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

Synthetic hexaploid wheat harbours STB resistance-associated loci with multi-isolate and isolate-specific effects, with partly independent genetic control of pycnidia suppression and necrosis. Septoria tritici blotch (STB), caused by Zymoseptoria tritici, is a major constraint on wheat production. Erosion of host resistance and declining fungicide efficacy highlight the need to exploit new resistance sources, including synthetic hexaploid wheat (SHW). 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 UK variety Robigus to dissect the genetic basis of STB resistance under controlled conditions. Seedlings were challenged with five UK 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, consistent with partial genetic decoupling of pathogen reproduction and host tissue damage. GWAS identified a major multi-isolate association on chromosome 3D (qSTB-3D.1), contributed by SHW.035 and detected in response to four of the five isolates, defining a 23.7 Mb candidate resistance-associated interval. This interval encompasses the Stb16q region but also contains other plausible resistance candidates, including a WAK close to the strongest association at 609.21 Mb; the causal basis therefore remains unresolved. Additional isolate-specific resistance-associated intervals were detected on chromosomes 1B, 2D, 3A, and 6D. In a BC₂F₂ population derived from a resistant SHW.035-derived NAM line, pycnidia suppression segregated in a 3:1 ratio consistent with a single dominant factor, whereas necrosis showed more complex inheritance. These findings show that Niab SHWs are a valuable source of STB resistance and highlight the potential to select for reduced pathogen reproduction independently of visible leaf damage.