Genetic dissection of seedling resistance to septoria nodorum blotch resistance in a nested association mapping panel derived from synthetic hexaploid wheat lines and bread wheat.

Septoria nodorum blotch (SNB), caused by the necrotrophic fungal pathogen Parastagonospora nodorum, is a major foliar disease of wheat (Triticum aestivum) that significantly reduces grain yield and quality. In this study, we evaluated a modified nested association mapping (NAM) population for SNB resistance. This population consisted of 276 BC1F8 progenies derived from crosses between four synthetic hexaploid wheat (SHW) and ten hard red spring wheat (HRSW) varieties/lines. We screened the population using two P. nodorum isolates (Sn4 and Sn2000) and three necrotrophic effectors (SnToxA, SnTox1, and SnTox3). Genome-wide association studies using the 90K SNP markers identified 32 significant marker-trait associations (MTAs) across nine chromosomes, including nine markers associated with isolate responses and 23 with effector sensitivity. While several markers co-localized with known genes such as Tsn1 (5BL), Snn2 (2DS), Snn3 (5BS), and Snn7 (2DL), we also identified novel loci that expand our understanding of SNB resistance. Of the nine isolate-associated MTAs, the resistance alleles were contributed by different parents: four came from SHW, one from HRSW, and four from both parental types. Nine progeny lines exhibited resistance to both isolates and insensitivity to all tested effectors, indicating broad-spectrum and effective resistance. The SHW lines SW91 and SW93, as well as HRSW cultivars 'Bolles' and 'Linkert', and their progenies consistently showed increased resistance compared to other backgrounds. These lines, carrying novel SNB resistance loci derived from cultivated emmer and Aegilops tauschii, provide valuable germplasm for improving SNB resistance in wheat breeding programs.