On the third day of the Advanced Training in Plant Health: From Field Surveillance to Molecular Technologies, jointly organized by the Faculty of Agriculture, Universitas Gadjah Mada (UGM), and the World Vegetable Center (WorldVeg), participants explored advanced molecular diagnostics, plant virus detection, and bioinformatics applications. Building upon previous sessions on field diagnostics, pest identification, disease screening, and resistance evaluation, the third day focused on equipping participants with cutting-edge molecular techniques for rapid, accurate, and genomics-based plant pathogen detection.
The day began with a lecture entitled Molecular Diagnostics & Introduction to Major Vegetable Viruses, delivered by Lourena Maxwell, Ram, Dr. Widhi Dyah Sawitri (UGM), and Dr. Ady Bayu Prakoso (UGM). Participants were introduced to the fundamentals of molecular diagnostics, including the principles of Polymerase Chain Reaction (PCR), Reverse Transcription PCR (RT-PCR), quantitative PCR (qPCR), as well as emerging technologies such as Loop-mediated Isothermal Amplification (LAMP) and CRISPR-based diagnostics. The session also covered the use of FTA cards for field sample collection, primer selection and design, and an overview of major viruses affecting vegetable crops.
The lecture was followed by Lab Session 1: RNA & DNA Workflows, facilitated by Ram, Owen, and Dr. Widhi Dyah Sawitri. During this practical session, participants learned nucleic acid purification techniques by extracting viruses from infected plant tissues and obtaining clean virus isolates suitable for downstream molecular analyses. Emphasis was also placed on good laboratory practices to minimize contamination and maintain sample integrity throughout DNA and RNA extraction procedures.
Participants then continued with Lab Session 2: RNA Extraction (Viruses), led by Jo, Owen, and Dr. Widhi Dyah Sawitri. The hands-on exercise introduced standardized RNA extraction protocols using extraction buffers, isopropanol, and ethanol. Participants practiced tissue preparation, sample homogenization, nucleic acid purification, and RNA recovery while learning important considerations for maintaining RNA quality for reliable molecular diagnostics.
In the afternoon, Owen, Dr. Widhi Dyah Sawitri, and Dr. Ady Bayu Prakoso delivered a session on qPCR: Principles & Applications. Participants gained an understanding of real-time PCR technology, interpretation of cycle threshold (Ct) values, and the application of qPCR in plant disease diagnostics and resistance selection. The session demonstrated how quantitative molecular detection provides rapid, sensitive, and highly accurate diagnostic results for plant health management.
The practical program continued with Screening Tomato Genotypes for Potyvirus, facilitated by Owen and Ram in the greenhouse. Participants learned mechanical virus inoculation techniques using phosphate buffer and carborundum, followed by observations of early infection symptoms and discussions on evaluating tomato genotype resistance to viral diseases. The activity highlighted the importance of resistance screening in supporting breeding programs for disease-resistant vegetable cultivars.
The third day’s program concluded with Bioinformatics & Phylogenetics, presented by Lourena Maxwell, Ram, Dr. Ady Bayu Prakoso, and Dr. Widhi Dyah Sawitri. Participants explored the use of NCBI databases, BLAST sequence analysis, primer design, phylogenetic tree construction, and bioinformatics software such as Geneious for analyzing molecular data. The session demonstrated how bioinformatics has become an essential component of modern plant health diagnostics by supporting pathogen identification, evolutionary analysis, disease surveillance, and evidence-based decision-making.
The third day of the Advanced Training in Plant Health: From Field Surveillance to Molecular Technologies further reinforced the program’s contribution to the United Nations Sustainable Development Goals (SDGs). By strengthening participants’ expertise in molecular diagnostics, bioinformatics, and early pathogen detection, the program supports SDG 2 (Zero Hunger) through improved crop protection and sustainable agricultural production. It also contributes to SDG 4 (Quality Education) through advanced laboratory-based learning, SDG 9 (Industry, Innovation and Infrastructure) by promoting biotechnology and bioinformatics innovation in agriculture, and SDG 17 (Partnerships for the Goals) by strengthening collaboration among the Faculty of Agriculture UGM, the World Vegetable Center, and national and international experts in advancing plant health research and capacity building.
