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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS, POPULATION BIOLOGY, AND HOST-PARASITE INTERACTIONS OF CEREAL RUST FUNGI AND THEIR DISEASES

Location: Cereal Disease Laboratory

2012 Annual Report


1a.Objectives (from AD-416):
New funds will be used to expand the current research objectives for this ARS project to prepare for the possible appearance of Ug99 in North America. Those objectives are:

Objective 1: Monitor and characterize races of cereal rust pathogens, particularly the new East African strain, Ug99. This includes the sub-objective of characterizing races of cereal stem rust, particularly Ug99 and related mutants, which represent a threat to the production of wheat, oat, and barley cultivars in the United States.

Objective 2: Identify features essential for cereal rust pathogensis including sub-objectives of characterizing the genome of Puccinia graminis (stem rust). Research for this objective will be expanded to characterize the Ug99 genome sequence and to develop detection methods for the new Eastern African stem rust mutants.

Objective 3: Identify resistance genes and develop effective strategies for deploying host-resistance genes to control cereal rust diseases. Research for this objective will be expanded to identify new sources of Ug99 resistance and to accelerate the development of Ug99-resistant wheat and barley varieties adapted for U.S. production.


1b.Approach (from AD-416):
Cereal rust pathogens continuously evolve to overcome existing host resistance genes in wheat, barley, and oats. Cereal germplasm with durable rust resistance, and other control strategies are needed to minimize yield losses due to cereal rusts. Variation in cereal rust populations will be analyzed by assessing virulence polymorphism to important rust resistance genes and by using molecular polymorphism to determine the relatedness and relationships between these populations. Migration patterns of cereal rust populations will be established using virulence and molecular markers. Virulence shifts in cereal rust populations in major cereal-producing areas of the U.S. in relation to use of rust resistance genes will be analyzed. Cereal germplasm with rust resistance will be evaluated in seedling plant tests and in adult plant field tests. Advanced germplasm lines with combinations of rust resistance genes will be selected. Cereal germplasm with durable resistance will be genetically analyzed to determine the identity and expression of the rust resistance genes. A genetic map of P. graminis will be constructed using AFLPs, SSRs, and SNPs. Physical maps of regions with avirulence genes will be developed using BAC and cosmid libraries. Genetic determinants of early infection processes in cereal rusts will be characterized. Crosses will be made with other cereal rust fungi to determine the genetics of avirulence/virulence to important rust resistance genes.


3.Progress Report:
Progress was made on all three objectives. Under Objective 1, surveys of stem rust in the U.S. indicated population in east of the Rocky Mountains showed a decline in incidence, and that a single race, QFCSC, remains dominant, and the population in northwestern U.S. remains diverse with multiple races found. Mahonia repens and M. aquifolium were found to serve as alternate host, which may play a role in generating/sustaining the genetic diversity. Oat stem rust evolved rapidly in North America in last five years with virulence combinations attacking all resistance genes in US oat cultivars. Surveys of wheat leaf rust indicated that over 50 races are identified annually in the U.S., and the most common races have virulence to genes that are present in the leading soft red winter and hard red winter wheat cultivars. As a result most of the leading winter wheat cultivars are susceptible to leaf rust. In 2010, the first races with virulence to Lr21 were found in the U.S. As a result, many hard red spring wheats are now susceptible to leaf rust. Under Objective 1B, the wheat leaf rust populations from North America and South America were determined to be highly related for molecular and virulence variation, indicating migration, and populations from Europe, Central Asia, and the Middle East were more closely related, indicating little if any recent migration of these regions with the Americas. New races in the Ug99 race group, as well as other races attacking important stem rust resistance gene combinations, such as TRTTF, were identified in eastern Africa. Genetic analysis of the Ug99 race group demonstrated that this is a unique lineage and individual phenotypic races contain multiple genotypes. Stem susceptible barberry was found in highlands of Ethiopia and Kenya, close to cereal production fields. Barberry was found to be the alternate host of stripe rust. Under Objective 1C, P. triticina isolates collected from A. speltoides, durum wheat, and common wheat, varied little for sequence variation at one gene locus, confirming that these diverse collections can be considered as a single species. Under Objective 2, P. graminis genome was sequenced, assembled, and annotated. Gene expression was characterized across different developmental stages and samples. Candidate effector genes involved in pathogenicity were identified and characterized. Under Objective 3A, wheat, oat, and barley germplasm from breeding programs across the U.S. were evaluated for rust resistance in seedling greenhouse tests and field plots, and identity of rust resistance genes were postulated when possible. Under Objective 3B, diverse sources of rust resistance in wheat, oat, and barley, and cultivated and wild relatives of wheat and oat were genetically characterized for rust resistance. Molecular markers for rust resistance genes were developed, and new genes for rust resistance were mapped to chromosome locations. Germplasm developed from these studies can be used to improve rust resistance in cereal improvement programs in the U.S.


4.Accomplishments
1. Susceptibility of Mahonia species to stem rust and stripe rust pathogen. A key management practice for controlling wheat stem rust has been the regulation of susceptible ornamental varieties of Berberis species in regions of the U.S. growing wheat. ARS scientists at Saint Paul, Minnesota discovered that Mahonia eurybracteata variety "Minganpi" is susceptible to infection by the wheat stem rust pathogen, Puccinia graminis. In addition, they showed that this variety was also susceptible to Puccinia striiformis, the stripe rust pathogen. These discoveries identified new host in which these two major cereal rust pathogens can complete their life cycle and therefore increase the virulence diversity of these pathogens. This information was provided to Animal and Plant Health Inspection Services (APHIS) as well as the developer to determine whether this species can be released commercially into the barberry regulated states.

2. Genetic mapping of five Ug99 stem rust resistance genes. In order to mitigate the threat of Ug99, the African strain of the wheat stem rust fungus virulent on the majority of United States wheat, ARS researchers at the Cereal Disease Laboratory in Saint Paul, MN, in collaboration with an international team of scientists, have identified molecular markers linked to five wheat genes that provide resistance to Ug99. The genes, previously identified by ARS scientists and collaborators, originate from diverse wheat germplasm including U.S. hard red spring wheat, U.S. hard red winter wheat, European winter wheat, and a wild wheat relative. The molecular marker information will allow wheat breeders worldwide to efficiently breed for resistant wheat.

3. Evolutionary biology of host adaptation in Puccinia triticina. Strains of the wheat leaf rust pathogen, P. triticina show distinctly different ability to infect durum wheat and common bread wheat. ARS scientists at St. Paul, Minnesota used molecular markers to analyze populations of strains that were adapted to durum and common bread wheat. Their results indicated that the strains adapted to infect durum wheat have evolved more recently and were derived from the strains adapted to common bread wheat. This work will be used by scientists to better understand the evolution of the wheat leaf rust pathogens and the mechanism of adaption to new hosts.

4. Predicting risk of soybean rust in North American continental interior. Soybean rust continues to pose a significant risk to soybean production in the United States. Developing methods to analyze the risk of disease development in the main soybean growing areas of the Midwest has been problematic. ARS scientists at Saint Paul, Minnesota and scientists at Pennsylvania State University, University Park, Pennsylvania lead a group of international collaborators to develop a system that combines spore trap data and aerobiological modeling to predict development of seasonal soybean rust incursions into continental North America. This system provides a cost effective alternative to sentinel plots for soybean rust management. Accurate and timely information on risk of soybean rust development has become a key component in the management of this disease and has lead to effective control.


Review Publications
Rouse, M.N., Jin, Y. 2011. Genetics of resistance to race TTKSK of Puccinia graminis f. sp. tritici in Triticum monococcum. Phytopathology. 101:1418-1423.

Ghazvini, H., Hiebert, C., Zegeye, T., Liu, S., Dilawari, M., Anderson, J., Rouse, M.N., Jin, Y., Fetch, T. 2012. Inheritance of resistance to Ug99 stem rust in wheat cultivar Norin 40 and genetic mapping of Sr42. Journal of Theoretical and Applied Genetics. 125:817-824.

Olivera, P., Jin, Y., Rouse, M.N., Badebo, A., Fetch, T., Singh, R., Yahyaoui, A. 2011. Races of Puccinia graminis f. sp. tritici with combined virulence to Sr13 and Sr9e in a field stem rust screening nursery in Ethiopia. Plant Disease. 96:623-628.

Baenziger, P.S., Graybosch, R.A., Regassa, T., Nelson, L.A., Klein, R.N., Santra, D.K., Baltensperger, D.D., Krall, J.M., Xu, L., Wegulo, S.N., Jin, Y., Kolmer, J.A., Chen, M., Bai, G. 2011. Registration of 'NI04421' hard red winter wheat. Journal of Plant Registrations. 6:54-59. DOI: 10.3198/jpr2011.02.0102crc.

Edwards, J.T., Hunger, R.M., Smith, E.L., Horn, G.W., Chen, M., Yan, L., Bai, G., Bowden, R.L., Rayas-Duarte, P., Osburn, R.D., Kolmer, J.A., Jin, Y., Porter, D.R., Giles, K.C., Seabourn, B.W., Bayles, M.B., Carver, B.F., Klatt, A. 2011. 'Duster' wheat: A durable, dual-purpose cultivar adapted to the southern great plains of the USA. Journal of Plant Registrations. 6(1):1-12.

Baenziger, P.S., Graybosch, R.A., Regassa, T., Nelson, L.A., Klein, R.N., Santra, D.K., Baltensperger, D.D., Krall, J.M., Xu, L., Wegulo, S.N., Jin, Y., Kolmer, J.A., Chen, M., Bai, G. 2011. Registration of 'NE01481' hard red winter wheat. Journal of Plant Registrations. 6:49-53. DOI: 10.3198/jpr2011.02.0101crc.

Haley, S.D., Johnson, J., Westra, P., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Brawl CL Plus' wheat. Journal of Plant Registrations. 6:1-5.

Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Byrd' wheat. Journal of Plant Registrations. 6:1-4.

Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Martin, T.J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Denali' wheat. Journal of Plant Registrations. 6:311-314. DOI: 10.3198/JPr2011.12.0675crc.

German, S.E., Kolmer, J.A. 2012. Leaf rust resistance in selected Uruguayan common wheat cultivars with early maturity. Crop Science. 52:601-608.

Kolmer, J.A., Long, D., Hughes, M.E. 2012. Physiologic specialization of Puccinia triticina on wheat in the United States in 2010. Plant Disease. 96:1216-1221.

Kolmer, J.A., Hanzalova, A., Goyeau, H., Bayles, R., Morgounov 2012. Genetic differentiation of the wheat leaf rust fungus Puccinia triticina in Europe. Plant Pathology. Available: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3059.2012.02626.x.

Isard, S., Barnes, C., Hambleton, S., Ariatti, A., Russo, J., Tenuta, A., Gay, D., Szabo, L.J. 2011. Predicting soybean rust incursions into the North American continental interior using crop monitoring, spore trapping, and aerobiological modeling. Plant Disease. 95(11):1346.

Nirmala, J., Drader, T., Lawrence, P.K., Yin, C., Hulbert, S., Steber, C.M., Steffenson, B.J., Szabo, L.J., Von Wettstein, D., Kleinhofs, A. 2011. Concerted action of two avirulent spore effectors activates Reaction to Puccinia graminis 1 (Rpg1)-mediated cereal stem rust resistance. Proceedings of the National Academy of Sciences. 108(35):14676-81.

Pretorius, Z.A., Szabo, L.J., Boshoff, W., Herselman, L., Vissar, B. 2012. First report of a variant within wheat stem rust (Puccinia graminis f. sp. tritici) race TTKSF in South Africa and Zimbabwe. Disease Note. 96(4):590.

Saunders, D., Win, J., Cano, L., Szabo, L.J., Kamoun, S., Raffaele, S. 2012. Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi. PLoS One. 7(1):e29847.

Last Modified: 10/1/2014
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