Race‐Specific Reaction of Wheat Germplasm to Current European Virulence of Common Bunt (Tilletia spp.) and Fine‐Mapping of Causal Resistance Genes Using SNP Markers

Common bunt of wheat (Tilletia spp.) remains a significant threat to wheat production in low-input and organic farming systems, where chemical seed treatments are restricted or avoided. Host resistance represents a key component of sustainable disease control, but it’s effective deployment requires detailed knowledge of race-specific virulence and the genetic basis of resistance. In this study, we analysed the reaction of a large and diverse wheat germplasm collection to current European populations of common bunt and mapped the underlying resistance genes using SNP-based approaches. A total of 2,731 wheat accessions were phenotyped from 2012 to 2025 using up to 42 purified bunt races with well-defined virulence profiles. Based on phenotypic responses to race-specific resistance patterns , accessions were grouped, and compared with established differential lines. A total of 1504 selected accessions were genotyped using Illumina 26k SNP arrays, and resistance loci were identified by genome-wide association studies followed by fine mapping using recombination analysis. All classical Bt resistance genes from Bt1 to Bt10 and Bt13 were mapped to defined physical intervals, and the genomic positions of 16 additional race-specific resistance genes were identified in the panel of germplasm. Our results confirm that several historically defined Bt genes including Bt11 and Bt12 represent multi-gene resistance complexes rather than single loci. Also, genes established as separate genes may possibly be identical, including Bt4 being identical to Bt6, Bt10 being identical BtZ and Bt9 possibly being identical to one of the genes in the Bt11 complex. These finding highlights the need for revised nomenclature of genes and differetial set of varieties. The identified resistance haplotypes provide an improved tool for marker-assisted selection, and support the development of wheat cultivars with durable resistance to common bunt.