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We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.

Wheat (Triticum aestivum L.) yields are commonly affected by foliar infection by fungal pathogens. Of these, three wheat leaf blotch fungal diseases, septoria nodorum blotch (SNB), tan spot (TS) and septoria tritici blotch (STB), caused by Parastagonospora nodorum (Pn), Pyrenophora tritici-repentis (Ptr) and Zymoseptoria tritici (Zt), respectively, induce major yield losses. Infection results in necrotic areas on the leaf, and it is often difficult to determine the underlying causative pathogen from visible symptoms alone, especially in mixed infections. Here, a regional survey of 330 wheat samples collected across three seasons (years 2015–2017) from four north-west European countries was undertaken. Using quantitative polymerase chain reaction (qPCR) assays specific for each pathogen, as well as disease assessment of leaf materials, distinct regional differences were identified. Two-thirds (65%) of all samples harbored at least two of the three pathogens. Norway had high SNB abundance, but also showed mixed infections of SNB, TS and STB. In Germany, TS was prevalent, with STB also common. Danish samples commonly possessed all three pathogens, with STB prevalent, followed by TS and SNB. The UK had a major prevalence of STB with minimal occurrence of TS and SNB. Across all samples, qPCR identified Zt, Pn and Ptr in 90%, 54% and 57% of samples, respectively. For each pathogen, average disease levels via visual assessment showed modest positive correlation with fungal DNA concentrations (R2 = 0.13–0.32). Overall, our study highlights that the occurrence of mixed infection is common and widespread, with important implications for wheat disease management and breeding strategies.

A modified eight-founder multiparent advanced generation intercross population (MAGIC) in winter wheat was found to be equivalent to a MAGIC population with a labor-intensive mating design. Genetic analysis of resistance to powdery mildew, septoria tritici blotch, and tan spot detected six, seven, and nine quantitative trait loci (QTL), respectively. Most QTL were trait-specific. Genomic regions involved in resistance to all three diseases were identified on chromosomes 1AS and 7AL. Multiple candidate genes were identified for resistance QTL., Es wurde gezeigt, dass eine auf acht Eltern basierende multiparentale Winterweizen-Population (MAGIC) mit modifiziertem Kreuzungsschema vergleichbar zu einer MAGIC Population mit einem arbeitsintensiven Kreuzungsdesign ist. Genetische Resistenzanalysen gegenüber Mehltau, STB- und DTR-Blattdürre detektierten jeweils sechs, sieben und neuen „Quantitative Trait Loci“ (QTL). Die meisten QTL waren merkmalsspezifisch. Auf den Chromosomen 1AS und 7AL wurden Genomregionen gefunden, die mit allen drei Resistenzen assoziiert waren. Mehrere Kandidatengene wurden für die Resistenz-QTL identifiziert.

A modified eight-founder multiparent advanced generation intercross population (MAGIC) in winter wheat was found to be equivalent to a MAGIC population with a labor-intensive mating design. Genetic analysis of resistance to powdery mildew, septoria tritici blotch, and tan spot detected six, seven, and nine quantitative trait loci (QTL), respectively. Most QTL were trait-specific. Genomic regions involved in resistance to all three diseases were identified on chromosomes 1AS and 7AL. Multiple candidate genes were identified for resistance QTL., Es wurde gezeigt, dass eine auf acht Eltern basierende multiparentale Winterweizen-Population (MAGIC) mit modifiziertem Kreuzungsschema vergleichbar zu einer MAGIC Population mit einem arbeitsintensiven Kreuzungsdesign ist. Genetische Resistenzanalysen gegenüber Mehltau, STB- und DTR-Blattdürre detektierten jeweils sechs, sieben und neuen „Quantitative Trait Loci“ (QTL). Die meisten QTL waren merkmalsspezifisch. Auf den Chromosomen 1AS und 7AL wurden Genomregionen gefunden, die mit allen drei Resistenzen assoziiert waren. Mehrere Kandidatengene wurden für die Resistenz-QTL identifiziert.

© The Author(s). Septoria nodorum blotch (SNB) is a disease of wheat (Triticum aestivum and T. durum) caused by the necrotrophic fungal pathogen Parastagonospora nodorum. SNB resistance is a typical quantitative trait, controlled by multiple quantitative trait loci (QTL) of minor effect. To achieve increased plant resistance, selection for resistance alleles and/or selection against susceptibility alleles must be undertaken. Here, we performed genetic analysis of SNB resistance using an eight-founder German Multiparent Advanced Generation Inter-Cross (MAGIC) population, termed BMWpop. Field trials and greenhouse testing were conducted over three seasons in Norway, with genetic analysis identifying ten SNB resistance QTL. Of these, two QTL were identified over two seasons: QSnb.nmbu-2A.1 on chromosome 2A and QSnb.nmbu-5A.1 on chromosome 5A. The chromosome 2A BMWpop QTL co-located with a robust SNB resistance QTL recently identified in an independent eight-founder MAGIC population constructed using varieties released in the United Kingdom (UK). The validation of this SNB resistance QTL in two independent multi-founder mapping populations, regardless of the differences in genetic background and agricultural environment, highlights the value of this locus in SNB resistance breeding. The second robust QTL identified in the BMWpop, QSnb.nmbu-5A.1, was not identified in the UK MAGIC population. Combining resistance alleles at both loci resulted in additive effects on SNB resistance. Therefore, using marker assisted selection to combine resistance alleles is a promising strategy for improving SNB resistance in wheat breeding. Indeed, the multi-locus haplotypes determined in this study provide markers for efficient tracking of these beneficial alleles in future wheat genetics and breeding activities.