The Rise of the Bakanae Disease of Rice in the Philippines

Christian Joseph R. Cumagun | University of the Philippines Los Baños

Bakanae or “foolish seedling” in Japanese is a common seedling disease in rice caused by the fungus Fusarium fujikuroi. (Gibberella fujikuroi). Infected seedlings exhibit abnormal elongation and in severe cases stunting leading to death (Figure 1a and b). The elongation is attributed to gibberellins ( a plant growth hormone) and stunting  to fusaric acid, both of which are produced by the fungus. The type of symptom produced and the severity of the disease is dependent on the amount of the two metabolites produced, which varies with different strains of the fungus and the resistance imposed by rice cultivars. The pathogen is both seed-borne and soil-borne which means that infection may occur by: (1) sowing infected seeds in non-infested rice fields, (2) sowing uninfected seeds in inoculum infested fields, and (3) sowing infected seeds in inoculum infested fields.The disease is considered minor in most rice growing fields in the Philippines, however  bakanae is found to be increasing in incidence and severity in certain areas of the country, specifically in Ilocos Norte, Agusan and Nueva Ecija. What is the cause of the upsurge of the disease? According to a survey conducted by the Philippine Rice Research Institute (PhilRice), 46% of farmer-respondents in IIocos Norte, 39% in Agusan, and 54% in Nueva Ecija use PSBRc82 - a popular high yielding but highly susceptible rice variety. Due to the threat this pathogen poses to rice security and safety, knowledge about its population structure, aggressiveness and toxin produced may provide knowledge on the biology and evolution of F. fujikuroi and may aid in the development of sustainable disease management strategies.

Pathogen Diversity in  Farmers’ Fields

The fungus is highly diverse on the basis of DNA fingerprinting analysis.  Using universally primed polymerase chain reaction (UP-PCR), Our research team at the University of the Philippines Los Baños (UPLB in collaboration with PhilRice) characterized a population coming from Nueva Ecija, Central Luzon and found a diverse fingerprinting profile coming from a single rice field.  The fungus is considered heterothallic, meaning two compatible mating types exist in the population in which sexual reproduction occurs as confirmed by another aspect of our study.

We concluded that the high variation of the population generated at the DNA level is due to the sexual reproduction of the fungus occurring in the farmer’s fields. High diversity of F. fujikuroi poses a risk in terms of the development of fungicide resistance and susceptibility of modern cultivars, especially PSBRc82 and IR42. Establishing genetic diversity is essential in evaluating risk associated with management of the disease, selecting strains used in resistance screening and development of strategies for deployment of resistance.

Mycotoxin fumonisins, mating types and aggressivenessAside of gibberellins and fusaric acid, the fungus also produces fumonisins, a potent mycotoxin detected in considerable amounts in corn but fortunately is minimal in rice.  Although minimal, the risk cannot be underestimated, especially if it infects one of the world’s most important crops. We tested the ability of F. fujikuroi to produce fumonisins using two methods: by enzyme linked fragment length polymorphism (ELISA) and by Real Time RT-PCR and found a good association between the two. The FUM1 gene, a gene responsible for the production of fumonisins, was detected in F. fujikuroi in rice - although only for half of the strain population.

F. fujikuroi is indistinguishable morphologically with another species, F. proliferatum, but both are closely related. Phylogenetic analysis revealed the separation of these species into two groups.  It was reported previously that the sexual phase of F. fujikuroi is naturally occurring in the field. We confirmed the occurrence of the sexual stage by determining the mating type (MAT) of the isolates that were collected in Nueva Ecija. The population consisted of both MAT1 and MAT2 with MAT2 having twice as much frequency of occurrence than MAT1. Although the ratio is distorted, the finding supported the view that F. fujikuroi is undergoing sexual reproduction in the field.

There is no correlation between fumonisin production and aggressiveness in the form of elongation and stunting induced by F. fujikuroi, confirming the well established role of the gibberellins and fusaric acid in symptom expression.  Variety-isolate interaction was observed in some isolates as evidenced by the significant difference in the mean amount of disease they induced on two rice varieties PSBRc54 and PSBRc18. The significant isolate-environment interaction led to a medium heritability (0.54-0.55) in both varieties being tested due to significant genotypic variation of isolate by environment interaction. The most important sources of variation are isolate and isolate-environment interaction accounting to about 34% and 42%, respectively of the total variance for both varieties.

Implications for Disease Management

Information generated from this study could be useful in future bakanae disease resistance breeding programs in the Philippines. For example, isolates with stable aggressiveness could be used in evaluation of disease resistance. High variation in aggressiveness of the isolates of F. fujikuroi and widespread use of susceptible varieties that are high yielding and with good eating quality could explain the resurgence of bakanae disease. Based on the data on genetic diversity, aggressiveness, and fumonisin production of F. fujikuroi isolates, development of control strategies such as breeding of resistant varieties is deemed necessary to minimize or even eliminate the threat that the pathogen poses to the Philippine rice industry.

Variety Isolate: Variety-isolate interaction is an interaction effect between the rice variety and  fungal isolate. For example, an isolate may react differently  ( in terms of virulence) to variety 1 as compared to variety 2.