Description

The team's deep-rooted appreciation for farmers and agricultural practices serves as the inspiration for our project. The abundance of pepper farms in our region has brought to light the alarming problem surrounding their cultivation. Pepper foot rot is a condition that plagues plantations around the world. In India, infection typically occurs during the monsoon and progresses under high humidity and cooler temperatures. Early signs include the yellowing of leaves, defoliation, and quick wilting, ultimately resulting in vine mortality (TNAU Agritech Portal : Crop Protection, n.d).

The impact of the disease cannot be overstated, as over 561,500 tonnes of black pepper are grown in 26 countries every year. The damage is particularly evident in states like Kerala and Karnataka. In some districts of Kerala, annual losses go up to 1,000 tonnes, which is nearly half of the total vines being grown (Sreethu et al., 2025). On the West Coast of India, the average vine mortality is about 9.64%, translating to economic losses of over $900 per hectare. In severe cases, these losses can double to $1838 per hectare (Bhat et al., 2025). Pepper cultivation is deeply engraved in the culture of the community, which is now threatened by P. capsici. Despite being one of the largest cultivators, India's net pepper yield falls fifth, mainly due to the heavy toll taken by this pathogen. The disease does not know borders either, as Vietnam, Ethiopia, Malaysia, and Indonesia also report significant losses. Vietnam, the world's largest producer and exporter, cultivates over 131,000 ha (as of 2020) in the Central Highlands and Southeast region. Foot rot is black pepper's most destructive disease globally, with up to 95% vine infection reported in cases. In 2016, over 10,000 ha of black pepper in Vietnam were damaged by this infection (Thao et al., 2024). In southwestern Ethiopia, it affects up to 95% of vines on some farms, with vine loss reaching 21.4% (Jibat M et al., 2023). The problem extends to Indonesia and Malaysia, where yield losses go up to 40% and 10% respectively (Nguyen, 2015).

To combat P. capsici, a combination of biological and chemical solutions has been explored. Farmers tend to rely on chemical fungicides such as metalaxyl and mancozeb, copper oxychloride, nitrogen-phosphorus-potassium (NPK), and propiconazole. However, these measures are ineffective and come with long-term risks such as soil degradation and accumulation, disruption of microbiota, etc. Therefore, despite being fairly effective, the current methodologies are harmful to the environment.

Understanding the life cycle of Phytophthora capsici is essential to developing an effective biocontrol measure. The pathogen reproduces both sexually and asexually, which helps in its survival and spread. In the sexual cycle, two mating types (A1 and A2) form the gametangia that produce oospores, which survive under harsh conditions. During the asexual phase, reproduction occurs through the formation of sporangia that release zoospores under favourable conditions. These zoospores are the primary infectious agents that use their negative geotropism and chemotaxis to move towards the roots of the plants. On reaching the root, they germinate and form the appressoria to penetrate host cells. These structures then secrete effector proteins such as RxLRs and CRNs, which inhibit key cellular functions (Nguyen, 2015; Lamour et al., 2011).

Our project aims to develop an efficient and sustainable solution to combat pepper foot root by targeting Phytophthora capsici at its zoospore stage. An extensive research process identified bZIP1 as a gene that could be targeted to curb infection, as it plays a key role in appressorium formation, zoospore motility, and cyst germination. (Blanco & Judelson, 2005).

We aim to silence this gene using the RNA interference (RNAi) mechanism, using small interfering RNA (siRNA). The approach allows for the reduction of gene expression at the mRNA level (knockdown), which will not create irreversible changes, making it safer for environmental release.
The siRNA we have designed is highly specific to bZIP, ensuring that no unintended effects occur in the surrounding environment. To increase stability in the soil and assist the uptake of siRNA into the pathogen, chitosan nanoparticles are used to encapsulate the siRNA. Chitosan is a biodegradable and non-toxic polymer, which can form stable complexes with siRNA. Nanoparticles of varying sizes have been produced in our lab, which were further optimized for better size regulation using a tripolyphosphate cross-linker (Van Bavel et al., 2023). Larger particles will destabilize the cell wall of P. capsici (Ana Niurka Hernández-Lauzardo, 2011), allowing the siRNA to enter the cell. The nanoparticles degrade at a pH of 5.5-6 (Tığlı Aydın & Pulat, 2012), which aligns with the natural pH of P. capsici as well as the soil. This allows for the effective and precise delivery of siRNA. By employing these siRNA-chitosan complexes, we aim to eliminate the infection in P. nigrum plants to a degree much greater than any current solution.

At present, determining the stability of siRNA-nanoparticle complexes relies on experimental trial and error as well as extensive scientific literature review. Although techniques like docking simulations and molecular dynamics offer valuable insights, they produce fragmented results that are hard to interpret and compare across scenarios. To streamline this process, we have developed a software tool to assist with siRNA design and predict the interaction of siRNA-nanoparticle complexes for drug delivery. S.E.N.S.E., our machine learning model, predicts the stability of siRNA-nanoparticle complexes based on various parameters, utilising data from molecular dynamics simulations and docking studies as its training data.

Additionally, we found that the process of siRNA design is long, labour-intensive and requires a great deal of technical knowledge. There also doesn't exist a unified software solution for siRNA design that accounts for off-target effects and secondary structure stability. Our tool, siUltimate solves this by integrating several computational tools into a single and automated design pipeline. As a result, the task that earlier took several weeks can now be accomplished in a few minutes.

Aydın, R. S. T., & Pulat, M. (2012). 5‐Fluorouracil encapsulated chitosan nanoparticles for pH-stimulated drug delivery: Evaluation of Controlled Release Kinetics. Journal of Nanomaterials, 2012(1). https://doi.org/10.1155/2012/313961

Bhat, S., Arunachalam, V., Paramesha, V., & Gaonkar, N. (2025). Quantifying the economic impact and management strategies for foot rot (Phytophthora capsici L.) disease on black pepper cultivation in West Coast India: Farm-level insights. Plant Science Today. https://doi.org/10.14719/pst.6764

Blanco, F. A., & Judelson, H. S. (2005). A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection. Molecular Microbiology, 56(3), 638–648. https://doi.org/10.1111/j.1365-2958.2005.04575.x

Hernández Lauzardo, A. N. (2011). Current status of action mode and effect of chitosan against phytopathogenic fungi. African Journal of Microbiology Research, 5(25), 4243–4247. https://academicjournals.org/journal/AJMR/article-full-text-pdf/594FEEA15014.pdf

Jibat, M., & Asfaw, M. (2023). Management of foot rot (Phytophthora capsici) disease of black pepper (Piper nigrum L.) through fungicides and cultural practices in Southwestern Ethiopia. International Journal of Agricultural Research, Innovation and Technology (IJARIT), 13(1), 48-50. https://doi.org/10.3329/ijarit.v13i1.67973

Lamour, K. H., Stam, R., Jupe, J., & Huitema, E. (2011). The oomycete broad‐host‐range pathogen Phytophthora capsici. Molecular Plant Pathology, 13(4), 329–337. https://doi.org/10.1111/j.1364-3703.2011.00754.x

Nguyen, V. L. (2015). Spread of Phytophthora capsici in Black Pepper (Piper nigrum) in Vietnam. Scientific Research, 07(08), 506–513. https://doi.org/10.4236/eng.2015.78047

Sreethu, P. T., Paul, M. M., Gopinath, P. P., Shahana, I. L., & Radhika, N. S. (2025). Foliar symptom-based disease detection in black pepper using convolutional neural network. Phytopathology Research, 7(1). https://doi.org/10.1186/s42483-024-00305-1

Thao, L. D., Khanh, T. N., Van Liem, N., Hien, L. T., Thanh, H. M., Binh, V. T. P., Trang, T. T. T., Anh, P. T., Van Chung, N., Hien, P. H., Van Long, N., Duy, N. Q., Lesueur, D., Herrmann, L., & Brau, L. (2024). Current species of oomycetes associated with foot rot disease of black pepper in Vietnam. Tropical Plant Pathology, 49(5), 633–648. https://doi.org/10.1007/s40858-024-00662-4

TNAU Agritech Portal :: Crop Protection. (n.d.). https://agritech.tnau.ac.in/crop_protection/pepper_diseases_1.html

Van Bavel, N., Issler, T., Pang, L., Anikovskiy, M., & Prenner, E. J. (2022). A Simple Method for Synthesis of Chitosan Nanoparticles with Ionic Gelation and Homogenization. Molecules, 28(11), 4328. https://doi.org/10.3390/molecules28114328