Evidence map›Paper›PMID 41762226›Full record

ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2026

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.

Janam Prabhat Acharya, Md Ali Babar, Naeem Khan, Kathy Esvelt Klos, Flavia Furlan, Stephen Harrison, Noah DeWitt, Amir Ibrahim, Shuyu Liu, Ellen Melson and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Janam Prabhat AcharyaDepartment of Agronomy, University of Florida, 3105 McCarty Hall B, Gainesville, FL, 32608, USA.
Md Ali BabarDepartment of Agronomy, University of Florida, 3105 McCarty Hall B, Gainesville, FL, 32608, USA. mababar@ufl.edu.ORCID http://orcid.org/0000-0001-9951-6856
Naeem KhanDepartment of Agronomy, University of Florida, 3105 McCarty Hall B, Gainesville, FL, 32608, USA.
Kathy Esvelt KlosSmall Grains and Potato Germplasm Research Unit, USDA-ARS, Pacific West Area, Aberdeen, ID, USA. kathy.klos@usda.gov.
Flavia FurlanSchool of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Stephen HarrisonSchool of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Noah DeWittSchool of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Amir IbrahimAgriLife Research, Texas A&M University, College Station, TX, 77843, USA.
Shuyu LiuAgriLife Research, Texas A&M University, College Station, TX, 77843, USA.
Ellen MelsonAgriLife Research, Texas A&M University, College Station, TX, 77843, USA.
Daniel HathcoatAgriLife Research, Texas A&M University, College Station, TX, 77843, USA.
Raja Sekhar NandetyCereal Crops Improvement Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA.
Jason FiedlerCereal Crops Improvement Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA.
Yue JinCereal Disease Lab, USDA-ARS, St Paul, MN, 55108, USA.
Pablo Olivera FirpoCereal Disease Lab, USDA-ARS, St Paul, MN, 55108, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

key messageIn 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.

Indexed as

AvenaDisease ResistancePlant DiseasesBasidiomycotaChromosome MappingGenome-Wide Association StudyGenotypePhenotypePolymorphism, Single NucleotidePucciniaQuantitative Trait LociSeedlings

Identifiers

PMID41762226
PMCPMC12950007

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.