Research

The morphological traits used for species-level identification of plant pathogens and beneficial microbes are tedious, time-consuming, and are not always accurate due to the ambiguity in morphological characters. The morphological-based identification of plant pathogenic and beneficial microbes at the species level is often erroneous. Nucleic acid-based amplification systems like polymerase chain reaction (PCR) are promising methods for the rapid and precise identification of microbes at the species level. Among different PCR-based techniques, the use of gene sequences such as 16S rRNA in prokaryotic organisms, internal transcribed spacer (ITS) region, and translocation elongation factor (TEF) genes in eukaryotic are the most extensively studied target sequences for microbial identification. The developed countries have included PCR-based techniques in routine plant disease diagnosis. In contrast, the use of these techniques in plant disease diagnosis is still at the infant stage in Nepal. The current project will establish a molecular laboratory to develop, update, and establish the protocols for the use of molecular tools in routine plant disease diagnosis.

Some soils are known to have very specific pathogen-suppressive properties known as soil suppressiveness where pathogens do not thrive or persist; therefore, are unable to cause damage to plants even though the pathogen persists in that soil. Being a country of diverse agro-climatic domains, Nepal might harbor several pockets of suppressive soil which deserve to be explored for commercial applications. The project is aimed at exploring the suspected suppressive soil from Salyan and Palpa districts and investigating their capacity to suppress rhizome rot diseases in a zinger. High throughput sequencing technologies will be utilized to underpin the microbial community structures responsible for disease suppressiveness of the soil. Finally, the promising soil will be studied for its transmissibility in regard to its suppressive capacity in other disease-infested fields.

Plant viruses are the major group of emerging pathogens globally with significant damage and annual crop losses. The diagnosis and identification of plant viruses are still primitive stages in Nepal due to the lack of sensitive detection methods. The availability of sensitive detection methods contributes significantly to deploying appropriate control strategies for viral disease management. The current project is targeted to employ high-throughput sequencing and PCR-based methods to identify plant viruses infecting citrus and solanaceous crops in Nepal. Comprehensive surveys will be conducted in Bagamati and Sudurpaschim provinces. The plant samples will be collected from the suspected plants, then nucleic acids (RNA and DNA) will be isolated from samples for sequencing. The project will enhance NARC-NPPRC capacity for plant virus diagnosis and detection and a standard protocol will be developed for future routine virus diagnosis. This will develop a comprehensive list of plant viruses present in solanaceous and citrus crops in Nepal, which will be helpful in designing the IPM strategies for viral disease management in solanaceous and citrus crops in Nepal.

Banana is a major fruit commodity grown commercially in all the plain districts of Nepal and contributes more than 21% of summer fruit production in Nepal. Banana cultivation is severely challenged by several biotic stresses; among them, Panama wilt and banana blasts are two major factors for declining banana cultivation in Nepal. NARC-NPPRC recently confirmed the association of Fusarium oxysporum f.sp. cubense race 1 with Panama wilt and Pyricularia spp. with blast or black pit in Nepal. However, further works are under action to confirm the species of Pyricularia associated with the banana blast in Nepal. The project has been continued for five years and has made huge progress. There is still a lack of effective measures recommended for both of these diseases in Nepal. The current year's activities are planned to share the achievements in banana disease research in Nepal among commercial banana growers in different regions. It also includes regular surveys and surveillance of the Panama wilt and banana blast to assess the economic impacts, distribution, and extent of severity in different regions of Nepal. The project will also evaluate the effectiveness of Anaerobic Soil Disinfestation and some novel biocontrol agents to control Panama wilt and selected a few chemicals to manage banana blasts in greenhouses conditions. The project is expected to document the extent of damage caused by these diseases in Nepal, and contribute towards developing novel management strategies for Panama wilt and blast disease. Consequently, these endeavors will enhance farmers' capacity to tackle major problems in banana cultivation through workshops designed for the extension and dissemination of information.

Potatoes play a major role in Nepalese agriculture contributing 9.4% of national agriculture gross domestic product. Late blight is one of the major constraints in potato production in our country. The estimated loss from late blight is around 15%, however, 100% loss has been reported frequently under unmanaged conditions. Phytophthora infestans have shown the ability to evolve faster and also are reported to develop fungicide resistance in no time. Therefore, there is an imminent need to study the P. infestans populations in Nepal in order to understand its ability to cause disease and devise proper management. The broad objective of this project is to study the genotypic makeup and fungicide sensitivity of the late blight pathogen Phytophthora infestans in Nepal. We have a collection of more than 150 P. infestans DNA in FTA cards which will proceed with genotyping to assess the genetic diversity of the isolates using microsatellite markers. In addition, the mating type will be assessed along with its fungicide sensitivity.

Tomatoes and potatoes are Nepal's most important crops for food and nutritional security. Both of these crops are devastatingly damaged by late blight caused by oomycetes Phytophthora infestans annually. The disease can cause 100% yield loss under favorable conditions. The use of resistance variety and the application of fungicides are two important strategies to manage diseases. However, the rapid evolution of new pathotypes causes the frequent breakdown of resistance with late blight. Furthermore, the over-application of fungicides increases the financial burden and environmental cost and possess the risk of developing fungicide resistance in Phytophthora infestans. Therefore, the judicial application of fungicides is very important for the economic management of late blight in both tomatoes and potatoes. The current project will develop, test, and validate a model creating efficient forecasting of late blight in Nepal with which evidence-based advisory could be provided to the farmers before the onset of the disease. We will be collaborating with Tej Shahi, a computer scientist at the University of Queensland, and Hem N. Chaudhary, a mathematician at the Massachusetts Institute of Technology, USA, Awasar Agrotech Pvt. Ltd. for developing models and National Agricultural Environmental Research Center for testing and validation of the model.

Early, rapid, and accurate plant disease detection is critical in deploying effective management strategies. The application of multispectral imaging in plant disease diagnosis is getting priority due to the ease of application in a large area, high confidence in disease detection, and considerably low cost. Considering the significant variation in the spectral response of leaf tissues, due to the biochemical and physiological impact of pathogen infection in plants, this study is focused on determining the potential application of multispectral imaging in the early and accurate detection of various pathogens. We are using a DJI P4 Multispectral drone in collaboration with Awasar Agrotech Pvt. Ltd. for acquiring field images and will employ a support vector machine as a classifier to estimate and detect the diseases.

Yellow rust is one of the major threats to wheat production in Nepal with estimated grain yield losses between 30–80%. The disease is caused by a biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst). Pst is notoriously known for the rapid incursion in a new location, the rapid evolution, and the generation of new races virulent to prevailed resistance varieties in a short period of time. The new races are also reported as more aggressive being able to thrive even at higher temperatures and are moving rapidly from the northern hills to the southern plain in Nepal. We are using MARPLE (mobile and real-time plant disease diagnostics) technology developed by Dr. Diane Saunders and her team at John Innes Centre, UK for race identification of yellow rust pathogen in Nepal using Oxford Nanopore-based third-generation sequencing in collaboration with JIC, UK, and CIMMYT International.