CRISPR-based metabolic pathway editing for enhanced fungal disease resistance in crops

Overview

This solution offers a genome editing approach to enhance fungal disease resistance in staple crops such as potato, wheat, and barley. Despite decades of conventional breeding, most commercial cultivars lack acceptable resistance to fungal pathogens. The underlying cause is often mutated resistance (R) genes within metabolic pathways that compromise the plant's natural defense response. By combining transcriptomics and metabolomics to identify these mutations, specific gene segments can be replaced with functional versions to restore and strengthen resistance. The approach targets broad-spectrum disease resistance rather than pathogen-specific traits, enabling stacking of multiple edited genes for durable protection.

Technical specifications

Key features:

• RNAseq and metabolomics workflows to identify mutated resistance genes in metabolic pathways based on molecular function
• CRISPR-Cas9 editing demonstrated in potato via the StCCoAOMT gene in the phenylpropanoid pathway
• Transgene-free editing methodology under development for potato, strongfield wheat, and advanced breeding line barley
• Edited plants trigger lignin-related defense compounds within 72 hours of pathogen inoculation, containing infection to small lesions instead of full blight
• Gene stacking strategy to enhance multiple disease resistance simultaneously, as the mechanism is not pathogen-specific
• Application potential across existing high-yielding cultivars without disrupting agronomic performance

How it works:

The phenylpropanoid pathway produces defense metabolites that are deposited around infection sites to contain pathogens. In susceptible cultivars, key genes such as StCCoAOMT are mutated, breaking this defense. The team uses RNAseq and metabolomics to pinpoint these mutated segments, then employs CRISPR-Cas9 to replace them with functional gene versions. This restores the plant's ability to produce resistance metabolites rapidly upon pathogen attack.

Technology readiness level

Proof of concept has been demonstrated in Russet Burbank potato, where editing of the StCCoAOMT gene significantly enhanced resistance and contained pathogen spread to a small lesion. The current stage involves extending the transgene-free editing approach to wheat and barley. With industry collaboration and co-funding, the team aims to pursue an NSERC-Alliance grant to scale the approach across additional cultivars. A resistant cultivar is projected within 3-4 years of collaborative development. The technology is at a validation stage transitioning toward broader cultivar application.