Identification of septoria nodorum blotch sensitivity genes in hard winter wheat

The necrotrophic fungus Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) of wheat. P. nodorum effectors recognition by wheat sensitivity genes leads to susceptibility. Limited information exists on SNB sensitivity genes in contemporary U.S. hard winter wheat (HWW). The objective of this study was to determine the prevalence of SNB sensitivity genes in 619 HWW breeding lines and cultivars. This HWW panel was evaluated against five P. nodorum isolates and five necrotrophic effectors (NEs) SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, and genotyped using genotyping-by-sequencing (GBS) and diagnostic KompetItive-allele specific PCR (KASP) markers for the sensitivity genes Tsn1, Snn1, and Snn3. Genome-wide association studies (GWAS) were conducted using phenotypic data, 34357 GBS-single nucleotide polymorphism (SNP) markers, and KASP markers linked to Tsn1, Snn1, and Snn3. Evaluations against P. nodorum isolates showed that 40-67% of the genotypes were susceptible. Toxin infiltration assays showed that 54%, 2%, 37%, 13%, and 15% of the genotypes were sensitive to SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, respectively. The diagnostic KASP markers for Tsn1, Snn1, and Snn3 showed accuracy of 98%, 75%, and 92% in predicting sensitivity/insensitivity to the corresponding effectors SnToxA, SnTox1, and SnTox3, respectively. The GWAS confirmed the presence of the known sensitivity genes Tsn1, Snn1, Snn2, Snn3, and Snn5. In addition, GWAS identified other unknown loci to be associated with responses to P. nodorum isolates and NEs. Of which, Qsnb.osu-2AS on chromosome 2AS was found to be associated with responses to all five isolates. As Tsn1 and Snn3 are present in high frequencies in contemporary HWW, their elimination should be prioritized using high-throughput KASP markers. We also developed the marker KASP_S4B_643615365 for the locus linked to Snn5, which could be used to eliminate this gene with an accuracy of 89%. Marker-assisted selection for SNB resistance should also target the novel locus, Qsnb.osu-2AS.