LOS BAÑOS, PHILIPPINES (March 12, 2025) – Bacterial panicle blight (BPB), caused by the seed-borne and seed-transmitted pathogen Burkholderia glumae, is an emerging threat to rice production. Aside from yield losses, which can result in up to 70%, BPB also poses significant risks to seed production, international seed trade, and biodiversity. Although its prevalence remained low for many years, BPB outbreaks have become more frequent and widespread, now affecting over 2 0 countries across Asia, Africa, and the Americas (Azzahra et al., 2024).
To respond to this challenge, IRRI’s Seed Health and Logistics Unit (SHU) developed a rapid and simple diagnostic test for bacterial panicle blight using the Loop-mediated Isothermal Amplification (LAMP) method. LAMP is a technique that rapidly amplifies specific DNA sequences, allowing for the quick and accurate detection of Burkholderia glumae. This method is performed at a constant temperature without the need for complex laboratory equipment, making it ideal for use in the field.
As part of scaling out this method, IRRI-SHU introduced it to the Bureau of Plant Industry-National Seed Quality Control Services (BPI-NSQCS) through a Capacity Development Workshop on the Rapid Detection of Bacterial Panicle Blight of Rice. The workshop aimed to enhance the seed health diagnostic skills of BPI seed analysts and facilitate the adoption of LAMP technology to strengthen seed quality management and plant quarantine efforts.
About the Development of Innovation System for Climate Smart Pest Management in Rice (CSPM)
Opening the training, IRRI’s Senior Associate Scientist Dr. Nancy Castilla emphasized that while rice cultivation is a victim of climate change, it also contributes to its worsening impacts.
“Methane emissions from rice cultivation, particularly pesticide application, contribute to greenhouse gas effects. Therefore, there is a need for climate-smart pest management to improve rice productivity while minimizing environmental impacts,” she said.
Dr. Castilla also introduced the project of the Department of Agriculture, the Development of Innovation System for Climate-Smart Pest Management in Rice (CSPM). The project adopts an agricultural innovation system framework where various institutions collaborate to introduce new methodologies in pest management. Key approaches include using sustainable pest detection methods such as LAMP technology; tailored-fit resources to enhance pest identification and management at the farm level; and expansion of CSPM’s reach through policy integration, institutional partnerships, and farmer adoption programs.
Addressing the emerging threat of bacterial panicle blight (BPB) through LAMP Method
SHU Associate Manager Sheryl Catausan provided an overview of the LAMP method and its advantages over current detection methods such as PCR and culture-based techniques.
"LAMP is faster and more efficient than traditional PCR, providing results in minutes. It doesn’t require thermal cycling or complex equipment, making it suitable for low-resource settings. This is particularly beneficial for laboratories in developing countries, where resources and equipment for sophisticated diagnostic testing are often limited," she explained.
In addition to rapid detection, LAMP achieves high sensitivity and accuracy by using multiple primers targeting different DNA regions. It also supports various detection methods, such as fluorescence, turbidity, and colorimetric assays, making it particularly effective for rapid pathogen detection, including during outbreaks like COVID-19. LAMP assays undergo tests for specificity, sensitivity, and robustness, confirming their effectiveness in detecting pathogens, even in infected tissue samples.
Seed analysts from BPI-NSQCS participate in hands-on laboratory exercises during the capacity development training on Burkholderia glumae detection using the LAMP method. As part of the method validation, each participant analyzed coded samples with varying contamination levels to assess accuracy, precision, and reproducibility.
Aside from lectures, BPI analysts learned the practical applications of LAMP-PCR technology through hands-on exercises in sample preparation, reagent mixing, and PCR setup. They also explored lab readiness, equipment setup, good laboratory practices, and safety protocols. The training culminated in the presentation and discussion of results, followed by a forum on next steps and strategies for scaling the technology for broader seed health testing.
Scaling LAMP-PCR Adoption and Training for BPI-NSQCS Laboratories
In response to the three-day activity, Arian Jane Nanta, Agriculturist II at BPI-NSQCS, stated that the activity provided an opportunity to adopt modern detection techniques, particularly LAMP-PCR technology, which they plan to implement themselves. Their team is now adjusting the protocol to align the current capabilities of their laboratory with requirements for regulatory testing.
"By the end of the year, we aim to include B. glumae detection by LAMP-PCR in our seed health tests. We also plan to adopt methods for other plant pathogens and train strategic regional and satellite BPI-NSQCS seed health laboratories," she said.
SHU Senior Manager Dr. Martina Castellion supported this, noting that "BPI-NSQCS is the perfect scaling partner in this project," which aims to include BPB evaluation in standard rice seed certification tests in the Philippines.
She added, "This technology is quite simple to carry out, compared to other molecular techniques, and does not require highly experienced manpower, making it suitable for young scientists and technicians. Other high-risk pathogens can be detected using the same technology, contributing to farmers' access to quality seed."
Reference:
Azzahra, R. S. N., Miranti, M., Prismantoro, D., Mohd Suhaimi, N. S., Alizadeh, M., Mispan, M. S., & Doni, F. (2024). Bacterial panicle blight caused by Burkholderia glumae: a major disease in rice cultivation. Cogent Food & Agriculture, 10(1). https://doi.org/10.1080/23311932.2024.2381600