Genetic analysis of Puccinia graminis f. sp. tritici in Bhutan highlights the need for increased surveillance

Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has historically caused devastating yield losses in wheat-dependent regions of South Asia, but has been under control in recent decades largely due to the use of resistant cultivars. In this study, we set out to investigate Pgt occurrence within Bhutan, where we recorded a total of four Pgt samples recovered from the Haa district in 2025, confirming Pgt presence in the country. To compare these Pgt samples to global isolates of Pgt, each sample was genotyped using our Mobile And Real-time PLant disEase (MARPLE) diagnostics genotyping platform. Subsequent phylogenetic analysis indicted a close genetic relationship between all four Bhutanese Pgt samples and other Pgt strains previously identified within neighbouring Nepal. Furthermore, we identified several mutations in target genes (Cyp51 and SdhD) for two major fungicides used to control wheat rust worldwide. This included mutations in Cyp51 (S208T and V490L) that were ubiquitous in all 102 additional Pgt representative isolates analysed that represent the major Pgt race groups in the MARPLE diagnostics pipeline and are analogous to mutations previously reported to lower sensitivity to demethylation inhibitor (DMI) azole fungicides in Zymoseptoria tritici. This initial analysis indicates that Pgt, with genetic similarity to Clade IV, is present in Bhutan and that enhanced surveillance effects are needed to comprehensively define the Pgt population structure and further monitor for any potential changes in fungicide efficacy in the region.