Progress 06/01/24 to 05/31/25
Outputs
Target Audience:Researchers: Graduate students, collaborators, and the PIs shared research outcomes from this project at conferences/workshops, including North American Cereal Rust Workshop, Wheat Initiative Webinar: The Control of Wheat Pathogens Expert Working Group, American Phytopathological Society - Plant Health 2024. Three graduate students also presented their research at the 21st Annual Symposium on Biological Sciences and Food and Agricultural Products Center (FAPC) Research Symposium, organized by Oklahoma State University. Two of the investigators (Aoun and Alderman) presented results from this project in Partners in Progress Reports published by Oklahoma State University. Students: Three graduate students (1 MS and 2 PhD students), working on this project, were trained on leaf rust, stripe rust, septoria nodorum blotch evaluations in the greenhouse/growth chamber and in the field, GWAS, high-throughput phenotyping, and data analysis. An MS student has successfully passed the FAA Part 107 Certification Exam and has been issued a Part 107 Remote Pilot certificate. Wheat breeders: We communicated our project results with the OSU hard winter wheat breeder (Carver, collaborator) to inform him about identified rust resistance sources and septoria nodorum blotch sensitivity genes in the OSU breeding lines and cultivars. This information is intended to help the breeder with selection. Wheat growers and extension professionals: The PI (Aoun) talked about this project to 463 growers, county educators, and students at eight wheat field days across Oklahoma in 2025. The PI also provided five E-Pest alerts, two TV/Radio interviews, and two extension journal articles to growers to inform them about wheat disease situations in Oklahoma, including leaf rust, stripe rust, septoria nodorum blotch, and wheat streak mosaic. The PI presented an extension talk to ~ 45 growers and extension professionals at the Wheat Growers Association Annual Meeting in Oklahoma. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training activities:Three graduate students have been trained on wheat disease ratings, GWAS, data analysis, KASP marker development, and high-throughput phenotyping. Professional development: Graduate students and the PIs presented this project results at conferences and workshops, including North American Cereal Rust Workers Workshop, American Phytopathological Society - Plant Health 2024, Wheat Initiative Webinar: The Control of Wheat Pathogens Expert Working Group. Three graduate students also presented their research at the 21st Annual Symposium on Biological Sciences and Food and Agricultural Products Center (FAPC) Research Symposium, organized by Oklahoma State University. How have the results been disseminated to communities of interest?The results of this project were disseminated in seven oral and poster presentations and in two Partners in Progress Reports. 1. Ara A.M., Carver, B.F., and Aoun, M. 2025. Genome-wide association mapping identified Septoria nodorum blotch susceptibility genes in hard winter wheat. Food and Agricultural Products Center Research Symposium. Oklahoma State University, Stillwater, OK. March 27, 2025 (Poster). 2. Ara, A. M, Carver, B., Friesen, T.L. Holmes, D., and Aoun, M. 2024. Unraveling the genetic basis of Septoria nodorum blotch sensitivity in hard winter wheat. American Phytopathological Society, Plant Health. 2024. Memphis, TN, July 27-31 (Poster). 3. Aoun, M. 2025. Stripe rust resistance in hard winter wheat. North American Cereal Rust Workshop 2025, Fargo, ND. March 12-13, 2025 (Oral presentation). 4. Aoun, M. 2025. Stripe rust resistance in hard winter wheat. March 6, 2025. Wheat Initiative Webinar. The Control of Wheat Pathogens Expert Working Group (oral presentation). https://www.wheatinitiative.org/ewg-pathogens 5. Ara A.M., and Aoun, M. 2025. Genome-wide association studies identified genomic regions associated with septoria nodorum blotch susceptibility in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 28, 2025 (Oral presentation) 6. Adepoju, P. and Aoun, M. 2025. Identification of leaf rust resistance loci in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 27, 2025 (Poster, 3rd prize in graduate student poster competition). 7. Mobin M. A. and Aoun, M. 2025. Genome-wide association studies to identify stripe rust resistance loci in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 27, 2025 (Poster). 8. Alderman, P. D. 2025. Evaluating Image Processing Methods for High-Throughput Phenotyping 2024. 2024 Partners in Progress Wheat Research. Oklahoma State University. https://agresearch.okstate.edu/research/wheat-report/2024/evaluating-image-processing-methods-for-high-throughput-phenotyping-2024.html 9. Aoun, M. 2025. Wheat Pathology Report for 2024. Oklahoma State University. https://agresearch.okstate.edu/research/wheat-report/2024/wheat-pathology-2024.html Outreach activities The PI (Aoun) talked about this project to 463 growers, county educators, and students at eight wheat field days across Oklahoma in 2025. The PI also provided five E-Pest alerts, two TV/Radio interviews, and two extension journal articles to growers to inform them about wheat disease situations in Oklahoma, including leaf rust, stripe rust, septoria nodorum blotch, and wheat streak. The PI presented an extension talk to 45 growers and Extension professionals at the Wheat Growers Association Annual Meeting in Oklahoma. 1. Aoun, M. 2025. Pest alert -Wheat disease update: https://extension.okstate.edu/e-pest-alerts/2025/wheat-disease-update-april-1-2025.html 2. Aoun, M. 2025. Pest alert - Wheat disease update: https://extension.okstate.edu/e-pest-alerts/2025/wheat-disease-update-april-28-2025.html 3. Aoun, M. 2025. Pest alert - Wheat disease update: https://extension.okstate.edu/e-pest-alerts/2025/wheat-disease-update-may-7-2025.html 4. Aoun, M. 2025. Pest alert - Wheat disease update: https://extension.okstate.edu/e-pest-alerts/2025/wheat-disease-update-may-22-2025.html 5. Aoun, M. 2025. Pest alert - Wheat disease update. https://extension.okstate.edu/e-pest-alerts/2025/wheat-disease-update-may-8.html 6. Aoun, M. 2025. SUNUP TV video. https://www.youtube.com/watch?v=TtttwZXyrDw 7. Aoun, M. 2025. Low Disease Pressure Seen in Oklahoma Wheat Despite Recent Rains, Says OSU Pathologist. Farm report Radio. https://www.oklahomafarmreport.com/okfr/2025/04/28/low-disease-pressure-seen-in-oklahoma-wheat-despite-recent-rains-says-osu-pathologist/ 8. Aoun, M. and Carver, B.F. 2025. Lahoma Field Day brings wheat growers together for crop update. High Plains Journal: Fusarium head Blight. https://hpj.com/2025/05/09/wet-humid-conditions-make-fusarium-head-blight-a-concern-for-wheat/ 9. Aoun, M. 2025. Wet, humid conditions make fusarium head blight a concern for wheat High Plains Journal: https://hpj.com/2025/05/09/wet-humid-conditions-make-fusarium-head-blight-a-concern-for-wheat/ 10. Aoun, M. 2025. Bust the Rust. Oklahoma Wheat Growers Association Annual Meeting. Oklahoma City, OK. Feb 12, 2025 (oral presentation, 45 attendees). What do you plan to do during the next reporting period to accomplish the goals?Objective 1. We plan to phenotype the OSU GWAS panel of 619 breeding lines and cultivars against three additional Puccinia tricina races, two P. nodorum isolates, and three P. nodorum effectors (Tox267 and Tox5). Furthermore, septoria nodorum blotch (SNB) phenotyping in the field (leaf blotch and glume blotch) is ongoing in 2025. An additional SNB testing in the field will be performed in 2026. GWAS for leaf rust, stripe rust, and SNB should be completed in the next reporting period. KASP markers will be developed for large-effect SNP markers associated with leaf rust and stripe rust resistance and SNB resistance/susceptibility. QTL analysis in Gallagher/Iba and Green Hammer/Lonerider will be completed using 2024 and 2025 field data and available genotypic data to identify stripe rust resistance genes in the cultivars Gallagher and Green Hammer. KASP markers linked to the identified resistance genes will be developed for potential use in marker-assisted selection. Objective 2. We plan to address the aforementioned prediction issues in the coming year in several ways. First, to address the imbalance in data across BYD ratings, we plan to test the use of alternative models and model fitting approaches. In particular, we plan to explore the use of machine learning (ML), Bayesian hierarchical and quasi-Bayesian modeling to implement models with one or more levels that target the expected proportion of plots across BYD rating categories and additional levels that model the rating for specific plots. We will also explore alternative objective functional forms (other than sum of squared error) that will better address the imbalance across categories. Second, to address the mismatch in the scale of symptoms (sub-plot) and predictors (currently whole-plot), we will generate new predictors to capture features at the sub-plot scale. Specifically, we plan to calculate additional field-plot-level statistics (e.g. standard deviation, skewness, kurtosis) and extract additional features using image processing methods (e.g. Gabor filters). Objective 3. Additional virus-infected samples will be collected for the upcoming 2 years. A MS student will be hired in fall 2025 to complete this project as described in the project initiation methods. Objective 4. We will continue to provide training and presentations at extension meetings in Oklahoma and nationally. We will educate stakeholders and county educators on wheat disease diagnosis and management during field days and by providing real-time disease updates during the season. OSU wheat variety trials and disease nurseries will continue to serve as demonstration plots for variety/experimental line reactions to different diseases. We will continue to produce new extension videos, newsletters, current reports, and factsheets.
Impacts
What was accomplished under these goals?
Objective 1. Characterize wheat genetic resources for resistance/susceptibility to leaf rust, stripe rust, and Septoria nodorum blotch. We created a germplasm collection of 619 breeding lines and cultivars from the wheat breeding program at Oklahoma State University (OSU). This collection was evaluated at the seedling stage in the greenhouse against United States leaf rust and stripe rust pathogen races and the adult plant stage in leaf rust and stripe rust nurseries in Oklahoma, Kansas, and Washington in 2024. We observed higher frequencies of lines with leaf rust resistance at the adult plant stage than at the seedling stage. This suggests the presence of adult plant resistance (APR) in OSU breeding lines. Stripe rust resistance was mainly due to the presence of APR genes. In the fall of 2024, this germplasm was planted in rust nurseries in Oklahoma (Stillwater and Lahoma) and Washington (Pullman and Central Ferry) for leaf rust/stripe rust evaluations in the spring of 2025. We genotyped this germplasm using genotyping by sequencing (GBS), and 39,286 molecular markers were retained for genome-wide association mapping (GWAS) to identify genomic regions associated with leaf rust and stripe rust resistance in OSU hard red winter wheat. GWAS, using molecular markers and stripe rust data collected in 2024, identified 113 genomic regions associated with stripe rust response. Among these loci, genomic regions on chromosome arms 3BS and 4BL showed the most significant associations with stripe rust response in multiple field environments. Our results identified known and possibly novel effective Yr genes in the OSU hard red winter wheat. The GWAS identified 26 genomic regions associated with leaf rust resistance, with two loci on chromosomes 1D and 2B associated with seedling leaf rust response against races MNPSD and MPPSD. A locus on chromosome 6B was associated with leaf rust resistance against race TNBJS. Genomic regions on chromosome arms 5BL and 7AS were associated with leaf rust response at the adult plant stage in Stillwater in 2023 and 2024. The three bi-parental populations Gallagher/Iba, OK12D22004-016/Baker's Ann, and Green Hammer/Lonerider, used to identify APR stripe rust resistance genes in the OSU HWW cultivars 'Gallagher', 'Baker's Ann', and 'Green Hammer', were genotyped using Genotyping by Sequencing and phenotyped in stripe rust nurseries in Oklahoma, Washington, and Kansas in 2024 and 2025. Genetic mapping was completed for the population OK12D22004-016/Baker's Ann, and four Quantitative trait loci (QTLs) were detected, two of which had major effects, with one on chromosome 2DL from Baker's Ann, and another one linked to Yr17 on 2AS from OK12D22004-016. The SNPs flanking the major QTL from Baker's Ann were converted into kompetitive allele-specific PCR (KASP) markers to facilitate marker-assisted selection. Septoria nodorum blotch (SNB) is caused by Parastagonospora nodorum. This fungusis a necrotroph, which interacts with wheat in an inverse gene-for-gene manner. The recognition of P. nodorum necrotrophic effectors (NEs) by wheat sensitivity genes leads to host susceptibility. To date, five sensitivity genes (Tsn1, Snn1, Snn3-B1, Snn3-D1 and Snn5) and five effector genes (SnToxA, SnTox1, SnTox3, SnTox5 and SnTox267) have been cloned. Our objectives were to identify the reactions of OSU breeding lines and cultivars against SNB and to identify genomic regions associated with SNB response using GWAS. The OSU panel of 619 wheat experimental lines and cultivars was evaluated at the seedling stage for their reactions against two P. nodorum isolates and three P. nodorum effectors (ToxA, Tox1, and Tox3). In addition, this germplasm was screened using diagnostic markers for the susceptibility genes Tsn1 and Snn1. The results showed that 55% and 73% of the OSU panel do not carry Tsn1 and Snn1. OSU cultivars like Big Country, Uncharted and Green Hammer do not carry the sensitivity gene Tsn1, whereas multiple OSU cultivars do not carry Snn1. Molecular markers generated from genotyping by sequencing and the phenotypic data were used for GWAS to identify genomic regions associated with response to SNB. The GWAS confirmed the presence of three sensitivity genes Tsn1, Snn1 and Snn3 in OSU wheat. Tsn1 has the largest effect in explaining sensitivity to the two P. nodorum isolates. Objective 2. Develop high-throughput phenotyping system for large-scale selection of barley yellow dwarf resistance in wheat breeding programs. Regular flights of the Stillwater locations for the Dual-Purpose Observation Nursery by the OSU Wheat Improvement Team commenced after planting using a DJI Phantom 4 Multispectral Unmanned Aircraft System (UAS). Flight frequency was approximately once per week during the fall and spring and twice per month during the winter. For each flight, multiple raw multispectral images were collected, covering the whole field with approximately 80% overlap between images. Imagery data were combined with field-based barley yellow dwarf (BYD) severity rating (0-6 scale) for previous seasons (2022-2023 and 2023-2024), and current season imagery data will be combined once the field-based BYD data are available at the end of the season (expected July 2025). BYD severity rating was predicted based on plot-level averages of a variety of vegetation indices. Notably, predictions were best for BYD rating of 2 (63.5 to 75.9%), second best for rating 0-1 combined (37.2 to 49.0%) followed by ratings 5-6 combined (5.9 to 31.3%). Interestingly, the worst prediction was for rating 3 (4.2 to 18.9 percent). The low level of correct predictions for rating 3 seems to be due to observed BYD 3 ratings being misclassified as BYD 2 ratings. We hypothesize two likely causes contributing to these results. First, the distribution of ratings was not even across all categories. That is, there were far more observed level 2 BYD ratings than the other levels. This imbalance presents a challenge to the model fitting process. We attempted to address this imbalance by combining level 0 with 1 and level 5 with 6. However, a more robust approach appears to be necessary. The other likely cause is the use of field-plot-level averages as predictors. Disease ratings are based on symptoms that manifest at a sub-plot scale (e.g. within a plant or within a leaf). Thus, by averaging across the whole plot it is likely that the information about disease symptoms was distorted or lost in the averaging process, thereby resulting in poor prediction. Objective 3. Identify the occurrence and diversity of viruses infecting wheat in Oklahoma using E-probe Diagnostic Nucleic Acid Analysis (EDNA). In 2025, wheat streak mosaic (WSM) has been reported in several Oklahoma wheat fields in Blaine, Kay, Caddo, Garfield, Texas, Harper, Beaver, Alfalfa, Kingfisher, Washita, Woods, Kiowa, Custer, and Payne Counties. About 2/3 of the infected samples with WSMV were also infected with Triticum mosaic virus (TriMV) based on diagnosis performed at the OSU Plant Disease and Insect Diagnostic Lab. To date, we have collected 38 samples infected with diverse wheat viruses across wheat-growing regions in Oklahoma. Objective 4. Broder impacts: educate and train growers, county educators, and students on wheat disease diagnosis and effective management strategies The PI (Aoun) provided wheat disease updates and management to 463 growers, county educators, and students at eight wheat field days across Oklahoma in 2025. The PI also provided five E-Pest alerts, two TV/Radio interviews, and two extension journal articles to growers to inform them about wheat disease situations in Oklahoma, including leaf rust, stripe rust, septoria nodorum blotch, and wheat streak. The PI presented an extension talk about stripe rust to 45 growers and Extension professionals at the Wheat Growers Association Annual Meeting in Oklahoma in 2025.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
Ara, A. M, Carver, B., Friesen, T.L. Holmes, D., and Aoun, M. 2024. Unraveling the genetic basis of Septoria nodorum blotch sensitivity in hard winter wheat. American Phytopathological Society, Plant Health. 2024. Memphis, TN, July 2731 (Poster).
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Aoun, M. 2025. Stripe rust resistance in hard winter wheat. North American Cereal Rust Workshop 2025, Fargo, ND. March 12-13, 2025 (Oral presentation).
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Aoun, M. 2025. Stripe rust resistance in hard winter wheat. March 6, 2025. Wheat Initiative Webinar. The Control of Wheat Pathogens Expert Working Group.
https://www.wheatinitiative.org/ewg-pathogens
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Ara A.M., and Aoun, M. 2025. Genome-wide association studies identified genomic regions associated with septoria nodorum blotch susceptibility in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 28, 2025 (Oral presentation)
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Adepoju, P. and Aoun, M. 2025. Identification of leaf rust resistance loci in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 27, 2025 (Poster, 3rd prize in graduate student poster competition).
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Mobin M. A. and Aoun, M. 2025. Genome-wide association studies to identify stripe rust resistance loci in hard winter wheat. 21st Annual Symposium on Biological Sciences. Oklahoma State University. Feb 27, 2025 (Poster).
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Aoun, M. 2025. Bust the Rust. Oklahoma Wheat Growers Association Annual Meeting. Oklahoma City, OK. Feb 12, 2025.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2025
Citation:
Ara A.M., Carver, B.F., and Aoun, M. 2025. Genome-wide association mapping identified Septoria nodorum blotch susceptibility genes in hard winter wheat. Food and Agricultural Products Center Research Symposium. Oklahoma State University, Stillwater, OK. March 27, 2025 (Poster).
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