Genome-wide association study uncovers the genetic basis of stem rust resistance in the southern US oat (Avena sativa L.) germplasm at different growth stages

KEY MESSAGE: In the 440-line Southern Oat Association Panel (SOAP), GWAS detected 17 QTL, with ten in the adult stage, five in the seedling stage, and two expressed at both stages. The chromosome 1A region that aligns with Pg13 was the dominant signal. Effects combined additively, and stacking five stable adult plant loci nearly halved the disease severity Six QTL correspond to known regions, and eleven are newly reported. Stem rust (SR), caused by Puccinia graminis f. sp. avenae, threatens global oat production and remains a priority for resistance breeding in the southeastern USA. We conducted a multi-environment genome-wide association study of 440 Southern Oat Association Panel (SOAP) lines, pairing multi-year, multi-location adult plant phenotyping with seedling evaluations. Adult plant resistance response was measured as severity (SV) and infection response (IR). Seedling resistance was evaluated as infection type (IT) using isolates of four pathogen races (DBD, SGD, TGN, and TJS). In total, we detected 17 quantitative trait loci (QTL), including 10 expressed at the adult plant stage, five at the seedling stage, and two shared across stages. The strongest signal was a four-peak cluster on chromosome 1A (370.8-464.4 Mb) within the Pg13 interval. Conditional analysis showed that these peaks were not explained by a single effect, indicating multiple independent determinants within the interval. Two loci affected both seedling IT to TGN and adult field reactions, consistent with at least one race-specific all-stage component, whereas two others were restricted to adult plants. Additional, smaller-effect loci on chromosomes 1D and 6D contributed additively to adult plant field resistance. In contrast, race-specific seedling resistance loci were detected on chromosomes 2A, 2D, and 3C. Stacking stable adult-stage QTL produced cumulative effects on SV and IR, with reductions only when multiple favorable alleles were combined. Candidate intervals were enriched for nucleotide-binding site leucine-rich repeats and receptor-like kinases. Once, validated these SNPs can support marker-assisted selection for SR resistance in southeastern oat breeding programs.