Wheat (Triticum aestivum) chromosome 6D harbours the broad spectrum common bunt resistance gene Bt11

KEY MESSAGE: A major QTL on chromosome 6DL corresponding to bunt resistance gene Bt11 was identified in four mapping populations generated through crosses with Bt11-carriers PI 166910 and M822123. ABSTRACT: Common bunt in wheat has witnessed a renaissance with the rise of organic agriculture that began in the 1980s. The abandonment of systemic fungicides in organic farming, together with a lack of resistant cultivars, has led to wide-spread problems due to common bunt infections. Knowledge about genetic sources for resistance is still scarce and only few of the known bunt resistance factors are currently used in breeding. We therefore aimed to map the resistance factor harboured by the Turkish landrace PI 166910, which is the resistance donor for the Bt11 bunt differential line. Four mapping populations (MPs) with 96–132 recombinant inbred lines (RILs) were phenotyped for common bunt resistance over 2, 3 or 4 years with one or two local bunt populations and genotyped with the 25K SNP array. A major bunt resistance locus on the distal end of chromosome 6D designated QBt.ifa-6DL was identified in all MPs and experiments. Additional QTL contributing to resistance were detected on chromosomes 4B, 1A, 1B, 2A and 7B. QBt.ifa-6DL mapped to a region overlapping with the Bt9-locus identified in previous studies, but results indicate that QBt.ifa-6DL is different from Bt9 and convincing evidence from haplotype comparisons suggests that it represents the Bt11 resistance allele. Markers for the distal region of chromosome 6D between 492.6 and 495.2 Mbp can be used to select for QBt.ifa-6DL. This resistance factor confers high and stable resistance against common bunt and should be integrated into organic and low-input wheat breeding programs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-023-04452-5.