Host-selective toxins, or necrotrophic effectors, are important determinants of disease in both wheat-Stagonospora nodorum and wheat- Pyrenophora tritici-repentis pathosystems. This study describes the identification, validation, and genomic analysis of compatible host gene-effector interactions in these systems. In the wheat-S. nodorum system, the Snn4-SnTox4 interaction was identified and validated using the hexaploid wheat ( Tri ti cum aestivum L.) recombinant inbred populations 'Arina' x 'Forno' ( AF) and Salamouni x 'Katepwa' (SK), respectively. The single dominant gene, Snn4, which mapped to the short arm of chromosome 1 A in both populations, governs sensitivity to the proteinaceous effector, SnTox4, which is estimated to be 10-30 kDa in size. The compatible Snn4-SnTox4 interaction played a significant role in disease development in both the AF and SK populations accounting for 41 % and 23.5% of the phenotypic variation, respectively. Effects of the additional minor QTL were largely additive in both genetic backgrounds. Molecular mapping in the SK population using microsatellites and markers developed using bin-mapped expressed sequence tags (ESTs), and from ESTs identified based on colinear studies with rice (Oryza sativa L.) and Brachypodium, delineated Tsc2 to a 3.3 cM interval and confirmed its location on 2BS of hexaploid wheat. The compatible T.~c2-Ptr ToxB interaction accounted for 54% of the disease variation in the SK population. The marker XBE44454 l, which co-segregated with Tsc2 is diagnostic of the gene and will be useful in marker-assisted selection (MAS).