A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), threatens global food security. Using Oxford Nanopore sequencing, researchers rapidly genotyped field samples in under 48 hours, detecting lineage and fungicide resistance. This approach enables full-gene coverage, variant phasing, and is deployable in low-resource settings — supporting faster, more informed disease control strategies against this ‘cereal killer’.

Key points:

• Savva et al. introduce the Pgt MARPLE diagnostics platform: a portable, real-time genotyping tool designed to close the wheat stem rust surveillance gap

• 165 Pgt isolates were collected from 25 countries across the world

• Using Oxford Nanopore sequencing of a targeted panel of 276 genes and a standard laptop, MARPLE delivered lineage typing and fungicide resistance profiling within 48 hours of leaf sample collection

• The method has already been successfully deployed in Kenya and Ethiopia, placing powerful genomic tools in the hands of local teams and enabling faster, more informed responses to emerging outbreaks

Sample type: fungal isolates

Kit: Rapid Barcoding Kit