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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Research Project #423040


Location: Cereal Disease Lab

2014 Annual Report

Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogen populations. Sub-objective 1.A. Monitor, collect and characterize cereal rust pathogen populations in the U.S. for virulence phenotypes to rust resistance genes in cereal cultivars. Sub-objective 1.B. Determine levels of genetic variation in P. triticina and P. graminis populations. Sub-objective 1.C. Refine phylogenetics and systematics of P. graminis and P. triticina. Objective 2: Discover and characterize fungal genes that are involved in pathogenesis and the obligate biotrophic interactions of cereal rust pathogens and their hosts. Objective 3: Identify and characterize rust resistance genes in novel and elite germplasm to assist in the development of resistant cereal cultivars. 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. The proposed research objectives are central to the mission of the USDA ARS Cereal Disease Laboratory (CDL): to reduce losses in wheat, oat, and barley to major diseases using host resistance. Research is focused on genetic variation in both the host cereals and their rust pathogens that determine the resistance/susceptible phenotype of the interaction. Isolates of rust fungi obtained from annual surveys of the wheat, barley, and oat crops are used to inform the breeding process. Successful control of cereal rusts with host resistance cannot be achieved without knowledge of variation in cereal rust populations. Studies of virulence and molecular variation in cereal rust populations can answer questions that range from the applied, such as which host resistance genes are effective against the current rust population and what resistance genes are in current cereal cultivars, to more basic questions like what are the origins of new races and how do they spread. Discovery of the molecular determinants of pathogenesis and obligate biotrophy in cereal rust fungi via genomic approaches offers intriguing leads in the development of novel resistance mechanisms. Identification, characterization, and introgression of new host resistance to cereal rusts are key to increasing the diversity of resistance genes in our cereals and staying ahead of these "shifty" pathogens.

Cereal rust fungi are dynamic leading to constant changes in the U.S. population which leads to the erosion of effective rust resistance in cereal crops. In addition, the introduction of foreign isolates, such as Ug99, further threaten cereal production. Development of cereal cultivars with effective rust resistance and management strategies of these diseases will depend on the monitoring and characterization, virulence phenotypes and molecular genotypes, of cereal rust pathogen populations. Rust resistant cereal germplasm will be selected by testing wheat, oat, and barley lines from breeding programs throughout the United States for resistance to Puccinia coronata, P. graminis, and P. triticina, using the prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. Testing with selected isolates of the cereal rust pathogens and host genetics studies will identify the rust resistance genes in breeding lines and germplasm. Advanced germplasm lines with combinations of rust resistance genes will be selected. Rust fungi produce a large arsenal of effector proteins in order to infect and colonize the plant host. Genetic and genomic approaches will be used to identify and characterize effector genes from P. graminis.

Progress Report
Progress was made on all three objectives. Annual survey of wheat stem and leaf rust, oat stem and crown rust, and barley leaf rust in the United States were completed. Survey samples were characterized for virulence phenotypes. Survey and race identification results were disseminated through an interactive map hosted at the Cereal Disease Laboratory website and through bi-weekly Rust Bulletins. Representative isolates from individual states were accessioned into Cereal Disease Laboratory culture collection. Stem rust sentinel plots were established in Texas, California and Arizona for the purpose of detecting potential Ug99 incursion into North America. Sentinel plots were also established in Ecuador. In 2014, races of wheat leaf rust with virulence to widely used plant resistance gene combinations (Leaf rust genes) were identified, which threaten the varieties in many of the major wheat growing regions (e.g., the Great Plains) of the United States. Additionally, in 2013 a leaf rust race that has high virulence to durum wheat cultivars was found in a wheat field in Kansas. This virulent isolate may eventually spread to North Dakota where majority of the United States durum wheat is grown. Leaf rust isolates collected from China (81) and Pakistan (100) were further characterized, in addition to isolates from Ethiopia (113). Races that are avirulent to Thatcher wheat and highly virulent to durum wheat were also found. These races are unique to Ethiopia. Leaf rust populations in Ethiopia are very unique for diversity of different race types and molecular genotypes. Furthermore, about 200 samples of the wheat stem rust pathogen were genotyped with a focus on isolates from Northeast Africa, Middle East, Central Asia and Europe. One genetic cluster contained samples from all four regions indicating pathogen movement between these regions. Two of the sample sets from Europe suggest that the sexual cycle is contributing to genetic diversity in this region. In contrast, the data suggest that the genetic variation observed within the Ug99 lineage is due to mutation rather than sexual recombination. Rust infections on Berberis vulgaris were surveyed and collected from Minnesota and Wisconsin, and P. graminis f. sp. secalis was identified and isolated. Native Mahonia/Berberis species (B. nevinii, B. haematocarpa, M. aquifolium, and M. repens) were surveyed in southern California for the first time, and aecial infections were not observed, likely due to severe drought experienced in southwestern United States. The role of these plants as potential sources for pathogen variations (generating new races) remains unknown. There is an urgent need to have a clear understanding of the rust flora on these plants from these regions and consistent surveillance on their roles for disease epidemiology and pathogen variations of cereal stem and stripe rusts. We derived a mutant isolate of P. graminis with virulence on wheat resistance gene Sr9e. The mutagenized isolate was verified as derived from the original isolate through genotyping. This mutagenesis procedure will be a valuable resource to identify candidate avirulence genes. The genetic map of the wheat stem rust pathogen was further refined in the region containing the effector gene AvrT28 and alleles of a candidate for this gene were cloned. DNA of 135 isolates of P. triticina were sequenced in collaboration with USDA-ARS Manhattan in Kansas and the Broad Institute in Cambridge, Massachussetts. Analysis of single nucleotide polymorphism showed that grouping of isolates based on previous SSR and virulence markers had excellent correlation with the whole genome data. Isolates from common hexaploid wheat were grouped separately from isolates of tetraploid durum wheat and diploid Aegilops speltoides. A total of 1600 wheat breeding lines from various nurseries and breeding programs were tested with multiple stem rust races in the greenhouse and in the field. Data were provided to nursery coordinators and posted at Cereal Disease Laboratory website. Close to 400 wheat breeding lines were tested for seedling leaf rust resistance with 10 different races. Entries from the various Spring wheat breeding programs were also evaluated for seedling/greenhouse and adult/field leaf rust resistance. Oat crown rust nursery with close to 200 entries from across the United States were planted and data provided to coordinators and posted at the Cereal Disease Laboratory website. Barley breeding lines were not tested because the stem rust testing was done by a university collaborator. Advanced and preliminary wheat breeding lines from the University of Minnesota were evaluated for leaf rust resistance in field plots. Hard red spring wheat entries in the Uniform spring wheat nursery were evaluated for seedling resistance with 10 leaf rust races and the leaf rust resistance genes were postulated for each entry. Substantial progress was made in understanding the genetics of resistance to Ug99 stem rust in the United States Spring wheat lines. A number of publications detail identified resistance loci and linked molecular markers. Additionally germplasm combining Ug99 resistance genes in coupling have been deposited in the National Small Grains Collection as CDL001, PI 670015. In addition to understanding the genetics of plant resistance, we conducted the Ug99 screening necessary to introgress two new genes or alleles from Ae. tauschii into wheat. Six populations of wheat lines (approximately 100 lines each) were evaluated for leaf rust resistance in field plots in 2014. This data will be combined with previously developed genetic maps and seedling tests to produce a comprehensive view of segregating resistance genes.

1. ARS researchers in St. Paul led the international efforts in analyzing the 2013 severe stem rust epidemic in southern Ethiopia. Results from race typing of a large number of stem rust samples from the epidemic region concluded that the 2013 stem rust epidemic was due to a new race, TKTTF. Genotyping using approximately 960 genetic markers demonstrated that isolates of the race TKTTF belong to a distinctly different lineage than Ug99 race group. In addition, the isolates of the race TKTTF is composed of at least two genetic subgroups. More than 5000 elite breeding lines from the United States and international centers were evaluated against this new race and data were distributed to breeding community. Due to differential virulence response of this new race as compared with Ug99, deployment of various resistance genes in the United States and worldwide breeding programs needs to be further scrutinized. The rapid determination of the new stem rust race enabled international community to develop strategies in pathogen monitoring and resistance breeding.

2. Germany observed stem rust epidemic for the first time in more than 50 years. Race analyses by ARS researchers in St. Paul identified multiple races with new and significant virulence combinations that have not been observed before in the world's stem rust population. Elite United States breeding germplasm (3000 lines) were evaluated. Race phenotyping and SNP genotyping of stem rust samples from Georgia indicated that an active sexual population is providing diversity to the wheat stem rust pathogen population, including virulence to the universal resistance gene Sr22. The identification of these new races has significant implications for breeding stem rust resistance. As new more virulent combination of races emerge, the old varieties rapidly become susceptible, and the need for more focused pro-active approach in breeding for new resistance becomes critical.

3. The genetics of resistance in wheat cultivar 'Thatcher' were described as the complementary interaction of 3 genetic factors. In order to observe a reduction in stem rust severity, presence of 2 or 3 of these QTL factors were necessary. In addition, resistance was enhanced by the gene Sr57 (Lr34) inherited from the variety 'McNeal'. 'Thatcher' is believed to be the source of adult plant resistance in United States spring wheat. Knowledge of the identified QTL, the co-localization of one of these QTL with defeated stem rust resistance gene Sr12, and the complementary gene action observed by these factors provide valuable information needed to select for adult plant resistance in conventional United States spring wheat.

4. Leaf rust of wheat is the most common rust of wheat in the United States and worldwide. The population of causal agent, P. triticina, in the United States is genetically variable and is characterized by distinct groups of races that differ for virulence to important resistance genes in wheat and DNA markers. Scientists at the ARS, Cereal Disease Laboratory studied the worldwide collection of P. triticina to determine if new races in the United States are a result of migration from other wheat growing regions. Collections from China (2009 and 2010) were tested for virulence and genotyped with DNA markers and found to be distinct from those in the United States, indicating that migration from this region had not recently occurred. Analysis of isolates from seven provinces showed that populations in China are not differentiated based on province of origin indicating regular migration of leaf rust between the wheat growing regions in China. This movement of isolates in China could lead to sexual recombination and emergence of new more virulent types with greater impact on wheat production.

5. Genetic mapping of plant resistance genes is critical to breeding efforts for improved resistance. Adult plant leaf rust resistance in the Uruguayan landrace wheat cultivar Americano 44d was mapped to chromosomes 3A and 3D. These are new leaf rust resistance genes that can be utilized in wheat. Adult plant resistance genes derived from the United States soft red winter wheat 'Caldwell' mapped to chromosomes 3B and 4A. The gene on chromosome 3B gives effective field resistance to the current P. triticina races and can be used in combination with other resistance genes to improve leaf rust resistance.

Review Publications
Liu, M., Szabo, L.J., Hambleton, S., Anikster, Y., Kolmer, J.A. 2013. Molecular phylogenetic relationships of the brown leaf rust fungi on wheat, rye and other grasses. Plant Disease. 97:1408-1417.
Lopez-Vera, E.E., Nelson, S., Singh, R.P., Basnet, B.R., Haley, S.D., Bhavani, S., Huerta-Espino, J., Xoconostle-Cazares, B., Ruiz-Medrano, R., Rouse, M.N., Singh, S. 2013. Resistance to Ug99 stem rust in six bread wheat cultivars maps to chromosome 6DS. Theoretical and Applied Genetics. 127:231-239.
Turner, K.M., DeHaan, L.R., Jin, Y., Anderson, J.A. 2013. Wheatgrass-wheat partial amphiploids as a novel source of stem rust and Fusarium head blight resistance. Crop Science. 53:1994-2005.
Graybosch, R.A., Baenziger, P.S., Dantra, D., Regassa, T., Jin, Y., Kolmer, J.A., Wegulo, S., Bai, G., St Amand, P., Chen, X., Seabourn, B.W., Dowell, F.E., Bowden, R.L., Marshall, D.S. 2014. Release of ‘Mattern’ waxy (amylose-free) winter wheat. Journal of Plant Registrations. 8:43-48.
Niu, Z., Klindworth, D.L., Yu, G., Friesen, T.L., Chao, S., Jin, Y., Cai, X., Ohm, J.-B., Rasmussen, J.B., Xu, S.S. 2014. Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum. Theoretical and Applied Genetics. 127:969-980.
Niu, Z., Puri, K.D., Chao, S., Jin, Y., Sun, Y., Steffenson, B.J., Maan, S.S., Xu, S.S., Zhong, S. 2013. Genetic analysis and molecular mapping of crown rust resistance in common wheat. Theoretical and Applied Genetics. 127:609-619.
Bruce, M.A., Neugebauer, K.A., Joly, D.L., Bakkeren, G., Migeon, P., Wang, S., Akhunov, E., Cuomo, C.A., Fellers, J.P., Kolmer, J.A. 2014. Using transcription of six Puccinia triticina races to identify the secretome during infection of wheat. Frontiers in Plant Science. 4:520.
Haley, S., Johnson, J., Peairs, F., Stromberger, J., Hudson-Ams, A., Seifert, S., Valdez, V., Kottke, R., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W., Dowell, F.E. 2014. Registration of 'Antero' Wheat. Journal of Plant Registrations. doi: 10.3198/jpr2013.12.0072crc.
Olson, E.L., Rouse, M.N., Bowden, R.L., Pumphrey, M.O., Gill, B., Poland, J.A. 2013. Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theoretical and Applied Genetics. doi: 10.1007/s00122-013-2148-z.
Mago, R., Verlin, D., Zhang, P., Bansal, U., Bariana, H., Jin, Y., Ellis, J., Hoxha, S., Dundas, I. 2013. Development of wheat-Aegilops speltoides recombinants and simple PCR-based markers for stem rust resistance genes on the 2S#1 chromosome. Theoretical and Applied Genetics. 126:2943–2955.
Jin, Y., Rouse, M.N., Groth, J. 2014. Population diversity of Puccinia graminis is sustained through sexual cycle on alternate hosts. Journal of Integrative Agriculture. 13(2):262-264.
German, S.E., Kolmer, J.A. 2013. Leaf rust resistance in selected Uruguayan late maturity common wheat cultivars. Euphytica. 52:606-608.
Liu, M., Kolmer, J.A. 2013. Population divergence in the wheat leaf rust fungus Puccinia triticina is correlated with wheat evolution. Molecular Phylogenetics and Evolution. 112:443-453.
Terefe, T.G., Visser, B., Prins, R., Negussie, T., Kolmer, J.A., Pretorius, Z.A. 2014. Diversity in Puccinia triticina detected on wheat from 2008 to 2010 and the impact of new races on South African wheat germplasm. European Journal of Plant Pathology. 139:95-105.
Rouse, M.N., Talbert, L.E., Singh, D., Sherman, J.D. 2014. Complementary epistasis involving Sr12 explains adult plant resistance to stem rust in Thatcher wheat (Triticum aestivum L.). Theoretical and Applied Genetics. Available:
Hunger, R., Edwards, J., Bowden, R.L., Yan, L., Rayas-Duarte, P., Bai, G., Horn, G., Kolmer, J.A., Giles, K., Chen, M., Jin, Y., Osburn, R., Bales, M., Seabourn, B.W., Klatt, A., Carver, B. 2013. 'Billings' wheat combines early maturity, disease resistance, and desirable grain quality for the Southern Great Plains of the USA. Journal of Plant Registrations. 8:22-31.