, Volume 250, Issue 5, pp 1387–1407 | Cite as

Sheath blight of rice: a review and identification of priorities for future research

  • Pooja SinghEmail author
  • Purabi Mazumdar
  • Jennifer Ann Harikrishna
  • Subramanian Babu


Main conclusion

Rice sheath blight research should prioritise optimising biological control approaches, identification of resistance gene mechanisms and application in genetic improvement and smart farming for early disease detection.


Rice sheath blight, caused by Rhizoctonia solani AG1-1A, is one of the most devasting diseases of the crop. To move forward with effective crop protection against sheath blight, it is important to review the published information related to pathogenicity and disease management and to determine areas of research that require deeper study. While progress has been made in the identification of pathogenesis-related genes both in rice and in the pathogen, the mechanisms remain unclear. Research related to disease management practices has addressed the use of agronomic practices, chemical control, biological control and genetic improvement: Optimising nitrogen fertiliser use in conjunction with plant spacing can reduce spread of infection while smart agriculture technologies such as crop monitoring with Unmanned Aerial Systems assist in early detection and management of sheath blight disease. Replacing older fungicides with natural fungicides and use of biological agents can provide effective sheath blight control, also minimising environmental impact. Genetic approaches that show promise for the control of sheath blight include treatment with exogenous dsRNA to silence pathogen gene expression, genome editing to develop rice lines with lower susceptibility to sheath blight and development of transgenic rice lines overexpressing or silencing pathogenesis related genes. The main challenges that were identified for effective crop protection against sheath blight are the adaptive flexibility of the pathogen, lack of resistant rice varieties, abscence of single resistance genes for use in breeding and low access of farmers to awareness programmes for optimal management practices.


Biological control Fungicide Genome editing Integrated disease management Smart farming Transcription factor 


As the world population is expected to reach over 9 billion by 2050, it has been predicted that total food production will only be sufficient for 60% of the population (FAO 2018). Rice (Oryza sativa L.), the world’s most widely consumed cereal crop, is especially important to the rapidly growing populations in South Asian countries (Pareja et al. 2011) and provides 20% of the dietary protein in the developing countries where rice is the staple to the diet (FAO 2004). Around 40,000 different varieties of rice (Oryza sativa L.) exist in the world ( China produces largest amount of rice (142.3 million tonnes) followed by India (110.4 million tonnes) (According to FAO: Rice Market Monitor 2018). Rice productivity is affected by several pathogens that often place major constraints on production,. among which, Rhizoctonia solani, the causative agent of sheath blight (ShB), is responsible for yield loss up to 45% (Margani and Widadi 2018). The pathogen Rhizoctonia solani Kunh AG1-IA (anamorph), Thanatephorus cucumeris (Frank) Donk (teleomorph) is a soil-dwelling saprotroph and facultative parasite. The pathogen causes lesions on the sheath affecting grain filling and yield in rice (Wu et al. 2012).

ShB in rice was first reported in Japan in 1910. ShB in rice subsequently spread across the region, particularly where rice was grown under intense cultivation (Srinivasachary Willocquet and Savary 2011). As the disease spread to other Asian countries it was referred to by different names such as ‘Oriental leaf and sheath blight’, ‘Sheath blight’, ‘Pellicularia sheath blight, ‘Sclerotial blight’ and ‘Banded blight of rice’ (Srinivasachary Willocquet and Savary 2011). The ShB pathogen, R. solani Kühn, survives in the soil and water as sclerotia that remain viable for up to 3 years and form mycelia when coming into contact with plants (Kumar et al. 2009). The disease emerges around the late tillering to joint elongation stages in rice and achieves an aggressive state at the time of panicle differentiation. The early disease symptoms are the formation of lesions on the sheath leading to softness and lodging of the sheath and inhibition of grain filling (Wu et al. 2012). The fungus spreads rapidly via contact between plant parts such as tillers and leaves, and also via sclerotia (densely packed hyphal masses) present in surface water (Tsiboe et al. 2017). The severity of the disease depends upon cultivation practices, growth stages of the plant at the time of infection, usage of nitrogen fertilisers (Norman et al. 2003) and rice variety susceptibility (Tang et al. 2007).

ShB in rice is difficult to control because of the wide host range of the pathogen and persistence of sclerotia on exposure to adverse environmental conditions. Most insidiously, the pathogen evolves with time, allowing the sclerotia to overcome the resistance that may have been the hard-won achievement of the farmers and breeders. In order to combat the spread of ShB, it is necessary to use information compiled from studies of the biology of the pathogen, of the infection process and to determine how this information can be applied and supported with ShB management practices. Here we provide a review of the current information on identification criteria, modes of infection, hosts range and molecular basis of pathogenicity along with current management practices.

Biology of the sheath blight pathogen

Taxonomy and host range of the pathogen

Rhizoctonia solani Kunh is a collective species belonging to the order basidiomycetes but rarely producing basidiospores (Parmeter and Whitney 1970). Julius Kuhn first observed this fungus on diseased potato tubers in 1858 and named it R. solani (Almasia et al. 2008). Rhizoctonia solani infects over 27 families of plants, causing root, crown, hypocotyl, pod and belly rot, sheath and leaf blight, banded leaf, brown patch and canker (Sneh and Ichielevich-Auster 1998; Fenille et al. 2002) (Table 1). The species is subdivided into anastomosis groups (AG) based on their compatibility for hyphal fusion with known tester isolates. Anastomosis between genetically similar isolates that are compatible, form a fused hyphal network involving fusion of cell wall, cytoplasm and nuclei, whereas genetically distant isolates may form anastamoses but show no changes in the hyphal organisation (Kuninaga et al. 2002). A total of 14 different anastomosis groups (AG1 to AG13 and AGBI), which exhibit high variation in colony morphology, host range, aggressiveness and nutritional requirement, have been reported in R. solani (Guillemaut et al. 2003; Ahvenniemi et al. 2009; Ajayi-Oyetunde and Bradley 2018). Based on sequence homology and on size and shape of sclerotia, R. solani AG1 isolates are subdivided into three subgroups, IA, IB and IC (Sneh et al. 1991), all of which cause ShB, with the AG1-IA most commonly reported as the causal agent (Bernardes-De-Assis et al. 2009; Gonzalez-Vera et al. 2010).
Table 1

Summary of hosts and the diseases caused by different anastomosis groups of Rhizoctonia solani




Part of the plant infected

Disease symptoms

Anastomosis group/Subset




Sheath blight

Leaf sheath

Immergence of lesions on sheaths of lower leaves near the water line


Miyake (1910)


Barley stunt disorder


Patches of chlorosis on leaves stunted plants


Roberts and Sivasithamparam (1986)


Sheath blight

Leaves, sheaths, stalks and ears

Stalk lesions (rind spotting), stalk breakage, clumping and caking of styles (silk fibres)


Ahuja and Payak (1982)


Root rot


Lesions with dark brown borders and pale, straw-coloured - centrrs on the lower portions of wheat stems (culm) near the base of the plant


Paulitz et al. (2002), Barnett et al. (2017)


Sheath blight

Stem (ground side of sheath)

Lesions which are cloud-shaped, ash brown to ash white with reddish brown border on stem


Pascual and Raymundo (1988), Kasuga and Inoue (2000)



Black scurf


Raised black patches


Beagle-Ristaino and Papavizas (1985)

Stem canker

Stem and colon

Sunken, brown lesions on the sprouts before they emerge from the soil



Leaf spot and root rot


Damping off and stem rot in young transplants, sore shin in older field plants and a foliar disease named ‘target spot’

AG-2-2 and AG-3

Lucas (1975), Gonzalez et al. (2011)


Sugar beet

Root and crown rot


Wilting of the leaves, scattered brown to black lesions on the root surface, blackening of petioles at the crown position

AG 2-2 IV and AG 2-2 IIIB

Pannecoucque et al. (2008)



Belly rot


Lesions which grow as sunken, cratered, irregular in shape on fruits


Flentje et al. (1963), Lewis and Papavizas (1980), Hassan et al. (2015)


Pod rot


Seed decay, dark, sunken lesions just below the soil line on stem


Thiessen and Woodward (2012)

Soya bean

Seedling blight, root and hypocotyl rot


Red-brown sunken lesions on hypocotyl, shrunken, reddish brown lesion or canker developing at or near the soil line

AG2-2IIIB, AG4 and AG5

Yang (2015), Ajayi-Oyetunde and Bradley (2018)


Root rot/wet rot


Root rotting, yellowing and wilting of leaves, rotted and discoloured tissues become wet

AG2 and AG3

Harveson (2011)



Necrotic leaf spot


Small and large necrotic spots on leaves


Priyatmojo et al. (2001)


Oilseed rape and canola

Seedling damping-off, seedling root rot and basal stem or foot rot (brown girdling root rot) of adult plants.

Seedling hypocotyls and roots

Light brown lesions on the roots which becomes sunken, dark, enlarge enough to girdle the taproot

AG2-1 and AG4

Kataria and Verma (1992)



Damping off


Damping-off kills seedlings, rot beneath soil, Lesion near the tender stem causing the seedling to collapse or the seedling may continue to grow even though the lesion girdles the stem. The lesion is quite sunken, and the stem resembles a wire, hence the name wirestem. The girdled seedling eventually dies


Pscheidt and Ocamb (2008)



Root rot


Damping–off, which included seed rot, lesions on the hypocotyls and root rot

AG4 and AG7

Rani et al. (2013)



Bottom rot disease

Leaf midribs and leaf parts in contact with soil

Small rust-coloured necrotic spots on leaf midribs and leaf parts, lesions expand into a rot

AG 1-IB AG 1-IC and AG 2-1

Grosch et al. (2004)

Rice sheath blight infection and disease cycle

Typical R. solani infections result from sclerotia from a previous cropping season (Kumar et al. 2009). Initially, hyphae from sclerotia in the soil form a network and roots of newly planted seedling are penetrated at or near the water line (Ou 1985). Infection is favoured by warm temperatures (~ 28–32 °C), high humidity (~ 95%) and high levels of nitrogen fertiliser (Savary et al. 1995). The disease progresses in classical phases of early to late necrosis, with the cycle completed by the infection of soil by sclerotia from the infected rice plants (Fig. 1). After entering plant tissues, R. solani produces RS toxin, a mixture that includes N-acetyl glucosamine, N-acetyl galactosamine, glucose and mannose (Vidhyasekaran et al. 1997) along with pathogen effectors (such as glycosyltransferase, cytochrome C oxidase CtaG/cox11 and peptidase inhibitor I9), which co-relate with the virulence of the pathogen (Zheng et al. 2013). The fungus spreads in infected plant with the hyphae penetrating the stomata, producing lobate appressoria or infection cushions (Groth and Nowick 1992; Singh and Subramanian 2017). The formation of appressoria triggers enzymatic degradation, causing necrosis of the host plant and assisting colonisation by the fungal pathogen (Groth and Nowick 1992). The green or grey ellipsoid lesions (0.5–3 cm) formed on the sheath of leaves in acropetal succession (reviewed in Srinivas et al. 2013) give the classical sheath blight symptoms. As plant colonisation by the pathogen extends from leaf sheath to leaf blades, panicles and tillers, the necrotic lesions enlarge to 2–3 cm length and 1 cm width, with beached centres and borders turning purple-brown (reviewed in Srinivas et al. 2013). Finally, lesions on the upper part of leaves coalesce, covering entire stem and sheath of the plant leading to stem lodging. Stem lodging blocks the water transport, which disturbs canopy architecture and reduces photosynthetic capacity. As a result, grain filling is reduced and ultimately the infection leads to plant death (Bahuguna et al. 2012).
Fig. 1

Disease cycle of Rhizoctonia solani showing different phases of sclerotia development and disease symptom on rice

After rice harvest, R. solani sclerotia from infected plants persist in the soil for periods of up to 3 years and act as a source of infection for subsequent crop cycles (Savary et al. 1995). Individual sclerotia typically range from 5 mm in diameter to much bigger masses formed by fusion of multiple sclerotia (Keijer et al. 1996). Sclerotia are white initially and gradually turn brown after maturation as a result of melanin formation in the cell walls. The resilience of sclerotia can be related to the mature form, which has impermeable cell walls and high nutrient content: Melanin is an oxidised phenolic with hydrophobic properties (Willetts and Bullock 1992) reducing cell wall permeability and protecting cells from biological degradation (Sneh et al. 1991). Sclerotia have a rich nutrient reserve of proteins, polyphosphate, glycogen and lipids in the cytoplasm (Willetts and Bullock 1992), which serves as an energy source during extreme environmental conditions and also supports reinfection process (Keijer et al. 1996). The sclerotia are generally transported to the surrounding field from infected crops via irrigation of infested soil. At the time of re-infection, sclerotia undergo myceliogenic germination (Webster 1980) and hyphae spread horizontally (average is recorded to be 20 cm/day) on the plants hence making the disease to spread very fast (Savary et al. 1995). ShB development is also accelerated by high seedling rate, dense canopy of plants in the fields and growing of high-yielding improved varieties (which requires nitrogen fertilisers) (Savary et al. 1995).

Molecular basis of pathogenicity

The publication of whole genome sequence assemblies of R. solani AG1-1A (Zheng et al. 2013; Nadarajah et al. 2017), as well as genome sequences for rice (Eckardt 2000), provide useful resources for determining key mechanisms underlying R. solani infection and disease. Initial stages of ShB infection involve recognition between the rice host and the fungal pathogen. While rice roots produce exudates, comprised of carbohydrates and protein molecules that act as a chemoattractant for soil-borne bacteria (Bacilio-Jiménez et al. 2003) and influence fungal diversity (Van Der Wal et al. 2013; Hugoni et al. 2018), there are no reports of any specific fungal pathogen attracting molecules and a molecular mechanism explaining the role of root exudates in attracting R. solani is unknown. Genome sequence studies predict an array of secreted proteins, enzymes of primary and secondary metabolism, carbohydrate-active enzymes and transporters (such as ATP binding cassette) associated with the necrotic phase of infection (Zheng et al. 2013). Following that, transcriptome analysis of R. solani=infected rice sheath also showed involvement of various plant genes such as extracellular protease, ABC transporter and transcription factors during establishment and sugar transporters, cellular metabolism and protein degradation-related genes during the necrotrophic phase of infection (Ghosh et al. 2018). Following attachment of the fungal hyphae to rice roots, enzymic degradation of the plant primary and secondary cell walls occurs. The breakdown of complex macromolecules of cell walls such as cellulose, hemicellulose and pectin into simple sugars via cell wall degrading enzymes (pectinase, laccase and xylanase) secreted by R. solani facilitates host cell penetration (Talbot 2010; King et al. 2011). In the later stages of the disease, the pathogen activates sugar membrane transporters to enable the transport of simple sugar molecules to the fungal cells (Zheng et al. 2013; Quistgaard et al. 2016; Ghosh et al. 2018).

Signal transduction mechanism in R. solani infection is not yet well understood, though it likely involves G protein-mediated signalling through second messengers including cAMP and a number of downstream pathogenesis effector molecules: The G protein (Rga1) homologue to Ga subunits reported in other fungi was identified in R. solani (Charoensopharat et al. 2008). The disruption of Rga1 resulted in slow growth and reduction in pathogenicity, changes in colony structure and inability to form sclerotia. G proteins are the largest group of cell wall receptors in fungi, well-known for their function in promoting survival, propagation and virulence (Brown et al. 2018). A loss in pathogenicity because of disruption in G protein function has been reported for other pathogenic fungi including Magnaporthe grisea (Fang and Dean 2000) and Fusarium oxysporum (Jain et al. 2002). Changes in cAMP levels upon disruption of G proteins during infection have been reported for other pathogenic fungi but are yet to be explored in R. solani. A few studies have identified R. solani secreted proteins that are upregulated during infection and may be downstream effector molecules involved in enhancing plant infection and/or suppressing plant defense responses (Zheng et al. 2013; Ghosh et al. 2018). Studies of effector molecules identified in different R. solani strains show high diversity in gene sequences which indicates its adaptative flexibility (via gene duplication, deletion and point mutation) to escape host recognition and optimise virulence function (Oliver and Solomon 2010; De Wit et al. 2012; Ghosh et al. 2018). This could be one of the possible factors underlying the broad host range of R. solani strains.

Management of sheath blight disease in rice

Field disease history, weather conditions and prior information on cultivar susceptibility are major checkpoints to minimise disease occurrence. Current management practices and research to improve crop protection are discussed below and can be considered as related to agronomic practices, to chemical and biological control and crop improvement (Fig. 2).
Fig. 2

Disease management approaches for sheath blight of rice

Agronomic practices

Rice cultivars have considerable variation in terms of morphological traits including plant height, days to heading (date of sowing to panicle emergence), plant compactness, tiller angle, flag leaf length and width and stem thickness, which each have been reported to be associated with susceptibility to sheath blight (Zou et al. 2000; Pinson et al. 2005; Willocquet et al. 2012; Dey et al. 2016). To increase the grain yield, rice varieties with short height and abundant tillers are generally used in the field. Such varieties are also commonly cultivated with a high use of nitrogen fertilisers (Norman et al. 2001), which together create a denser canopy than taller varieties and provides a microclimate that enhances R. solani infection (Tang et al. 2007). Hence a systematic study on variety selection and correlation of nitrogen fertiliser with the seedling stage as well as the frequency of ShB infection may provide better information for optimising the use of nitrogen fertiliser while minimizing infection.

Regular monitoring, early detection of inocula and removal of weed-hosts are important points to be considered for ShB management. ShB infection in rice is also associated with the spacing in the plantation: Field studies in China showed a wider space plantation method such as square (Yang et al. 2008) and sparse plantation (Sugiyama et al. 2007) to improve the canopy architecture, produce a higher leaf area index, increase the grain yield and reduce disease occurrence. Clearance of plant debris and tubers from rice fields and postharvest drying was found to be effective in minimising sclerotia movement (Ritchie et al. 2009). Following drainage, complete sanitation using fungicides and destroying host-weeds from field boundaries (Anand et al. 2014) and crop rotation with the non-host plant (Wright et al. 2017) should be practiced to reduce inoculum density for next cropping season.

Rice farmers are on the front line in responding to crop diseases in the field. It is, therefore, important for the farmer to understand the available options to mitigate crop damage and the possible control methods that can be applied in the field (Nelson et al. 2001). Farmers in many developing countries rely only on fungicides because of lack of information on alternative disease management techniques. Hence awareness programmes are needed for implementing more effective disease management systems (Khoury and Makkouk 2010). In the early 90s, a farmer field schools (FFS) programme was conducted by the FAO’s Intercountry Programme on Rice Integrated Pest Management in South and Southeast Asia (Van de Fliert 1993; Matteson 1996) and farmers were trained with integrated disease management systems. In the programme, farmers were involved in observing and performing experiments such as rice genotype mixing to produce disease resistant cultivars; optimum use of nitrogen fertiliser for increasing yield and avoiding disease development; optimal plant density to avoid fungal infections and suitable concentrations of fungicides to grow susceptible varieties (Nelson et al. 2001). Likewise, more training programmes should be conducted to educate the farmers on good agricultural practices, marketing strategies and financial management, modern technologies such as remote sensing with Unmanned Aerial Systems (UAS, commonly known as drones) for early detection of ShB in the field. UAS provides high-spatial resolution to perform plant phenotyping and disease diagnosis (Mulla 2013). UAS equipped with multiple types of sensors are used to measure plant phenotypic traits, physiological status and water stress (reviewed in Yang et al. 2017). During ShB infection, the infected leaf tissue usually changes its colour from green (healthy tissue) to brown-to-yellow (diseased tissue) with the development of the disease. UAS equipped with digital and multispectral camera and green Seeker handheld crop sensor showed efficient detection of the colour changes during ShB infection in rice compared to manual disease scoring (Zhang et al. 2018). UAS can be further used to quantify the phenotypic parameter such as plant height, leaf texture and canopy architecture and physiological parameters such as chlorophyll content, photosynthetic activity and biomass and pigment content associated with ShB symptoms. By providing quick and accurate data on disease development, at a low cost, deployment of UAS can alert farmers to effectively take necessary measures on time and minimise the risk of spread and re-occurrence. Compared to manual methods for disease detection, the application of Unmanned Aerial Vehicle technology has helped to reduce the use of chemical fungicide as well as reduce soil and water pollution (Mulla 2013). The adoption of this technology can contribute to cost-effective and eco-friendly rice farm management by facilitating site-specific fungicide and/or fertiliser application, soil health scanning, planning irrigation schedules and yield rate estimation. A strong effective networking system connecting scientific research, management practices and farmer awareness programmes are highly recommended (Shaw and Pautasso 2014). Such improvements will enhance the livelihoods of vulnerable farmers and contribute to food security (FAO 2018) (Table 2).
Table 2

Resistant rice cultivars generated using overexpression of defense-related genes





Transformation system



Chitinase gene

Antifungal activity by hydrolysis of internal β-1,4-linkages of chitin (a fungal cell wall component)


Polyethylene Glycol-mediated protoplast transformation of calli derived from mature rice seeds

Lin et al. (1995)


Chitinase gene


Agrobacterium-mediated transformation of embryogenic derived rice calli

Datta et al. (2000)


Chitinase gene


1. Biolistic method for transformation of rice immature embryos

2. Polyethylene Glycol-mediated protoplast transformation of rice

Datta et al. (2001)


Chitinase gene


Agrobacterium-mediated transformation of mature rice seeds



Chitinase gene


Biolistic method for transformation of mature seed

Richa et al. (2017)


Thaumatin-like protein

Antifungal activity by hydrolysis of β-1,3-glucan (a fungal cell wall component)


Biolistic method for transformation of immature rice embryo

Datta et al. (1999)

RCH10 and AGLU1

Chitinase and Alfalfa β-1,3-glucanase gene

Hydrolysis of fungal cell wall components chitin and β-1,3-glucan


Agrobacterium-mediated transformation of mature embryos callus

Mao et al. (2014)

chi11, tlp and Xa21

Rice chitinase, thaumatin-like protein and serine-threonine kinase

Cell surface recognition of a pathogen ligand and hydrolysis of fungal cell wall components chitin and β-1,3-glucan


Biolistic method for transformation of immature rice embryos

Maruthasalam et al. (2007)


Antifungal plant defensin

Antimicrobial peptides which damage cell wall and increase membrane permeability


Agrobacterium-mediated transformation of scutellum derived rice calli

Jha et al. (2009)


Ethylene biosynthetic gene

Ethylene regulate the defense-related pathways during fungal pathogenesis


Agrobacterium-mediated transformation of mature rice seeds

Helliwell et al. (2013)


Oxalate oxidase 4

Oxalate oxidase breakdowns to produce H2O2 (antioxidant) which triggers plant’s defense response


Biolistic method for embryo transformation

Molla et al. (2013)

OsOXO4 and OsCHI11

oxalate oxidase 4 and chitinase gene

Oxalate oxidase breakdowns to produce H2O2 (antioxidant) which triggers plant’s defense response and chitinase hydrolyzes the fungal cell wall component chitin


Agrobacterium-mediated transformation of embryo raised callus

Karmakar et al. (2016)


Brassica juncea Non-expressor of pathogenesis-related genes 1

NPR1 regulate salicylic acid mediated systemic acquired resistance for defense response


Agrobacterium-mediated transformation of rice calli

Sadumpati et al. (2013)


Arabidopsis thaliana Non-expressor of pathogenesis-related genes 1


Biolistic method for mature rice embryo transformation

Molla et al. (2016)


Polygalacturonase inhibiting proteins

PGIP inhibit polygalacturonase secreted by pathogen to degrade the plant cell wall


Agrobacterium-mediated transformation of the following:

1. Shoot apices, roots and calli derived from roots

2. Scutella, calli derived from scutella, and suspension cultures

3. Immature embryos

Wang et al. (2015b)



Agrobacterium-mediated transformation of rice callus

Chen et al. (2016)

chi11 and ap24

Rice chitinase and Tobacco osmotin

Chitinase hydrolyses fungal cell wall components chitin and osmotin diffuses across the fungal cell wall causing leakage of the cellular contents


Agrobacterium-mediated transformation of scutellum derived rice calli

Sripriya et al. (2017)

RPMK1-1 and RPMK1-2

Pathogenicity Map Kinases

PMK helps formation of appressorium for infection and overall viability inside host plant


Biolistic method for mature seed derived calli transformation

Tiwari et al. (2017)

Chemical control

The most widely applied method for control of ShB is through the application of fungicides (Kandhari et al. 2003). Fungicides are toxic substances, often chemical compounds (natural or synthetic) with unique modes of action, used to kill or inhibit fungi (reviewed in Gullino et al. 2000). Selection of fungicide depends upon the intensity of the disease and also the tolerance level of the rice cultivar (Biswas 2004). The most popular fungicide application methods practiced for ShB control are foliar spray (McGrath 2004) and seed treatment (Kabir et al. 2006). Fungicides restrict the disease development on rice sheaths, acting on R. solani and its sclerotia by various means such as damaging the fungal cell membrane (Roberts et al. 1998), acting as enzyme inhibitors (Kumar et al. 2018), interfering in key processes including respiration or energy production (Ichiba et al. 2000; Lal et al. 2017) or by interfering with metabolic pathways associated with sterol and chitin biosynthesis for cell wall formation (Morton and Staub 2008). The best time to apply fungicides in a field is from 7 days after panicle differentiation until heading reaches 50–75% (Uppala and Zhou 2018). For susceptible rice varieties, application of fungicide is needed early in the crop cycle, at the booting stage of rice, when the leaf stem bulges to initiate panicle emergence (Yeshi et al. 2013). Some of the commercially available fungicides that are used against ShB in rice, their active ingredients and their modes of action are shown in Table 3. Apart from chemical fungicides, a few natural fungicides such as strobilurins (also known as β-methoxyacrylates) or QoI (Quinone outside Inhibitors) derived from the wild mushroom Strobilurus tenacellus have been tested for ShB management (Bag et al. 2016). Among analogues of strobilurins, Azoxystrobin (Methyl(E)-2-2-[6-(2-cyanophenoxy) yrimidin-4 yloxy] phenyl-3- methoxyacrylate) (commercial name Quadris 2.08 SC, Syngenta, Raleigh, NC, USA) was reported to be effective in reducing ShB and increasing grain yield (Bag et al. 2016). The above-mentioned fungicides arrest fungal growth via disrupting the electron transport chain, preventing ATP synthesis and restricting respiration in fungi (Ichiba et al. 2000). A recent comparison of the effect of Azoxystrobin and of the chemical fungicides thifluzamide, pencycuron, validamycin and hexaconazole showed the chemical fungicides to completely inhibit sclerotia formation while the natural fungicide, Azoxystrobin, also reduced sclerotia formation and resulted in better grain yield (Kumar et al. 2018).
Table 3

Chemical control of sheath blight of rice

Trade name

Active ingredient


Mode of action

Gram active ingredient/hectare



Strobilurin 23% SC

Suspension concentrate

Targets cytochrome bc1 (ubiquinol oxidase) at Qo-site which blocks the electron transport chain in fungi and prevent ATP formation


FRAC (2017), Bag et al. (2016)


Carbendazim 50% WP

Wettable powder

Disrupts β-tubulin assembly in mitosis of fungi and inhibits development of the germ tubes, formation of appressoria, and the growth of mycelia


Xiuguo et al. (2009)


Hexaconazole 5% EC

Emulsifiable concentrate

Targets C14-demethylase in sterol biosynthesis (erg11/cyp51) and inhibits spore germination, mycelium development, and sporulation in fungi


FRAC (2017), Kumar et al. (2013)

Cursor 40 EC

Flusilazole 40% EC

Emulsifiable concentrate


FRAC (2017)

Kitazin 48 EC

Eprobenfos 48%EC

Emulsifiable concentrate

Prevents phospholipid biosynthesis and methyltransferase activity disrupting chitin layer of the fungi, inhibits spore germination and their penetration


Kumar et al. (2013)

Score 25EC

Difenconazole 25% EC

Emulsifiable concentrate (EC)

Inhibits sterol demethylation, prevents the development of the fungus by inhibiting cell membrane ergosterol biosynthesis.


Kumar et al. (2018)

Eurofil-NT 35% SC

Mancozeb 35 SC

Suspension concentrate

Multisite contact activity, chelates metal cations, interferes with the vital thiol compounds in the fungal cell wall


Morton and Staub (2008)

Monceren 25 SC

Pencycuron 22.9% SC

Suspension concentrate

Inhibits fungal cell division and spindle microtubules assembly


Mian et al. (2004), Pal et al. (2005)

Tilt 25 EC

Propiconazole 25% EC

Emulsifiable concentrate

Prevents development of fungi by interfering with the biosynthesis of sterols in cell membranes


FRAC (2017), Kumar et al. (2013)

Folicure 25EC

Tebuconazole 25.9% EC

Emulsifiable concentrate

Demethylation inhibitor (DMI) of fungal sterol biosynthesis.


Roberts et al. (1998)


Thifluzamide 24% SC

Suspension concentrate

Targets succinate dehydrogenase complex II in respiratory chain and affect the fungal respiration


FRAC (2017), Kumar et al. (2012)

Sheathmar 3L

Validamycin 3% L

Inhibits trehalase an important carbohydrate energy source in fungi


FRAC (2017), Kumar et al. (2012)

The use of fungicides has been highly effective for controlling fungal diseases of crops. However, this is not without important considerations over the choice of fungicide and application practices: The prolonged use of a single fungicide increases the risk of fungicide resistance (Uppala and Zhou 2018). Fungal genomes may mutate resulting in altered target sites of fungicide binding, increased production of the target protein, or reduced uptake or increased metabolic breakdown of the fungicide (reviewed in Gullino et al. 2000). The above processes result in varying levels of resistance described as quantitative fungicide resistance (Deising et al. 2008). Therefore, the composition of fungicides is frequently modified to enhance the specificity to recognise and attack target fungus (reviewed in Gullino et al. 2000). However, the process of screening and selection for more specific and durable fungicides creates a cost burden to developers that may end up being passed on to the farmers in terms of higher prices who may then continue to use less effective but lower-cost earlier generation fungicides. Another concern over fungicide use is associated with hazard to human health (reviewed in Kim et al. 2017) and to natural ecosystems (Mahmood et al. 2016) requiring appropriate risk management strategies for their safe use. Many fungicides are persistent in soil and in above and below ground water bodies, ultimately entering and affecting the food chain (Rodrigues et al. 2018). Application of fungicides in agriculture also has a negative impact on aquatic organisms since the active ingredients of the fungicide often become concentrated in lakes and ponds through spray drift or agricultural runoff during heavy rainfall (Schulz 2004). The lethal effect of fungicides on detrivores also slows down leaf decomposition and thus impacts nutrient recycling (Hanazato 2001; Chang et al. 2005). The detrimental effect derived from fungicide treatment prompted policy actions that impose stringent regulation in several countries (Neha et al. 2017). Beside policy development, research and development efforts have been deployed to explore alternatives to the use of chemical fungicides such as use of biological agents to control ShB.

Biological control

Biocontrol is the use of parasites, predators or microorganisms (biocontrol agents) to reduce the population of a pest or pathogenic organism and is often considered to be a safe and reliable option for plant disease management (reviewed in Etesami and Maheshwari 2018). Microorganisms such as plant growth-promoting rhizobacteria (PGPR) can provide protection to rice cultivation via reducing R. solani infection (reviewed in Prasad et al. 2019). PGPR are free-living bacteria from the rhizosphere, which have been reported to actively participate in the biosynthesis of phytohormones (indole acetic acid, gibberellic acid, abscisic acid), increase N uptake, cause phosphate solubilization and interfere with pathogen toxin production (reviewed in Prasad et al. 2019). PGPR strains that are effective at controlling ShB infection in rice include Pseudomonas fluorescens and various Bacillus spp. (reviewed in Kumar et al. 2009; Karnwal and Mannan 2018). Pseudomonas fluorescens has been reported to inhibit R. solani by producing the antimicrobial compound hydrogen cyanide; the extracellular lytic enzymes β 1,3-glucanase and chitinase (Radjacommare et al. 2004) and by inducing systemic resistance in plants (Bakker et al. 2007). Bacillus spp. secrete phenylalanine ammonia lyase, peroxidase and other pathogenicity-related proteins to inhibit R. solani growth (He et al. 2002). Foliar spray of B. subtilis and B. megaterium was found to be highly effective in inhibiting the formation of sclerotia (40–60%) and mycelial growth (Li et al. 2003; Chen and Kang 2006). Pseudomonas fluorescens was also reported to be highly effective in preventing mycelial growth and sclerotia development (45%) when applied as a foliar spray or soil amendment (Kazempour 2004). Application of another strain of Pseudomonas, GRP3, as a coating on rice seed, followed by root dipping of germinated seedlings showed inhibition of the R. solani sclerotia up to 46%. (Pathak et al. 2004).

Eukaryotic microbes, mainly fungi from the genera Trichoderma and Gliocladium, have also been used as antagonists for ShB management. Trichoderma spp. and Gliocladium spp. inhibit R. solani by competition for nutrients and by mycoparasitism involving antifungal secondary metabolites (Qualhato et al. 2013). The major antifungal secondary metabolites reported are volatile antibiotics (e.g. 6-pentyl-α-pyrone and isocyanide derivates), hydrophilic compounds (e.g. heptelidic acid or koningic acid) and amphipathic polypeptides (e.g. peptaibiotics and peptaibols) (reviewed in Lorito et al. 2010, Bailey and Lumsden 2014). Fungal antagonists in the form of conidial biomass are used in the preparation of talc formulations for application as fungicides (Singh and Nautiyal 2012). The formulations applied to soil, seeds, root dip and foliar spray have shown inhibition of sclerotia formation up to 59% (Nagaraju et al. 2002; reviewed in Kumar et al. 2009).

Integrated, or combination approaches have also shown effectiveness for ShB control. As an example, applying a combination of a PGPR with an antibiotic was found to be very effective in suppression of ShB infection in rice: B. subtilis NJ-18 strain with jinggangmycin (a glucosaminidase glycoside antibiotic produced by Streptomyces var. jinggangensis) showed suppression of R. solani infection in rice under greenhouse conditions (Peng et al. 2014). A combined application of PGPR and fungus also showed promising results in controlling R. solani infection. T. viride and P. fluorescens reduced the disease by 47.3% (measured based on percentage disease scoring) compared with the individual application of either P. fluorescens (42%) or T. viride (45.7%) (Mathivanan et al. 2005). Combined application of T. viride and P. fluorescens demonstrated escalation in phytoalexin production, callose deposition, lignification of the plant cell wall, antimicrobial secondary metabolite production and upregulation of pathogenesis-related (PR) proteins (Nanda et al. 2010; Singh et al. 2016). Despite the promising results with biocontrol agents, the introduction of new biocontrol agents involves various considerations such as the tedious work of selection and screening, optimization of mode of application to achieve best results (reviewed in Tabassum et al. 2017), shelf life of the organism, efficacy in the field trials, environmental safety, and registration to be used as a PGPR (reviewed in Etesami and Maheshwari 2018).

Molecular biocontrol agents, such as antibiotics and the cell derivative trehalose have also been used against ShB. Trehalose (α-d-glucopyranosyl-(1 → 1)-α-d-glucopyranoside) is a carbohydrate energy source (Jin et al. 2015) present in all organisms except mammals (Benaroudj et al. 2001). In fungi, it is reported to be an important component of energy conservation and is also used as a scavenger of ROS (reactive oxygen species) under stress conditions (Perfect et al. 2017). Although generation of ROS is related with stress, ROS production has been reported to be crucial for the formation of R. solani sclerotia (Wang et al. 2018). ROS production is accelerated at the hyphal branches during the initial stage of sclerotia formation (Georgiou et al. 2000). During the mycelial growth, fungal cells remain stable and the amount of intracellular oxygen remains low, but in the transition period between mycelial growth to differentiation, fungal cells produce free radicals [ROS: hydroxyl radicals (·OH), superoxide anion (O 2 · ), singlet oxygen (1O2), and hydrogen peroxide (H2O2), etc.], which stabilise the antioxidant level in the cells (Georgiou et al. 2006). The whole process leads to excessive accumulation of intracellular ROS, initiating the formation of sclerotia (Wang et al. 2018). The application of exogenous trehalose showed a prominent increase in the ROS-related enzyme activities and induced oxidative burst as well as the decline in R. solani sclerotial dry weight (Wang et al. 2018). In addition, application of other antioxidants such as β-carotene (Zervoudakis et al. 2003) and ascorbic acid (Georgiou et al. 2003) also showed inhibition of sclerotial biogenesis. Hence, application of antioxidant or mimetics (chemicals which can act as antioxidant) can be utilised to restrict the sclerotia biogenesis (Papapostolou and Georgiou 2010) (Table 4).
Table 4

Summary of putative genes/proteins involved in Rhizoctonia solani-rice interaction

Phase of infection


Role in infectiona

Establishment phase


Polygalacturonase secreted by R. solani degrades enzyme pectin which is a major plant cell wall component

Extracellular metalloprotease, Mpr1

Fungalysins (zinc metalloproteases) which protect the pathogen from the action of host chitinases

ABC3 (ATP-binding cassette) transporter

ABC3 helps to efflux of cytotoxic compounds such as phytoalexins produced by the host

CRaZy (calcineurin-responsive zinc finger) transcription factor

Transcription factors helps in regulating expression of pathogenicity-associated genes during host colonisation


GAS1, encodes β-1,3-glucanosyltransferase which helps in formation of infection cushions

Necrotrophic phase


AOX1 is involved in alternative oxidative pathway and provides resistance against oxidative stress during pathogenesis


SidH (Enoyl-CoA hydratase protein family) is involved in siderophore production, which in turn assists the pathogen to survive under iron starved oxidative stress conditions


DHOD (dihydroorotate dehydrogenase) is involved in maintaining cellular redox homeostasis to survive in anaerobic host conditions


MoCDIP4 encodes effector proteins and cell wall degrading enzymes that induce cell death

aSource: Rao et al. 2019; Ghosh et al. 2019 and Ghosh et al. 2018

Genetic improvement of rice for sheath blight resistance

A long history of human selection, then traditional breeding in rice, are now supported by molecular information that can be used, often together with biotechnological approaches, to develop improved varieties, including ShB resistant cultivars. Below we discuss the different strategies which have been implemented in genetic improvement of rice against ShB infection:

Selection and breeding

ShB resistance is a quantitative trait which is controlled by multiple genes (Li et al. 1995; Zeng et al. 2011). Mapping of QTLs (quantitative trait loci) has revealed associations between gene loci and traits which have been used for marker-assisted selection in breeding (Mulualem and Bekeko 2016). Li et al. (1995) identified six QTLs associated with ShB resistance using restricted fragment length polymorphism (RFLP) analysis. Following this, more than 50 QTLs were identified for ShB resistance (Lavale et al. 2018), using mapping of various populations such as double-haploid populations (Zeng et al. 2015), a backcross population (Li et al. 2009), recombinant inbred lines (Channamallikarjuna et al. 2010), an F2 population (Sharma et al. 2009), chromosomal segment substitution lines (Zuo et al. 2014) and near-isogenic introgression lines (Loan et al. 2004). Association mapping of simple sequence repeats in rice genomes including landraces, further identified several markers significantly associated with ShB resistance (Jia et al. 2012; Lavale et al. 2018). However, the reliability of those QTLs is variable, as most of the QTLs remain undetected in multiple environments and/or mapping populations (Zuo et al. 2014; Eizenga et al. 2015). A recent genome-wide association study predicted two reliable QTL in rice based on significant correlation of the identified loci with ShB resistance in 299 cultivars (Chen et al. 2019). However, to date no QTL for ShB resistance has been well characterised: Identification of ShB resistance genes in QTL loci, functional characterization and application in marker associated breeding will be useful for generating resistant cultivars.

Genetic modification through biotechnology: Defense-related proteins and peptides

Genetic modification to develop resistant lines is a potentially powerful strategy to combat ShB infection in rice. The first tissue culture regeneration of rice (Oryza sativa cv. ‘Nipponbare’) was reported in 1985, using protoplasts derived from rice seed scutellum (Fujimura et al. 1985). The first genetically modified rice, (Oryza sativa L.v Taipei 309), containing an antibiotic resistance gene neomycin phosphotransferase II (NPTII), was reported in 1988 (Zhang et al. 1988). Following this, several genetically modified lines were developed expressing biotic and abiotic stress-resistant genes (reviewed in Ansari et al. 2015). More recently, the use of RNA interference (Tiwari et al. 2017) and gene editing (Gao et al. 2018) has demonstrated the possibilities to precisely manipulate expression of target genes to generate resistance rice varieties. Plant defense mechanisms are induced upon perception of a pathogen attack and include a hypersensitive response, generation of reactive oxygen species (ROS), accumulation of secondary metabolites such as phytoalexins, phenolics and tannins, and production and accumulation of pathogenesis-related (PR) proteins (Helliwell et al. 2013; Jain and Khurana 2018). Among the defense-related metabolites, expression of PR proteins has demonstrated potential to reduce ShB infection in rice (Table 2). Examples include rice plants overexpressing PR genes, such as Oryza sativa chitinase 11 (PR3 family) to inhibit R. solani via hydrolysis of β-1,4 linkages of the N-acetylglucosamine polymer of fungal chitin and degradation of the cell wall (Datta et al. 2001). The use of multiple disease resistance genes is likely to provide more enduring resistance than use of single resistance genes. Plants expressing three PR genes; chitinase-11 (PR3 family), thaumatin-like protein (PR5 family) and Xa21 (receptor like kinase) together showed fewer lesions compared to plants expressing each individual gene (Maruthasalam et al. 2007), while Karmakar et al. (2017) showed plants expressing OsCHI11 and AtNPR1 together displayed fewer sheath blight symptoms than plants expressing either single gene.

Expression of small antimicrobial peptides (AMPs) (45–54 amino acids), such as defensins in rice, have also been demonstrated to inhibit R. solani infection (Jha et al. 2009). Plant defensins bind to the fungal hyphae damaging the cell wall and plasma membrane thereby inhibiting fungal growth (Van Der Weerden et al. 2008). Expressing Dahlia merckii derived defensin, Dm-AMP1 in the apoplast of rice, suppressed the growth of R. solani by destabilising the plasma membrane. Dm-AMP1 also reduced the hyphal proliferation inside the plant tissue creating a disease resistance cascade (Jha et al. 2009). Although the role of AMPs has been widely studied and well characterised against biotic stresses there is a concern on the stability and innate toxicity of AMP. Much research is needed to develop less toxic and more stable AMPs for plant protection against ShB (Tang et al. 2018).

The recent addition of gene editing technology to plant biotechnology has expanded the possibilities for gene targets for the inhibition of pathogenesis. CRISPR/Cas9 editing has been used to restrict the growth of the R. solani in rice (Gao et al. 2018): R. solani activates the OsSWEET11 sugar transporter in infected plant cells, to efflux the sugar molecules for nutrition. Pathogen infection experiments showed that CRISPR-Cas9-based OsSWEET11 knock-out mutants were less susceptible to ShB, compared to OsSWEET11 overexpressing and wild-type plants (Gao et al. 2018). The precision of gene editing methods makes them attractive for crop improvement, particularly for loss of function mutations.

Genetic modification through biotechnology: Transcriptional and post-transcriptional regulation of gene expression

Strategies for manipulating gene expression at the transcriptional and post-transcriptional level have shown promise for improving rice ShB resistance. The rice genome encodes around 63 families of transcription factors (Gao et al. 2006), proteins that are master regulators of gene expression. Overexpression of members of the WRKY family of transcription factors, including OsWRKY30 (Peng et al. 2012), OsWRKY4 (Wang et al. 2015a) and OsWRKY80-OsWRKY4 (Peng et al. 2016) in rice each showed a reduction in the level of infection by R. solani. The reduction in the level of infection was found to be associated with WRKY-mediated elevated expression of defense-related PR genes of jasmonic acid and ethylene-responsive pathways (Peng et al. 2012; Wang et al. 2015a). Other than WRKY, transient expression of a rice transcription factor from the MYB family, Osmyb4 in rice leaf also demonstrated to elevate the expression of disease-resistant genes (aminotransferase, ankyrin and WRKY 12) (Singh et al. 2015) associated with the R. solani resistance (Zhang et al. 2010).

Other than the manipulation of gene expression via transcription factors, post-transcriptional regulation via RNA silencing is an effective biotechnological approach that has been applied in various crop. RNA silencing exploits the innate mechanism of double-stranded RNA-mediated suppression of gene expression via targeted destruction of mRNAs (Guo et al. 2016). With recent advancements in dsRNA delivery methods such as topical application of crude bacterial extract of exogenous dsRNA (Tenllado et al. 2003; Lau et al. 2014) and clay nanosheets loaded with dsRNA (Mitter et al. 2017) RNA silencing has already shown effect in disease management, especially for crop viruses. Information for the application of RNA silencing-based control to manage fungal pathogens is expanding, and this method offers an additional tool against fungi for which existing fungicides have been ineffective (Mcloughlin et al. 2018). An RNA silencing approach was able to reduce infection and delay symptoms of ShB by expressing a hairpin construct designed from the coding sequence of the PATHOGENICITY MAP KINASE (PMK), PMK1 and PMK2 genes of R. solani in rice (Tiwari et al. 2017). PMK is required in the fungal developmental pathway including the formation of appressorium infection structures, penetration of plant cuticle and overall viability inside host plant (Mey et al. 2002; Jenczmionka et al. 2003).

Conclusion and future prospects

ShB in rice is favoured by warm climatic conditions and high humidity. The key factors behind ShB outbreaks are broad host range and absence of single resistance gene and lack of awareness and access to best management practices among farmers. The most common practice in the field is still the application of fungicide, which if not used with care and good management, has negative environmental consequences and harmful effects on human health. The persistent use of fungicides leads to accumulation in agricultural soil and to ground-water contamination. The prolonged use of a fungicide also induces pathogen resistance. A more sustainable approach for ShB management in rice, with less reliance on synthetic fungicides, is to make greater use of natural fungicides such as strobilurins and biological agents such as P. fluorescens, Bacillus spp., Trichoderma spp., Gliocladium spp. and trehalose to restrict ShB occurrence. Further, testing of combinations of natural fungicides with biological agents and/or antibiotics to inhibit R. solani infection will likely lead to improved strategies for ShB management and can be used to determine more cost-effective approaches for farmers in various different settings. As ShB spreads more quickly with a poor spacing between plants and with over use of nitrogen fertilisers, adopting a square method of spacing and sparse plantation to avoid plant to plant contact and a combination of management practices such as postharvest drying and clearing of the field, crop rotation with the non-host plant will aid in restricting the fresh infection or re-occurrence. Furthermore, early disease detection of phenotypic and physiological parameters using Unmanned Aerial Systems can minimise the disease spread.

Use of tolerant and ideally resistant varieties is another sustainable approach. While QTL analysis has identified some potential ShB resistance loci and transcriptomic studies have identified candidate resistance genes, the underlying mechanisms for pathogenicity and resistance are not well understood and should be a priority for further studies. Also, genes associated with different phases of R. solani pathogenesis have been identified and further validation of such genes will serve as a reference for developing ShB tolerant varieties. Biotechnological approaches have shown promise: Transgenic lines overexpressing pathogenesis-related genes PR3, PR5, OsCHI11 and AtNPR1 (Table 2) and TF family WRKY (Peng et al. 2012; Wang et al. 2015a; Peng et al. 2016) showed inhibition against R. solani infection. It will be important to demonstrate protection against disease in field testing of the transgenic lines including under-warm and humid climates (optimal condition for R. solani infection) to further screen and select elite resistant varieties. Also, it will be interesting to study the productivity of transgenic lines in a field setting, especially at ShB hotspot locations. Host-derived dsRNA mediated silencing of pathogen-related kinase (PATHOGENICITY MAP KINASE 1) also demonstrated promising inhibition of R. solani infection. Exploration of pathogen- related genes through the exploitation of recent alternative approaches such as topical application of dsRNA as crude bacterial extract (Tenllado et al. 2003; Lau et al. 2014) or RNA clay (Mitter et al. 2017) and CRISPR mediated knock-out are additional approaches that should be included to achieve efficient and cost-effective disease management.

With climate change, ShB, along with other important crop diseases will require strong and concerted efforts in many areas of research from fundamentals though to applications. Strengthening linkages between researchers, media, non-governmental and community-based organisations in publicising information on ShB disease and its management will further aid in raising awareness to improve adoption of current available technologies to minimise ShB infection.

Author contribution statement

PS and PM designed the outline of the article, composed the manuscript and figure. JAH and SB provided scientific feedback and critical comments to revise the content. All the authors read and approved the manuscript.



Author Pooja Singh acknowledges Jimmy John Lilly, School of Bio Sciences and Technology, VIT University for providing sheath blight infection images. (PS, PM and JAH are partially supported by CEBAR Research University grant (RU006–2018).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest in the publication.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Centre for Research in Biotechnology for AgricultureUniversity of MalayaKuala LumpurMalaysia
  2. 2.Faculty of Science, Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
  3. 3.VIT School of Agricultural Innovations and Advanced LearningVIT UniversityVelloreIndia

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