Identification of septoria nodorum blotch susceptibility genes in hard winter wheat

Key message Characterized and unknown septoria nodorum blotch susceptibility/resistance genes were identified in contemporary U.S. hard winter wheat. The necrotrophic fungus Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) of wheat. To determine the prevalence of SNB sensitivity genes in a contemporary U.S. hard winter wheat (HWW), we evaluated a panel of 619 breeding lines and cultivars against five P. nodorum isolates and five necrotrophic effectors (NEs), SnToxA, SnTox1, SnTox3, SnTox267 and SnTox5, and genotyped the panel using genotyping-by-sequencing (GBS) markers and diagnostic Kompetetive-allele specific PCR (KASP) markers for the sensitivity genes Tsn1-B1, Snn1-B1, and Snn3-B1/B2. GBS analysis identified 34,357 GBS-single nucleotide polymorphism (SNP) markers. Evaluations against P. nodorum isolates showed that 40-67% of the genotypes were susceptible in the panel. Toxin infiltration assays showed that 54%, 2%, 37%, 13%, and 15% of the genotypes were sensitive to SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, respectively. Diagnostic KASP markers for Tsn1-B1, Snn1-B1, and Snn3-B1/B2 showed prediction accuracies of 98%, 75%, and 92% for the corresponding effectors SnToxA, SnTox1, and SnTox3, respectively. Genome-wide association studies (GWAS) not only confirmed the presence of the previously characterized sensitivity genes Tsn1-B1, Snn1-B1, Snn2, Snn3-B1/B2, and Snn5-B1, but also identified new loci to be associated with responses to P. nodorum isolates and NEs. Of which, Qsnb.osu-2AS on chromosome 2AS was associated with responses to all five isolates. We developed KASP markers KASP_S4B_643615365, KASP_ S2D_16184991, and KASP_S2A_9833162 linked to Snn5-B1, Snn2, and Qsnb.osu-2AS, respectively. These findings should guide breeding for SNB resistance in hard winter wheat.