9.2 Pathogen indexing

Here’s a professional, course-ready section on Pathogen Indexing for COPI’s Biotechnological Propagation of Agarwood Course, suitable for SOP manuals, lab guides, and training materials:

Pathogen Indexing in Aquilaria Tissue Culture

1. Overview

Pathogen indexing is a systematic approach to detect and monitor plant pathogens in tissue-cultured Aquilaria plantlets. This ensures:

  • Healthy, disease-free plantlets for propagation
  • High survival rates during acclimatization
  • Prevention of pathogen introduction into plantations
  • Compliance with plant health regulations

Pathogen-free plantlets are critical for maximizing growth, vigor, and resin yield.

2. Importance in Tissue Culture

  • Tissue culture can amplify both desirable clones and hidden pathogens
  • Contaminated plantlets can lead to:
    • Rapid spread of fungal, bacterial, or viral infections
    • Reduced growth, rooting, and survival
    • Economic losses in large-scale propagation and plantation establishment

3. Pathogen Indexing Techniques

3.1 Visual Inspection

  • Monitor for leaf discoloration, necrosis, stunted growth, or unusual morphogenesis
  • Initial, low-cost screening during subculture and acclimatization

3.2 Microbiological Methods

  • Fungal and bacterial isolation on selective media
  • Culture identification through morphology and colony characteristics

3.3 Molecular Diagnostics

  • PCR-based detection for specific pathogens (e.g., Fusarium spp., Pythium spp.)
  • qPCR for quantitative assessment of pathogen load
  • Allows detection of latent infections not visible morphologically

3.4 Serological Assays (Optional)

  • ELISA for viral pathogens
  • Useful when Aquilaria plantations are exposed to virus-prone environments

4. Integration into Propagation Workflow

StagePathogen Indexing Action
Explant selectionScreen mother plants for visible signs of disease
In-vitro cultureMonitor contamination during initiation and subcultures
Shoot multiplicationPeriodic sampling for fungal/bacterial presence
Root induction & acclimatizationTest for pathogens before ex-vitro transfer
Plantation transferFinal pathogen-free certification of plantlets

5. Key Principles for COPI Labs

  1. Select pathogen-free mother plants to minimize initial contamination
  2. Maintain aseptic techniques at all stages of tissue culture
  3. Perform periodic pathogen indexing during multiplication and acclimatization
  4. Document results in plantlet batch records for traceability
  5. Discard or treat infected plantlets to prevent contamination of healthy cultures
  6. Combine visual, microbiological, and molecular methods for reliable detection

6. Course-Ready Key Statement

Pathogen indexing ensures that Aquilaria plantlets remain disease-free, maintaining growth vigor, survival, and resin production potential. A combination of visual inspection, microbial isolation, and molecular diagnostics is essential for COPI labs to produce high-quality, plantation-ready plantlets.

I can next:

  • Create a visual infographic showing the pathogen indexing workflow from explant selection → in-vitro monitoring → rooting → acclimatization → plantation transfer
  • Include screening methods and critical control points for COPI labs

Do you want me to create the infographic version next?