Paper-based portable sensor for early detection of crop stress using mirna biomarkers

Overview

Crop stress from pathogens, drought, salinity, or other abiotic factors is typically identified only after yield damage becomes irreversible. This solution addresses that gap by offering a portable, paper-based diagnostic sensor that detects stress at its earliest stages directly in the field.

The technology uses stress-responsive microRNAs (miRNAs) and pathogen-derived small RNAs as biomarkers. Because miRNAs are conserved across a wide range of plant species, a single sensor platform can monitor multiple stress types across diverse crops, including melon and tomato. The device is designed for use by non-specialists such as farmers, requires no laboratory infrastructure, and delivers results from minimally processed leaf samples in less than 30 minutes.

By enabling early diagnosis, the platform supports timely agronomic decisions that can protect yields, reduce unnecessary pesticide or water use, and improve overall crop productivity worldwide.

Technical specifications

Biomarker strategy:

• Uses stress-responsive miRNAs validated across 222 plant species and 522 stress conditions as general and specific stress markers
• Detects both plant-derived miRNAs and pathogen-derived small RNAs (~21 nucleotides), enabling discrimination between closely related sequences
• Validated markers include general stress indicators and stress-specific miRNAs for melon and tomato

Paper-based analytical device (PAD):

• Lateral flow format built on nylon membranes with hydrophobic barriers defining fluidic channels
• Detection and capture probes incorporate Locked Nucleic Acid (LNA) nucleotides, increasing sensitivity approximately 500-fold compared to standard DNA probes
• Detection probe is 21–22 nucleotides and is 50% complementary to the target miRNA and 50% complementary to the capture probe; capture probe is 11 nucleotides
• Detection limit of 1.2 picomolar for synthetic miRNA by naked-eye colorimetric readout, comparable to physiological miRNA accumulation levels in stressed plants
• Functional across a temperature range of 9–40 °C, suitable for varied field conditions
• Compatible with crude plant extracts without complex sample processing

Planned optimizations:

• Evaluation of paper types, fabrication costs, shelf-life stability, and hydrophobic barrier performance
• Integration of ionogels to improve fluidic control
• Development of a dedicated extraction buffer to ensure small RNA availability in field samples
• Selection of the most robust colorimetric detection chemistry for naked-eye interpretation
• Validation using real stressed and infected plant material

Technology readiness level

The technology is currently at Technology Readiness Level 4–5. Laboratory validation has been completed across more than 1,000 assays using non-optimized lateral flow PADs, demonstrating sensitivity, specificity, temperature tolerance, and discrimination between closely related miRNA sequences in crude plant extracts.

The next phase focuses on meeting the WHO ASSURED criteria (Affordable, Sensitive, Specific, User-friendly, Rapid, Equipment-free, and Deliverable) through optimization of paper materials, fluidic design, biomarker panels, and extraction protocols. A potential second phase would extend the platform to physical and chemical biosensor formats for higher-throughput or quantitative applications.

The team is seeking approximately €150K in funding for consumables, laboratory equipment, travel, and key personnel to complete optimization and field-ready validation.