Wheat stem rust disease (caused by fungus Puccinia graminis f sp tritici, or Pgt) has become a global food security threat, spreading across countries and continents from the Middle East into Europe, Africa, North America, South Asia, and elsewhere. Infections to wheat plants cause large-scale yield loss that can cause or exacerbate food insecurity, threatening the lives and livelihoods of civilian populations around the world.
Researchers leading the charge against wheat stem rust have found genetic analysis of both the Pgt pathogen and wheat plants to be an essential resource in reducing risks of food insecurity and famine. The protein products of avirulence genes (Avr) in a pathogen are recognized by specific resistance (R) proteins in the cereal grain, triggering an immune response in the plant and leading to pathogen resistance. By observing and describing the genetic information about Pgt disease strains and small grain crops, researchers can provide information that farmers globally can use to make educated decisions about which crop lines to grow in order to better withstand disease outbreaks, with less need to rely on fungicides and chemical intervention. A classic example of a Pgt race causing a large-scale threat is the Ug99 race, discovered in Uganda in 1998, which remains a threat to wheat production in African and South Asian countries.
Postdoctoral researcher Rebecca Spanner led the charge on recent University of Minnesota research that characterized the pathogen genetics of Pgt in major recent wheat stem rust epidemics, which occurred in 2013 and 2018 Ethiopia and Sicily, respectively. Spanner and colleagues obtained isolates of the Pgt pathogen from these epidemics and inoculated the pathogen samples onto wheat lines containing distinct genes providing resistance to wheat stem rust. Both genome sequencing technology and functional methods were used to assess the connection between avirulence gene sequence and disease outcome on the various resistance genes. To learn more about methods used and genes located when crafting whole-genome sequences, please read the original publication in full.
In this publication, Spanner et. al. have expanded the genomic resources for Pgt by generating reference genomes for the Ethiopian and Sicilian Pgt isolates, as well as full chromosomes for relevant Ug99 haplotypes. This enabled establishment of an Avr gene atlas compiling genetic variation in these Pgt strains’ known Avr loci. Detecting and identifying these Avr genes is an essential step to following and understanding the evolution of wheat stem rust disease. Avirulence traits are not always apparent in rust surveillance processes that rely solely on phenotyping, making genetic information like this an essential resource for disease defense.
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Spanner, R.E., Henningsen, E.C., Langlands-Perry, C. et al. Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69508-8