Breeding for wheat varieties resistant to Stagonospora nodorum blotch (SNB) is the most sustainable strategy for controlling the disease. In order to map quantitative trait loci (QTLs) for SNB resistance we analysed 204 recombinant inbred lines of the cross between the winter wheat (Triticum aestivum L.) variety Forno and the winter spelt (Triticum spelta L.) variety Oberkulmer. We determined the level of resistance of adult plants to leaf blotch (SNL) and glume blotch (SNG) as well as morphological traits for 2 years after artificial inoculation with S. nodorum. Using composite interval mapping and LOD > 3.7, we detected ten QTLs for SNG blotch resistance (six inherited from the susceptible parent Forno) and 11 QTLs for SNL resistance (four inherited from Forno) across 2 years. Both resistance traits were moderately correlated (r = 0.52) and had only one common QTL. For SNL resistance, seven QTLs were not associated with QTLs for morphological traits. Among them, QSnl.eth-2D, QSnl.eth-4B and QSnl.eth-7B3 had major effects (R(2) > 13%) and were potential candidates for marker-assisted selection. For SNG, the major QTL on chromosome 5A, explaining 36% of the phenotypic variance for resistance, was associated with the q locus conferring the spelt morphology (long lax ear, long culm and hard glumes). Only QSng.eth-1BS, which explained 7% of the variance for resistance to SNG blotch, was not associated with QTLs for morphological traits. The consequences for breeding programmes are discussed.

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