Multi-isolate GWAS identifies broad-spectrum and isolate-specific Septoria tritici blotch resistance loci in synthetic hexaploid wheat

Septoria tritici blotch (STB), caused by Zymoseptoria tritici , remains a major constraint on wheat production worldwide. Erosion of host resistance and declining fungicide efficacy highlight the need to exploit the new sources of resistance, including synthetic hexaploid wheat (SHW). Here, we used a three-family nested association mapping (NAM) population derived from Niab SHW donors (SHW.035, SHW.054, and SHW.075) crossed with the elite UK variety Robigus to dissect the genetic basis of STB resistance under controlled conditions. Seedlings were challenged with five Z. tritici isolates differing in virulence, and disease progress was quantified separately as necrosis (AUDPC_N) and pycnidia coverage (AUDPC_P). Many SHW-derived lines showed strong suppression of pycnidia despite visible necrosis, indicating partial genetic decoupling of pathogen reproduction and host tissue damage. Genome-wide association analysis identified a major broad-spectrum resistance locus on chromosome 3D ( qSTB-3D.1 ), contributed by SHW.035, that co-localised with the Stb16q region. Additional isolate-specific loci were detected on chromosomes 1B, 2D, 3A, and 6D. In an F ₂ population derived from a resistant SHW.035-derived NAM line, suppression of pycnidia segregated as a single dominant factor, whereas necrosis showed quantitative inheritance. These findings show that Niab SHWs are a valuable source of STB resistance and highlight the potential to breed for reduced pathogen reproduction independently of visible leaf damage.