Comparative mapping and validation of multiple disease resistance QTL for simultaneously controlling common and dwarf bunt in bread wheat

KEY MESSAGE: Resistance QTL on chromosomes 1AL and 7AL are effective against common and dwarf bunt, QTL on 1BS affects common bunt and QTL on 7DS affects dwarf bunt in bread wheat. ABSTRACT: Common bunt, caused by Tilletia caries and T. laevis, and dwarf bunt, caused by T. controversa, negatively affect grain yield and quality of wheat and are particularly destructive in low-input and organic production systems. Two recombinant inbred line (RIL) populations derived by crossing the highly and durably resistant cultivars ‘Blizzard’ and ‘Bonneville’ to the susceptible cultivar ‘Rainer’ were evaluated for their resistance to common and dwarf bunt in artificially inoculated field and greenhouse trials over two growing seasons and genotyped with a 15 K SNP array. Bunt resistance QTL were mapped to chromosomes 1AL, 1BS, 7AL and 7DS. Common bunt resistance was regulated by the major QTL QBt.ifa-1BS and QBt.ifa-1AL together with the moderate effect QTL QBt.ifa-7AL. Dwarf bunt resistance was on the other hand regulated by the QTL QBt.ifa-1AL, QBt.ifa-7AL and QBt.ifa-7DS. Common bunt resistance QTL exhibited pronounced epistatic effects, while epistatic effects were of smaller magnitude for dwarf bunt QTL. Kompetitive Allele-Specific PCR (KASP) markers were developed from SNPs associated with bunt resistance QTL and successfully used for QTL validation in an independent set of RILs. These KASP markers have the potential to support targeted introgression of QTL into elite wheat germplasm and accelerate breeding for enhanced bunt resistance. Durable protection against both common and dwarf bunt can be achieved by combining multiple resistance genes in the same genetic background. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00122-020-03708-8) contains supplementary material, which is available to authorized users.