The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat. SNB results in a reduction of photosynthetic area on the host that can lead to significant yield losses. P. nodorum facilitate infection by secreting a number of proteinaceous necrotrophic effectors (NEs) that cause necrosis on hosts carrying matching dominant susceptibility genes. Three NE-host gene interactions have been well-defined; ToxA encodes a 13.2 kDa mature protein that causes necrosis on wheat varieties that carry Tsn1 located on chromosome 5BL. Tox1 encodes a 10.3 kDa mature cysteinerich protein with a chitin-like binding motif at the C-terminus. Sensitivity to SnTox1 is conferred by Snn1 located on chromosome 1BS. Tox3 encodes a 17.5 kDa cysteine-rich mature protein. Sensitivity to Tox3 is conferred by Snn3-B1 and Snn3-D1 located on wheat chromosomes 5BS and 5DS, respectively. The role of these interactions in SNB are complex. Their expression in SNB are mediated by epistasis where effector interactions masked the action of others. In order to uncover novel quantitative trait loci (QTL) associated with SNB and sensitivity to undiscovered effectors, 1,500 wheat lines sourced from CIMMYT, ICARDA and the Vavilov collection were subjected to effector bioassays. A total of 142 wheat lines insensitive to ToxA, Tox1 and Tox3 were identified and genotyped using the Affymetrix 35K Axiom SNP array. Of the 35K gene-based SNPs, 16,115 were found to be suitable for genomic association analysis using GAPIT. The wheat panel was infected with the P. nodorum SN15 reference strain and FG114, a highly pathogenic strain. Both strains express ToxA, Tox1 and Tox3. GWAS revealed two very different QTL profiles between the two P. nodorum isolates. Novel QTL on 2B and 4B were detected with phenotype from SN15 infection whereas novel QTL on 5A, 2B, 1D and 6A were observed from the FG114 disease dataset. QTL associated with Tsn1, Snn1 and Snn3 were not detected from infection phenotypes of both strains. Newly identified QTL are currently being investigated and used for corresponding effector identifications. This reductionist approach can also be applied on other necrotrophic fungal pathogens of wheat such as Pyrenophora tritici repentis and Bipolaris sorokiniana where the ToxA-Tsn1 interaction is active.