Research Project: Surveillance, Pathogen Biology, and Host Resistance of Cereal Rusts

Location: Cereal Disease Lab

2025 Annual Report

Objectives
Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogen populations, and characterize foreign populations that threaten U.S. cereal production. • Sub-objective 1.A: Monitor, collect and characterize cereal rust pathogen populations in the U.S. for virulence that overcomes rust resistance genes in current cultivars. • Sub-objective 1.B: Characterize key exotic rust pathogen strains in advance of their introduction to the United States and contribute towards consortia for global pathogen surveillance through strategic partnerships and alliances. • Sub-objective 1.C: Development and/or improvement of molecular diagnostic tools for detection of cereal rust pathogen strains. Objective 2: Develop new genomic resources for cereal rust pathogens, identify links between pathogen phenotypes and genotypes, and improve understanding of the role of the sexual cycle in population dynamics. • Sub-objective 2.A: Develop genomic resources for population genetics and evolutionary studies of cereal rust pathogens. • Sub-objective 2.B: Identify linkages between phenotype and genotype of cereal rust fungi involved in pathogenicity and host resistance. • Sub-objective 2.C: Improve understanding of the roles of the sexual cycle in cereal rust fungal population dynamics. Objective 3: Improve host resistance in cereal crops to rust pathogens through investigations in sources and genetics of rust resistance, characterization of various germplasm, and incorporation into adapted germplasm. • Sub-objective 3.A: Evaluate wheat, oat and barley germplasm from U.S. breeding programs for rust resistance. • Sub-objective 3.B: Identify and characterize new sources of rust resistance in wheat, barley, and oat. • Sub-objective 3.C: Incorporate rust resistance into adapted germplasm.

Approach
Cereal rust fungi are dynamic leading to constant changes in the U.S. populations, which leads to the erosion of effective resistance in cereal crops. In addition, foreign isolates further threaten cereal production if they are introduced and established. Development of cereal cultivars with effective rust resistance will depend on the monitoring and characterization of virulence phenotypes of the rust pathogens with host differential lines containing single genes for rust resistance. Rust fungi have large, complex genomes and the uredinial stage is dikaryotic with two distinct haploid genomes. Genetic and genomic approaches will be used to (1) complete phased haploid genome assemblies for cereal rust fungi; (2) characterize population genetics of cereal rust pathogens; and (3) identify linkages between phenotype and genotype of cereal rust fungi involved in pathogenicity and host resistance. Surveys and identification of rust infections on Berberis and Mahonia species will be conducted to investigate the potential roles of alternate hosts in pathogen variations and disease epidemiology. Rust resistant cereal germplasm will be selected by testing wheat, oat, and barley lines from breeding programs throughout the U.S. for resistance to Pca, Pgt, P. hordei and P. triticina, using prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. The identity of rust resistance genes in breeding lines will be postulated in seedling tests using specific races of these rust fungi. Adult plant resistance of breeding lines will be evaluated in field plots. Genetic loci that mediate rust resistance genes will be identified along with molecular markers that facilitate plant breeding via marker assisted selection. Advanced germplasm lines with combinations of rust resistance genes will be derived and distributed for use in cultivar development.

Progress Report
Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogen populations, and characterize foreign populations that threaten U.S. cereal production. Field surveys were conducted across major wheat, barley, and oat growing regions of the U.S. Evaluations and sampling were performed at university research trials, farmer fields, and strategically located sentinel plots in California and Texas by USDA-ARS scientists and university collaborators. A total of 101 stem rust samples from wheat, barley, rye and oats were collected and analyzed in the 2024 crop season. Race QFCSC of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici-Pgt) was the only race identified from samples collected across the country. Rye stem rust pathogen (P. graminis f. sp. secalis-Pgs) was identified from infected rye and the alternate host, common barberry. Six races of the oat stem rust pathogen (P. graminis f. sp. avenae-Pga) were identified—SLN, TJS, TQL, TGN, KBD, and SGD—with race TGN continuing to be the predominant race east of the Rocky Mountains for a third year. In 2024, wheat leaf rust incidence was generally moderate to high across the 20 states. A total of 296 single pustule isolates were recovered from 170 wheat leaf rust samples collected from 20 states and 39 races were identified based on their infection responses on 20 differential wheat lines each carrying a single different wheat leaf rust resistance gene (Lr). Races MPPSD, MCTNB, TBTNB, TCTNB, TNBJS, MNPSD, and MBTNB were predominant across the U.S. with frequencies at 11.5%, 10.8%, 7.8%, 7.1%, 7.1%, 5.8%, and 5.1%, respectively, although their frequencies in different regions depended on the host resistance genes used in wheat cultivars in those regions. A total of 14 barley leaf rust samples were collected from six states (Texas, California, North Dakoka, Minnesota, Oregon, and Virginia), and 13 single pustule isolates were recovered and used to inoculate differential barley lines with individual resistance genes (Rph1 to Rph15). The data indicated that most of the Rph genes lost effectiveness to the tested isolates. All isolates except one were virulent on Rph3. However, virulence frequencies were very low for Rph5, Rph6, Rph7, Rph12, and Rph15 although the number of tested isolates was low. Seven samples of rye leaf rust were collected from four states. A total of 243 single pustule isolates of the oat crown rust pathogen (P. coronata f. sp. avenae-Pca) derived from 190 collections from 10 states, were tested on 40 oat varieties that carry different crown rust resistance genes. Similar to previous observations, high virulence diversity is present in the North American Pca population with approximately 90% of isolates being unique. The average number of ineffective resistance genes per isolate is 25, showing a continued trend for progressive increase in the ability of Pca to cause disease. We analyzed 26 rust samples from Spain to understand cereal rust epidemiology and monitor the evolution of virulence. The collection included 7 aecial barberry samples, 2 stem rust samples from the grass Elymus repens, and 15 stem rust samples from a wheat trap nursery planted adjacent to barberry bushes. Pgt isolates from wheat and barberry samples were highly diverse, although no new virulences were identified compared to the highly diverse and virulent sexual population collected in Spain in 2019. Two samples from E. repens yielded 13 unique Pgt races. Four new Pga races with unique virulence combinations were identified from aecial samples. Genetic analysis of 83 foreign wheat stem rust isolates from Ethiopia and Kenya found stable populations composed of Clade I (Ug99) and Clade IV-F. In contrast, all 21 evaluated wheat stem rust isolates from Nepal were unrelated to East African populations. Approximately 100 stem rust isolates were derived from infected fruits of Mahonia aquifolium collected from Northeastern Washington. Phenotypic analyses of these isolates have detected novel virulence to important stem rust resistance genes. This set of isolates will serve as an important genetic stock for population genetic studies of North American native sexual populations of the stem rust pathogen. Objective 2: Develop new genomic resources for cereal rust pathogens, identify links between pathogen phenotypes and genotypes, and improve understanding of the role of the sexual cycle in population dynamics. A total of 188 Pgt isolates derived from a sexual population from Spain were tested on a panel of 50 wheat stem rust resistance genes. Isolates were increased, DNA extracted, and sequenced. To develop high quality annotated genomes, we performed RNA sequencing using several stages: spores and infected wheat. Association analysis has identified candidate genes for AvrSr5 and AvrSr21, which suppress plant defense responses to cause disease. Research is underway to identify variants in the Pgt genome that underlie recognition in wheat and barley. Rust infections of common barberry (Berberis vulgaris) were observed and samples were collected from southeastern Minnesota and Wisconsin in 2023. Rye stem rust was identified but not wheat stem rust. Sequencing of rust samples collected from B. fendleri, a native barberry species collected in Colorado and New Mexico was performed to investigate the potential role of this plant in pathogen variations and disease epidemiology. Sequencing confirmed the presence of P. striiformis, the stripe rust pathogen of cereal crops and grasses. To understand diversity of domestic and foreign Pgt isolates, sequencing was completed on 34 isolates. Comparative analysis of these Pgt isolates is underway to understand wheat stem rust diversity, evaluate approaches the pathogen uses to evade recognition by crops, and develop new approaches for safeguarding US crops. Objective 3: Improve host resistance in cereal crops to rust pathogens by investigating resistant germplasm, characterizing genetics of rust resistance, and incorporating resistance into adapted germplasm. A total of 3,500 winter wheat, spring wheat and barley breeding lines from public and private breeding programs were tested for stem rust resistance with domestic and foreign races at the seedling stage, including Ug99 races. Candidate resistance genes were identified. A total of 35,000 data points were collected. Stem rust reaction at the adult plant stage is currently being evaluated in field trials. Data are distributed to breeders via regional nursery coordinators. A total of 832 spring wheat and 207 spring barley lines from 9 collaborating U.S. breeders were assessed for response to virulent strains of the stem rust pathogen (including Ug99) at the international stem rust nursery in Njoro, Kenya. We evaluated entries from the 2024 Northern and Southern Regional Performance, Uniform Southern and Eastern Soft Red Winter Wheat, and Uniform Southern Soft Red Winter Wheat nurseries with 12 races of leaf rust at seedling plant stage in greenhouse studies. Leaf rust resistance genes presented in the entries were postulated based on infection types to different races and molecular marker data. Gene postulations were distributed to the nursery coordinators and wheat breeders. In collaboration with USDA-ARS scientists in St. Paul, Minnesota, and Fargo, North Dakota, we evaluated 1,000 historic U.S. spring wheat cultivars and breeding lines for resistance to 8 domestic and foreign Pgt races (including Ug99) and stem rust resistance genes were postulated. Three mapping populations were phenotyped against foreign Pgt races to map wheat stem rust resistance genes in two durum wheat lines deposited at the National Small Grains Collection. In collaboration with USDA-ARS and university scientists, several novel sources of disease resistance were identified including a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111, mapping leaf rust resistance loci in hard winter wheat, and identification of novel leaf rust resistance genes in Aegilops umbellulata. Several new disease resistance genes were cloned, providing perfect markers for wheat breeders including wheat leaf rust resistance gene Lr39 and Yr87/Lr85 that confers resistance to wheat stripe rust and wheat leaf rust from wild relatives. A spring wheat cultivar, “MN-Rothsay” was released with high levels of resistance to wheat stem rust and wheat leaf rust. In 2024, over 3,441 oat breeding lines from various oat uniform nurseries and breeding programs in the U.S. and Canada were evaluated for crown rust resistance in the buckthorn nursery and nearby field plots. In 2025, over 3,244 lines have been planted in the buckthorn nursery and nearby field plots for evaluation. The 2024 lines included over 964 advanced oat breeding lines from the regional programs. Two oat lines carrying multiple APR genes to oat crown rust and linked molecular markers were released in 2024 for use in oat breeding programs. These APR genes are postulated to be more durable than seedling resistance genes. We are now evaluating additional combination of APR genes in the buckthorn nursery for oat crown rust resistance for release in 2026. Historical disease resistance data for East African trials with wheat and barley to wheat stem rust from 2011-2025 were curated to ensure compatibility with the Triticeae Toolbox (T3) database. To identify new resistance genes for leaf rust, a collection of 500 rye accessions deposited at USDA-ARS National Small Grains Collection were evaluated for resistance to seven cultures of the rye leaf rust pathogen (P. recondita f. sp. secalis) collected across the U.S. Collectively, this research will benefit US small grain farmers by improving disease resistance through the introduction of new sources of disease resistance into modern cultivars, the monitoring of cereal rusts in US fields, and surveillance of foreign cereal rust threats to US agriculture.

Accomplishments
1. The Southern Shield: Fortifying stem rust resistance in Southern U.S. wheat. Wheat is one of the most important food crops grown in the United States, forming a backbone of many diets and agricultural economies. Emerging races of the wheat stem rust pathogen are threatening wheat production. The Southcentral U.S. is an area of special concern because it is considered an overwintering region for the wheat stem rust pathogen and a source of inoculum to major wheat-growing regions in the Great Plains and Midwest. To fortify stem rust resistance in southcentral wheat cultivars, USDA-ARS researchers in Saint Paul, Minnesota, screened over 800 elite wheat lines from southern breeding programs for stem rust resistance in seedling and field evaluations and incorporated broadly effective stem rust resistance genes into 22 elite Southern U.S. lines. These genes, which confer resistance to all known domestic and highly virulent foreign strains of the stem rust pathogen, will enhance crop protection against stem rust for US farmers in the southern states and help reduce nation’s overall vulnerability to stem rust epidemics.

2. The Northern Shield: Delivering wheat stem rust resistance to upper Midwest U.S. farmers. Developing next generation crops that provide farmers with built in disease resistance will reduce operating costs and protect American crops. The sequential release of individual disease resistance genes threatens its long-term use due to erosion in resistance and increases risk for farmers from domestic and foreign pathogens. USDA-ARS researchers at Saint Paul, Minnesota, have developed novel combinations of wheat stem rust resistance, introduced these into elite wheat cultivars for the Upper Midwest, and delivered these improved cultivars to wheat breeders to generate next-generation resistant wheat varieties for U.S. farmers that safeguard U.S. wheat from domestic and foreign wheat stem rust including Ug99.

3. Identification of key adult plant resistance genes for oat crown rust. Crown rust is the most devastating disease affecting oat globally. The disease poses a severe threat to global oat production by significantly reducing yield and quality, where yield losses can exceed 50% during severe epidemics. Utilizing various published data, USDA-ARS scientists at the Cereal Disease Laboratory (CDL) in Saint Paul, Minnesota, identified 167 genetic loci linked to crown rust resistance. Through a detailed analysis, 23 key genomic regions associated with resistance were pinpointed. This study identified several important genes involved in stress response, plant defense, and hormone regulation. These findings provide valuable insights for breeders to develop more resistant oat varieties, enhancing protection against crown rust and securing improved crop stability.

4. New multi-rust disease resistance gene discovered. Safeguarding wheat in the United States involves the introduction of new sources of disease resistance. Leaf rust and stripe rust are common diseases on wheat in the United States, resulting in significant yield losses on an annual basis. USDA-ARS researchers in Saint Paul, Minnesota, working with collaborators in Minnesota and Israel discovered a new rust resistance gene in wheat that confers resistance to both leaf rust and stripe rust. This new gene gives resistance to all tested variants of leaf rust that occur in the U.S. This gene can be used by wheat breeding programs to develop new U.S. wheat cultivars that will be highly resistant to these two rusts.

5. Identification of a new disease resistance against wheat leaf rust. Identification of a new disease resistance against wheat leaf rust. Leaf rust is one of most important fungal diseases impacting wheat production in the United States, and it can cause significant yield losses each year. Use of host resistance is the most effective and environmentally sound approach for managing the rust disease. However, a single resistance gene bred into a wheat variety is often not good enough to fight against the rust disease because the pathogen creates new variants that can break the resistance. Cloning different leaf rust resistance genes and combining them into a wheat cultivar may make the rust resistance more effective and durable. USDA-ARS researchers in Saint Paul, Minnesota, isolated a leaf rust disease resistance gene (Lr39). This newly cloned gene encoded a resistance protein with a unique structure. Cloning of this gene can facilitate its utilization in wheat breeding programs and speed up the process of developing new U.S. wheat cultivars with durable resistance to the rust disease.

Review Publications
Sharma, D., Avni, R., Gutierrez-Gonzalez, J., Kumar, R., Sela, H., Prusty, M.R., Shatil-Cohen, A., Molnar, I., Holusova, K., Said, M., Dolezel, J., Millet, E., Khazan-Kost, S., Landau, U., Bethke, G., Sharon, O., Ezrati, S., Ronen, M., Maatuk, O., Eilam, T., Manisterski, J., Ben-Yehuda, P., Anikster, Y., Matny, O., Steffenson, B.J., Mascher, M., Brabham, H.J., Moscou, M.J., Liang, Y., Yu, G., Wulff, B., Muehlbauer, G., Minz-Dub, A., Sharon, A. 2024. A single NLR gene confers resistance to leaf and stripe rust in wheat. Nature Communications. https://doi.org/10.1038/s41467-024-54068-6.
Clare, S.J., Novakazi, F., Hayes, P.M., Moscou, M.J., Brueggeman, R.S. 2024. Colocalization of genetic regions that confer resistance/susceptibility against Puccinia species and association with Pyrenophora teres loci within the barley genome. Frontiers in Agronomy. 6. https://doi.org/10.3389/fagro.2024.1451281.
Cavalet-Giorsa, E., Gonzalez-Munoz, A., Athiyannan, N., Holden, S., Salhi, A., Gardener, C., Quiroz-Chavez, J., Rustamova, S., Elkot, A.F., Patpour, M., Rasheed, A., Kolmer, J.A., Lazo, G.R., Xu, S.S., Gu, Y.Q., Xu, X. 2024. Origin and evolution of the bread wheat D genome. Nature. 633:848-855. https://doi.org/10.1038/s41586-024-07808-z.
Singh, J., Gudi, S., Maughan, P. J., Liu, Z., Kolmer, J.A., Wang, M., Chen, X., Rouse, M.N., Lasserre-Zuber, P., Rimbert, H., Sehgal, S., Fiedler, J.D., Choulet, F., Acevedo, M., Gupta, R., Gill, U. 2024. Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement. Nature Genetics. 22(12): 3505-3519. https://doi.org/10.1111/pbi.14470.
Were, V., Yan, X., Foster, A., Sklenar, J., Langner, T., Gentle, A., Sahu, N., Bentham, A., Zdrzalek, R., Ryder, L., Kaimenyi, D., Gómez De La Cruz, D., Petit-Houdenot, Y., Eseola, A., Smoker, M., Bautista, M., Ma, W., Kourelis, J., Maclean, D., Banfield, M., Kamoun, S., Menke, F., Moscou, M.J., Talbot, N.J. 2025. The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity. The Plant Cell. Article koaf116. https://doi.org/10.1093/plcell/koaf116.
Leng, Y., Kummel, F., Zhao, M., Molnar, I., Dolezel, J., Logemann, E., Kochner, P., Xi, P., Yang, S., Moscou, M.J., Fiedler, B.A., Du, Y., Steuernagel, B., Meinhardt, S., Steffenson, B., Schulze-Lefert, P., Zhong, S. 2024. A barley MLA receptor is targeted by a specialized non-ribosomal peptide effector of the necrotrophic spot blotch fungus to induce disease susceptibility. New Phytologist. https://doi.org/10.1111/nph.20289.
Hewitt, T.C., Sharma, K.N., Zhang, J., Chunhong, C., Bajgain, P., Bhatt, D., Yang, J., Olivera Firpo, P.D., Singh, S., Wang, Q., Upadhyaya, N., Pozniak, C., Mcintosh, R., Lagudah, E., Zhang, P., Rouse, M.N. 2025. Divergent molecular pathways govern temperature-dependent wheat stem rust resistance genes. Nature Communications. 16.Article 4905. https://doi.org/10.1038/s41467-025-60030-x.
Klindworth, D.L., Rouse, M.N., Olivera, P., Jin, Y., Chu, C.N., Friesen, T.L., Zhong, S., Faris, J.D., Fiedler, J.D., Peters Haugrud, A.R., Gu, Y.Q., Elias, E.M., Liu, S., Cai, X., Xu, S.S. 2024. Registration of four durum wheat lines carrying Sr13 alleles for resistance to stem rust. Journal of Plant Registrations. 19(1). Article e20399. https://doi.org/10.1002/plr2.20399.
Kumssa, T., Baenziger, P.S., Rouse, M.N., Hussain, W., Belamkar, V., Wegulo, S.N., Poland, J. 2025. QTL mapping of stem rust resistance in a Bill Brown/Gage winter wheat population. Crop Science. 65(1).Article e21445. https://doi.org/10.1002/csc2.21445.
Yazdani, M., Rouse, M.N., Bajgain, P., Danilova, T.V., Motsnyi, I., Steffenson, B.J., Patpour, M., Rahmatov, M. 2025. Identification and Characterization of Sr59-Mediated Stem Rust Resistance in a Novel Wheat-Rye Translocation T2BL.2BS·2RL. The Crop Journal. 13(2025) 909-918. https://doi.org/10.1016/j.cj.2025.02.012.
Babar, M., Khan, N., Blount, A., Barnett, R.D., Harrison, S.A., Dewitt, N., Johnson, J., Mergoum, M., Boyles, R., Murphy, P., Mason, E., Shakiba, E., Ibrahim, A., Sutton, R., Brown Guedira, G.L., Marshall, D., Cowger, C., Baik, B.V., Santantonio, N., Cambron, S.E., Jin, Y., Mailhot, D. 2024. Registration of FL16045-25: An early-maturing, high-yielding, disease-resistant soft red facultative wheat variety for the Southern U.S.. Journal of Plant Registrations. 18(2):374-387. https://doi.org/10.1002/plr2.20343.
Massman, C., Hernandez, J., Clare, S., Brooke, M., Filichkin, T., Fisk, S., Helgerson, L., Del Blanco, I.A., Rouse, M.N., Steffenson, B.J., Brueggeman, R.S., Hayes, P. 2024. Registration of the 'Woodies' multi-rust resistant barley germplasm. Journal of Plant Registrations. 18(2):393-401. https://doi.org/10.1002/plr2.20373.
Shariatipour, N., Yazdani, M., Carlsson, A., Bengtsson, T., Kianian, S., Jalli, M., Rahmatov, M., The Ppp Roboat, C. 2025. Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes. The Plant Genome. 18(2). Article e70059. https://doi.org/10.1002/tpg2.70059.