Genome-wide association mapping of tan spot resistance in a modified NAM population derived from synthetic hexaploid wheat.

A total of 37 SNPs associated with resistance to five races of Pyrenophora tritici-repentis and two necrotrophic effectors were identified in a NAM population derived from synthetic and spring wheat. Tan spot, caused by Pyrenophora tritici-repentis, is a major foliar disease of wheat worldwide, and expanding the genetic basis of resistance remains a breeding priority. Synthetic hexaploid wheat (SHW) represents a valuable reservoir of novel alleles, yet its contribution to tan spot resistance has not been fully characterized. Here, a modified Nested Association Mapping population including 276 BC1F8 lines from crosses between four SHW parents and diverse hard red spring wheat (HRSW) cultivars was evaluated for reactions to five P. tritici-repentis races and two associated necrotrophic effectors (NEs) (Ptr ToxA and Ptr ToxB). The population exhibited broad phenotypic variation, with SHW parents and 66 BC1F8 lines showing resistance to all races. Genome-wide association analysis identified 21 marker-trait associations (MTAs) associated with tan spot resistance, of which, 6 resistance alleles were derived from SHW and 4 from HRSW parents, and 11 from both. Major-effect resistance loci were localized on chromosomes 5A, 2B, 5B, and 7D. Additionally, 14 MTAs were associated with Ptr ToxA sensitivity and 2 with Ptr ToxB sensitivity. Resistance alleles contributed by both parents showed a significant additive effect in reducing disease severity. Several loci colocalized with previously reported QTLs or genes, including Tsn1-B1 and Tsc2, while others represent potentially novel genomic regions. Notably, multiple lines were resistant to all races despite sensitivity to one or both NEs, indicating the presence of quantitative resistance other than those effector-sensitivity loci. These findings provide valuable genetic resources for facilitating marker‑assisted and genomic selection targeting tan spot resistance in wheat breeding.