Integrated isothermal system for on-site plant variant detection

Overview

This technology offers a rapid, cost-effective, extraction-free isothermal testing platform for on-site plant genetic analysis. By eliminating the need for laboratory DNA/RNA extraction, it enables real-time detection of specific gene sequences, SNPs (Single Nucleotide Polymorphisms), and SSRs (Simple Sequence Repeats) directly from plant tissue in the field. The platform supports agricultural decision-making by accelerating the identification of genetic variants linked to pathogen resistance, climate adaptation, and commercially important metabolites. It also enables on-site detection of plant pathogens, including bacteria such as Candidatus liberibacter asiaticus in citrus, which has a high agricultural impact.

Technical specifications

Core capabilities:

• Extraction-free nucleic acid amplification from raw plant samples (leaves, stems, seeds)
• Isothermal amplification methods including LAMP, RPA, and CRISPR-Cas12/13
• Multiple readout strategies: fluorescence, colorimetry, turbidimetry, and lateral flow assay
• Detection of constitutive genes (e.g., rbcL) for species identification
• Identification of transcription factors associated with pathogen resistance
• SNP and SSR detection for genetic diversity analysis and bioprospecting

Applications:

• Marker-assisted breeding programs for crops such as Vigna unguiculata
• Bioprospecting for genes linked to productivity, drought tolerance, and saline soil adaptation
• On-field pathogen detection for sustainable agriculture and climate change mitigation
• Genetic improvement of native plant species

Technology readiness level

The technology has been validated through preliminary work using isothermal tools for extraction-free gene amplification in plants. The team has demonstrated successful amplification of the rbcL gene in native Vigna unguiculata varieties, detection of pathogen-resistance transcription factors, and on-field detection of Candidatus liberibacter asiaticus in citrus. Prior clinical validation of RT-LAMP and RPA with raw samples (without purified RNA) for SARS-CoV-2 detection confirms the underlying methodology. Future development will optimize reaction conditions, cell lysis methods, starting material types, and readout formats, alongside the design of a portable device for fieldwork. The team is seeking a partner to finance supplies, reagents, and portable device design to advance toward field-ready deployment.