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

Authors: ARCHRYA, JANAM - UNIVERSITY OF FLORIDA; BARAR, MD - UNIVERSITY OF FLORIDA; KHAN, NAEEM - UNIVERSITY OF FLORIDA; ESVELT KLOS, KATHY; FURLAN, FLAVIA - LOUISIANA STATE UNIVERSITY; HARRISON, STEPHEN - LOUISIANA STATE UNIVERSITY; DEWITT, NOAH - LOUISIANA STATE UNIVERSITY; IBRAHIM, AMIR - TEXAS A&M UNIVERSITY; LIU, SHUYU - TEXAS A&M UNIVERSITY; MELSON, ELLEN - TEXAS A&M UNIVERSITY; HATHCOAT, DANIEL - TEXAS A&M UNIVERSITY; NANDETY, RAJA SEKHAR; FIEDLER, JASON; JIN, YUE; OLIVERA FIRPO, PABLO

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2026
Publication Date: 2/28/2026
Citation: Archrya, J.P., Barar, M.A., Khan, N., Esvelt Klos, K.L., Furlan, F., Harrison, S., Dewitt, N., Ibrahim, A., Liu, S., Melson, E., Hathcoat, D., Nandety, R., Fiedler, J.D., Jin, Y., Olivera Firpo, P.D. 2026. 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. Theoretical and Applied Genetics. Volume 139, article number 80, (2026). https://doi.org/10.1007/s00122-026-05180-2.
DOI: https://doi.org/10.1007/s00122-026-05180-2

Interpretive Summary: As a step towards delivering stem rust resistance solutions to oat growers, a set of 440 lines called the Southern Oat Association Panel (SOAP) was evaluated for evidence of quantitative trail loci (QTL) representing genes that influence stem rust response. This process detected 17 QTLs, with ten active in the adult stage, five in the seedling stage, and two expressed at both stages. The chromosome 1A region that aligns with the known stem rust resistance gene Pg13 was the dominant signal. Effects combined additively, such that lines carrying resistance alleles at more QTL tended to display greater field resistance than those carrying few resistance alleles. Stacking five stable adult plant resistance loci within a line nearly halved the disease level detected, compared with lines that did not carry any resistance alleles. Six QTLs correspond to known regions, and eleven are newly reported.

Technical Abstract: Stem rust (SR), caused by Puccinia graminis f. sp. avenae, threatens oat production worldwide and remains a priority for resistance breeding in the southeastern United States. We conducted a multi-environment genome-wide association study with 440 lines from the Southern Oat Association Panel (SOAP), pairing field phenotyping of adult plants across locations and years with a seedling study. Adult response was measured as severity (SV) and infection response (IR), while seedling reaction was scored as infection type (IT) with four isolates (DBD, SGD, TGN, and TJS). We detected 17 quantitative trait loci, with 10 expressed at the adult plant stage, 5 at the seedling stage, and 2 shared across stages. The most prominent 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 of these loci affected both seedling infection type to TGN and adult field reactions, consistent with at least one race-specific all-stage component, while the other two were restricted to the adult stage. Smaller-effect loci on 1D and 6D contributed additively to field resistance, and additional race-specific seedling loci were detected on 2A, 2D, and 3C. Stacking five stable adult-stage QTL nearly halved disease severity and infection response relative to the null group, underscoring their cumulative value for durable resistance. Candidate intervals were enriched for nucleotide-binding site leucine-rich repeats and receptor-like kinases, and the associated SNPs, once validated, may be deployed in marker-assisted selection to improve SR resistance in southeastern oat breeding programs.