homology to components of the Type VI secretion system, a mechanism involved in bacterial competition and host interactions in several Gram-negative pathogens. However, the precise role of this system in P. ananatis pathogenesis has yet to be fully elucidated [83, 84].

Unlike better-characterized host-pathogen systems, there is a scarcity of mechanistic studies detailing how these molecular pathways contribute to infection, colonization, or symptom development in rice. Further research is needed to elucidate the virulence strategies of P. ananatis in this crop, particularly under field conditions where interactions with the plant microbiome and environmental stressors may influence disease expression. As highlighted by Weller-Stuart et al. [69], genomic data provides a foundation for such investigations, but functional validation through mutagenesis and transcriptomic analyses in rice-specific contexts is still lacking.

3.2 Disease symptoms

In rice, the bacterium typically acts as a pathogen, associated with diseases such as sheath rot, grain discoloration, and systemic infections that can reduce yield and grain quality. Symptoms observed in leaves and sheaths of infected rice plants include elongated brown streaks spanning the full length of affected tissues (Figure 2a-d), which often progress from inside out and lead to complete necrosis. In other monocot hosts, symptoms generally present as streaks or blotches parallel to the main leaf veins [85, 86]. Occurrences of P. ananatis-related diseases in rice are generally sporadic in Asia and other production regions, including in the United States, likely reflecting its opportunistic nature.

A particularly noteworthy feature of P. ananatis is the variation in symptom expression on the same host across different geographic regions. In maize, for instance, Brazilian strains cause necrotic or white leaf spots and streaks [85, 87], while in South Africa, the disease manifests primarily as stalk rot [88]. A similar trend is observed in rice: in Japan and several other regions, P. ananatis infects developing seeds, resulting in palea browning, whereas in Australia, it causes stem necrosis [89]. In the United States, divergent symptomatology has also been noted; rice fields in Arkansas exhibit different symptoms compared to those in Louisiana, reinforcing the notion that both environmental conditions and strain-specific factors contribute to this variability [63, 90].

3.3 Epidemiology

The epidemiology of plant diseases caused by P. ananatis remains poorly understood, especially across its diverse range of hosts. Current knowledge suggests that the pathogen can enter host tissues through flowers [91], insect feeding wounds [92], mechanical injuries [93], or direct plant-to-plant contact facilitated by strong winds [89].

Pantoea ananatis is both seed-borne and seed-transmitted in several crops, including onions [94], sudangrass [86], and rice [95]. The recent emergence of bacterial blight and die-back symptoms in eucalyptus in countries that imported seeds from South Africa further supports the likelihood of seed transmission [75]. Similarly, outbreaks of center rot in onions have been associated with the introduction of infested seed into new environments [94]. Although this pathway has not yet been officially documented in rice, it represents a potential phytosanitary risk, particularly as international seed trade intensifies.

Environmental conditions have a substantial impact on disease incidence and severity caused by P. ananatis. In crops such as maize and eucalyptus, the pathogen thrives under moderate temperatures (20–25°C) and high humidity [75]. On sudangrass, however, the most severe infections occur at higher temperatures (32°C) and elevated humidity levels [86]. This trend is mirrored in onion, where P. ananatis becomes active during bulb formation under high moisture conditions and temperatures between 28 and 35°C [96]. In rice, ongoing studies are attempting to define the precise environmental parameters that favor disease development, but preliminary evidence suggests that high humidity and elevated temperatures similarly increase pathogen aggressiveness [97].

3.4 P. ananatis detection

Detection protocols for P. ananatis are still under development. Although primers for detection and diagnosis have been developed, they require further optimization to ensure reliability and specificity for isolates from rice [98]. A semi-selective medium for isolating bacteria of the genus Pantoea has been developed, facilitating preliminary identification and purification of new isolates [99].

3.5 Disease management

Disease management strategies for P. ananatis typically rely on resistant or tolerant cultivars when available. In South Africa, blight and die-back in eucalyptus are effectively managed through the deployment of resistant clones, selected in high-disease nurseries [75]. In maize, Paccola-Meirelles et al. [100] demonstrated that artificial inoculation trials were effective in identifying resistant genotypes. Chemical control of white spot disease in maize with the fungicide Mancozeb has also proven effective when applied early in the disease cycle [101]. In onions, cultural practices such as mulching and modified irrigation systems have been tested. While irrigation method had little impact on disease incidence, using straw mulch or bare soil delayed symptom development by 7–14 days compared to black plastic [102]. For rice, the most practical approach currently available is the early identification, avoidance, and eradication of initial inoculum sources. These preventative actions are considered the most appropriate strategies to manage P. ananatis-associated diseases in rice under field conditions.

4.1 Global distribution and pathogen characterization

The rice Cercospora diseases are caused by the ascomycete fungus Cercospora janseana (syn. Cercospora oryzae and Passalora janseana; telemorph: Sphaerulina oryzina) [103, 104, 105]. Cercospora disease in rice was first reported as narrow brown leaf spot in Japan in 1906 [104]. The disease has a global distribution, including most rice-growing regions in Asia, Africa, Australia, North America, Central America, and South America [106]. Cercospora janseana was first reported in the United States in 1935 in Texas [107]. Once considered a minor disease, the incidence and severity has been increasing over the past few decades, mainly in the southern United States rice belt, including major producers like Louisiana, Mississippi, Texas, and Arkansas [108, 109, 110].

Cercospora janseana is classified within the Kingdom Fungi. It belongs to the phylum Ascomycota, which includes fungi that produce spores in sac-like structures called asci [111]. Within this phylum, it falls under the class Dothideomycetes, known for many phytopathogenic species [112, 113, 114]. The pathogen is further categorized in the order Capnodiales and the family Mycosphaerellaceae, which comprises numerous foliar pathogens [115, 116]. Within the genus Cercospora, the species C. janseana is recognized as the causal agent of diseases in rice. Morphologically, C. janseana produces hyaline to light brown conidia, multicellular, and borne on pigmented conidiophores, typical of Cercospora species [117]. This pathogen exhibits a slow growth rate and low sporulation on commonly used culture media, such as potato dextrose agar (PDA) [108, 118]. As a result, efforts have been made to develop a reliable protocol for culturing and inducing sporulation, aiming to facilitate both laboratory and field studies of C. janseana [108].

The infection process of C. janseana begins with the germination of conidia under conditions of high humidity and temperatures ranging from 20 to 28°C [119]. Germ tube grows towards the stomata, where it forms appressoria and penetrates the rice tissues [106, 110, 120]. Cercospora janseana then colonizes the intercellular spaces, spreading longitudinally, with conidiophores emerging through the stomata [110]. This pathogen has a potentially long latent period, leading to delays in the observation of disease symptoms [106]. It has been reported to require from 7 to 66 days after inoculation for the expression of disease symptoms on rice leaves [106, 121].

The molecular mechanisms deployed by C. janseana to decoy the host immune system and successfully invade rice plants are yet to be elucidated. Recently, the reference genome for C. janseana was assembled, and 10,850 genes were identified, including 955 predicted secreted proteins and 361 predicted effector proteins [122]. Future studies will contribute to a better understanding of rice-C. janseana interactions.

4.2 Cercospora diseases

Narrow brown leaf spot (NBLS), caused by the fungus Cercospora janseana, is a recurrent foliar disease of rice that was initially observed affecting only the leaves, where it produced narrow, elongated lesions ranging in color from brown to reddish-brown [109, 123]. However, as the disease has expanded to other parts of the plant, including the sheath and panicle, a revision of both its terminology and management recommendations has become necessary. Following the naming convention used for blast disease, the nomenclature for C. janseana-induced symptoms now reflects the specific plant tissue affected. Thus, the term narrow brown leaf spot (NBLS) is now restricted to lesions on the leaves (Figure 3a). Symptoms appearing on the leaf sheath are referred to as Cercospora net blotch (CNB) (Figure 3b), while those on the panicle rachis and branches are identified as Cercospora panicle blight (CPB) (Figure 3c). When referring to the disease complex as a whole—encompassing symptoms across all tissues—the term Cercospora is being used. This updated terminology improves clarity and facilitates disease management, as recent studies have demonstrated that host resistance and control strategies may differ depending on the infected tissue [124, 125, 126, 127].

4.3 Epidemiology

Cercospora janseana conidia are dispersed by wind and rain splashes, infecting leaves through stomata or wounds [106, 110, 124]. This pathogen survives between seasons on crop residues and is favored by warm, humid environments—conditions common in rice-growing regions [126, 127]. Several gaps persist in the epidemiology of the Cercospora diseases. On the host side, factors such as planting date, nutritional imbalances, cultivar susceptibility, and growth stage susceptibility remain under investigation. Regarding the pathogen, the roles of potential alternative hosts and tillage practices in the life cycle of C. janseana, particularly related to survival mechanisms, have yet to be fully elucidated.

4.4 Disease identification and pathogen detection

The identification of diseases caused by C. janseana in rice is based on the symptomology wherein long, narrow, brown lesions on leaves, sometimes with a yellow halo indicate NBLS. Dark brown blotches in net-like patterns on leaf sheaths suggest CNB, and discoloration and decay in panicles, often confused with other panicle diseases, indicates CPB. There is a single report of C. janseana molecular detection and quantification by real-time PCR, aiming to quantify the inoculum build-up over time in treated and non-treated varietal plots at three different planting times [128]. However, there is no description of the specific primers and probe used.

4.5 Disease management

Integrated disease management for C. janseana involves a combination of cultural, chemical, and genetic strategies. Although host resistance is currently limited, ongoing research is investigating resistant rice varieties as a potential long-term solution. Rice varieties carrying the CRSP2.1 resistance gene [129] have been deployed in the southern United States, such as PVL03 [130], CLL16 [131], CLL17 [132], and Avant [133]. These varieties confer different levels of resistance to NBLS, although CNB and CPB can still occur [134].

Crop rotation and residue management are important practices that help reduce inoculum levels in the field by disrupting the pathogen’s life cycle. Lately planted rice develops more NBLS than earlier planted rice [126]. NBLS severity in hybrid genotypes is significantly lower than in inbred genotypes [125]. Chemical control using fungicides such as triazoles and strobilurins can provide partial disease suppression; however, proper resistance management is essential to maintain their effectiveness. The fungicides propiconazole and fluxapyroxad are more effective for NBLS control [124].

Finally, accurate diagnosis is essential for effective disease management, as it allows for proper differentiation of C. janseana from other foliar pathogens, ensuring that control measures are appropriately applied. Similarly, precise identification of panicle diseases is important, as they are often easily mistaken for neck blast in rice [109].

5.1 Global distribution and pathogen characterization

Rice false smut (RFS) is caused by the fungal pathogen Ustilaginoidea virens (Cooke) Takahashi (syn. Villosiclava virens), a nonobligate biotrophic ascomycete that infects rice floral organs. U. virens was first reported in India in 1878 as the causal agent of a minor disease with sporadic occurrence in rice fields [135, 136]. Currently, the RFS pathogen has spread throughout most important rice-growing regions, with reports on six continents and in 57 countries [137]. The RFS worldwide distribution includes 18 countries in Africa, 20 countries in Asia, 2 countries in Australia and Oceania, 1 country in Europe, 8 countries in North America, and 8 countries in South America (Figure 4) [137, 138].

The infection strategy of U. virens is unique. Unlike many foliar pathogens, U. virens invades the spikelets and forms characteristic smut balls that replace developing grains [135]. During the sexual cycle, the fungus forms sclerotia externally on false smut balls [139]. These sclerotia play a pivotal role in the pathogen’s survival and dissemination [4]. Under favorable environmental conditions (increased moisture, light, temperature), sclerotia germinate to produce asci and ascospores, which initiate primary infections and can generate secondary conidia, further promoting disease spread [137, 140]. At the late booting stages, the pathogen spores germinate on the lemma and palea of the developing spikelets, without forming appressoria, and invade the inner space of the spikelet to infect the staminal filaments [141, 142, 143]. In the asexual cycle, U. virens produces thick-walled chlamydospores on the surface of false smut balls, which generate secondary conidia that contribute to disease development as well as serve as a major inoculum source between rice seasons [137].

Ustilaginoidea virens conidia are round to elliptical with diameters ranging from 3 to 5 μm [144]. Conidia are ornamented with spines, usually pointed at the apex or irregularly curved, and approximately 200–500 nm long [144]. In contrast, sclerotia are flat and irregularly oblong or horseshoe-shaped, commonly developing when large temperature differences occur between day and night [135, 145]. This structure can remain dormant and be viable in the field for long periods [140].

Ustilaginoidea virens holds sophisticated mechanisms of infection and survival. Several effectors acting as virulence mechanisms have been identified to be crucial for U. virens. Effectors known to induce necrosis or suppress rice immunity, like SCRE1 and SCRE2, have already been reported [135, 146, 147, 148]. SCRE6, for example, is secreted and translocated into rice cells during infection, where it interacts with OsMPK6 to enhance its stability, suppress rice immunity, and facilitate U. virens infection [149]. OsWRKY31-OsAOC module, a key regulator of broad-spectrum disease resistance, was found to be hijacked by the U. virens secreted effector UvSec117, resulting in the suppression of jasmonic acid-mediated immunity [150]. Also, rice chitin-triggered immunity is suppressed by the U. virens-secreted cytoplasmic effector UvGH18.1 [151, 152]. This virulence factor acts as a chitinase by degrading chitin oligomers and reducing the plant’s reactive oxygen species (ROS) burst, which usually occurs upon pathogen sensing. Despite the findings to date, U. virens molecular mechanisms undermining rice immunity are still an undergoing investigation.

The RFS fungus is an exception among the biotrophs. Unlike other biotrophic fungi, U. virens can be cultured in the laboratory under nutrient-rich conditions such as Richard’s medium or Potato Dextrose Agar [4, 135]. By adopting a temperature range of 25–28°C and a pH of 5.5–7.0, U. virens mycelium and chlamydospores can be obtained on synthetic media [135, 153]. This characteristic can facilitate the study of pathogenicity mechanisms, enhancing the management strategies.

5.2 False smut disease

Recent reports have drawn attention to the increase in RFS incidence levels, thereby turning this pathogen into a re-emerging threat with the potential to cause yield losses commonly ranging from 0.01 to 8.6% [4, 135]. During epidemic seasons, yield losses can reach up to 70%, depending on weather conditions and rice cultivars [137, 154].

False smut affects the rice panicle during the booting to heading stage and is considered an emerging threat due to its increasing incidence in high-yielding and hybrid varieties, especially under favorable environmental conditions. The disease typically starts as small, pale-gray spots on the surface of developing grains (Figure 5a). As the infection progresses, one or more kernels on a panicle are transformed into large, yellowish-green spore balls that replace the normal grain [155]. These smut balls gradually enlarge and turn orange (Figure 5b), olive green, and eventually dark green to black (Figure 5c) as masses of chlamydospores accumulate on the surface [137]. Each smut ball may reach 1–2 cm in diameter and is composed of fungal mycelium, host tissue, and spores. Unlike true smut diseases, where the entire inflorescence is usually affected, false smut affects only a few kernels per panicle, often in a scattered pattern [142, 143]. This patchy infection pattern makes the disease difficult to manage and detect early. The smut balls are covered with a velvety mass of spores and sometimes exhibit a powdery texture. In severe cases, infection leads to grain yield and quality loss, and the presence of mycotoxins such as ustiloxins A and B can pose a food safety concern [135, 156].

5.3 Epidemiology

Ustilaginoidea virens survives in rice fields through the production of sclerotia, which have been found in high numbers even in subtropical regions. Although few sclerotia successfully overwinter, each can produce large quantities of ascospores that serve as the primary inoculum during the rice booting stage [140].

Dormant for 2–5 months, but viable up to 5 years under dry and low-temperature conditions, sclerotia germinate under favorable light, temperature, and humidity conditions [145]. Yellow fruiting bodies are produced under a light intensity higher than 250 Lux, combined with day and night temperatures around 31°C and 19°C, respectively [4, 135]. The conducive conditions also include recurrent rainfall periods along with cloudy weather until the next day and a relative humidity above 90% [4, 143]. Also, chlamydospores can germinate under high humidity conditions and produce a high amount of secondary conidia, which may spread by air and rain to infect rice flowers at the late booting stage [4].

Conidia serve as the primary inoculum, and wind and rain aid their dispersal [4, 137]. High nitrogen fertilization, dense planting, and prolonged booting-to-flowering periods increase disease severity [155]. Disease development is closely linked to environmental conditions during the panicle emergence and grain-filling stages, making false smut an unpredictable but recurrent problem. Sclerotia and chlamydospores are responsible for U. virens overwinter survival and serve as a primary inoculum source for the next season [135, 139].

The RFS pathogen can infect seedling roots, but the role of this mechanism in false smut ball epidemiology remains to be elucidated [140, 157]. Additionally, several weed species can act as alternative hosts and pathogen reservoirs during the rice off-season, potentially contributing to the long-term pathogen persistence [135, 137, 139]. Also, the specific contributions of germinating ascospores and chlamydospores in initiating the RFS infection at the booting stage remain unresolved [137].

5.4 Disease identification and pathogen detection

RFS early detection is challenging due to the cryptic nature of infection, which often remains asymptomatic until late stages [157, 158]. Traditional detection relies on visual observation of smut balls during the heading or maturity stage. Molecular methods such as PCR-based assays targeting U. virens-specific genes have improved early detection [159, 160]. Chlamydospores detection in field soil has been successfully achieved through real-time PCR [157]. Also, U. virens infection of rice roots and shoots was detected using a nested PCR with species-specific primers [157]. This advancement may support further investigations to elucidate the missing aspects of the disease cycle, such as the timing and impact of root and leaf sheath colonization and its role in RFS epidemiology. Furthermore, Loop-Mediated Isothermal Amplification (LAMP) detection provides sensitive and rapid diagnostics, supporting laboratory and field-level applications such as quarantine and breeding programs [161].

5.5 Disease management

Integrated disease management is essential to reduce the incidence and severity of rice false smut, relying on a combination of cultural, chemical, biological, and genetic strategies [4, 162]. Cultural practices such as the use of resistant or moderately resistant varieties, maintaining optimal planting density, and applying balanced fertilization, particularly managing nitrogen levels, can help limit disease development [162]. Chemical control remains a key strategy, although fungicide applications at the booting stage have only shown limited effectiveness in suppressing the disease; triazoles (e.g., tebuconazole, propiconazole) and strobilurins (e.g., azoxystrobin) are commonly used [137, 162, 163]. Biological control using antagonistic microorganisms like Bacillus spp. and Trichoderma spp. offers a promising but still underdeveloped alternative, requiring more field-level validation [164]. Efforts in host resistance breeding continue, but progress is hindered by the complex, polygenic nature of resistance and the limited availability of fully resistant rice cultivars [4, 162].