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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

2010 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
In 2010, monitoring for leaf rust (wheat), stem rust (wheat, barley, oat) and crown rust (oat) in the US was conducted. Updates were provided to agricultural professionals and growers. Race identification was completed for 2009 collections. Forty-one races of wheat leaf rust pathogen were described with five common races accounting for three-quarters of the samples. The predominantly grown hard red and soft red winter wheat cultivars are susceptible to these common races of leaf rust pathogen. Approximately 300 isolates of P. graminis were derived from 190 stem rust samples of wheat, barley and oat collected from 20 states. East of the Rockies a single race of the wheat stem rust pathogen continues to dominate as it has in recent years. High level of race diversity was found in collections of wheat stem rust pathogen from the Pacific Northwest. The mean virulence of P. coronata isolates in the U.S. is increasing. An increase in virulence to a new resistance gene, used in Canadian oat cultivars, indicates that its effective lifespan will be short. Virulence to the resistance gene in the popular oat variety HiFi remains low indicating that this resistance maybe stable.

Collections of Puccinia triticina (wheat leaf rust pathogen) from Turkey, the United Kingdom, and the Czech Republic were characterized for virulence and for molecular variation. Genetic characterization of worldwide P. triticina populations will be used to determine migration patterns of this wind-borne fungus and detect races that are virulent to wheat cultivars grown in the U.S.

To understand the molecular mechanism of pathogenicity and host resistance in wheat stem rust fungus, an effector gene was genetically mapped in the Puccinia graminis genome. Studies of gene expression in this fungus have identified additional candidate effector genes.

The wild slender oat, Avena barbata, has been found to be a rich source of new resistance genes to crown rust, Puccinia coronata. Resistant accessions of A. barbata have been successfully used to create synthetic hexaploid oats. This novel approach will allow the rapid introgression of novel resistance genes into the cultivated oat genome without the difficulties associated with previous attempts at introgressing genes from A. barbata.

The landrace derived wheat cultivars Americano 25e and Americano 44d from Uruguay have been very resistant to leaf rust since release in 1918. Genetic analysis identified a new source of leaf rust resistance for use in US wheat breeding programs.

Evaluated germplasm of regional nurseries and critical breeding programs in southern U.S., the Great Plains and spring wheat region with races of the TTKS lineage and U.S. races. Genes effective against Ug99 were postulated. Evaluated stem rust reaction of US spring germplasm for Ug99 resistance in the Njoro stem rust nursery. Characterized stem rust resistance in germplasm from international programs that have been introduced into US wheat germplasm. These phenotyping data provide critical information to facilitate breeding stem rust resistance in the US. Evaluation data of the international germplasm helps US breeders to select appropriate material to use.


4.Accomplishments
1. The Century-Old Mystery of the Life Cycle of Wheat and Barley Stripe Rust is Solved. The identity of the alternate host of stripe rust fungus (Puccinia striiformis) has baffled scientists for over a century. Some have even speculated that either it doesn’t exist or is extinct. ARS scientists in St. Paul, Minnesota have demonstrated conclusively that several species and hybrids of barberry (Berberis spp.) serve as alternate hosts to this important cereal rust. This may explain why this rust species is so variable and difficult to develop durable host resistance to. This discovery also paves the way for genetic studies of this organism that has heretofore been impossible.

2. Development of a Rapid Diagnostic Assay for the Identification of the Highly Virulent Race (Ug99) of Puccinia graminis: The Causal Agent of Wheat and Barley Stem Rust. The standard method of race identification requires using live isolates of P. graminis f. sp. tritici to screen wheat lines under controlled environmental conditions and takes 2-4 weeks. ARS scientists in St. Paul, Minnesota in collaboration with scientists in Cambridge, Massachussetts developed a DNA-based assay, which is able to identify the Ug99 race-group. The assay provides a phenotypic fingerprint using 13 different loci in the Puccinia graminis genome. This assay provides a rapid laboratory method that will speed up identification of this economically important race of wheat stem pathogen.

3. Determined the Leaf Rust Resistance Genes in Two Wheat Cultivars Shown to Have Stable Resistance. Leaf rust is the most common disease of hard red winter wheat in the U.S. Yield losses regularly occur and can reach up to 14% as in Kansas in 2007. Most of the commonly grown cultivars are susceptible since the leaf rust fungus is highly variable for virulence to resistance genes in host cultivars and virulent races quickly increase in response to cultivation of wheat cultivars. The cultivars Santa Fe and Duster have stayed highly resistant to leaf rust since release, even though other cultivars have become susceptible during this time. ARS scientists in St. Paul, Minnesota determined that the wheat cultivar Santa Fe and Duster contain unidentified adult plant resistance genes that likely provided resistance to the current races of Puccinia triticina as well as three known resistance genes. The unidentified adult plant resistance gene(s) present in these cultivars are likely new sources of leaf rust resistance. This information will be of value to plants breeders when selecting germplasm for developing new leaf rust resistance cultivars of wheat.

4. Identified Novel Stem Rust Virulence Combinations in Ethiopia that Overcome Ug99-Resistant Durum Cultivars. Durum wheat of North America generally has a higher frequency of resistance to the highly virulent race (Ug99) of Puccinia graminis f. sp. tritici than common wheat based on evaluations conducted in Kenya. However, Ug99-resistant selections of North American durum wheat became susceptible when evaluated in Ethiopia. ARS scientists in St. Paul, Minnesota identified two new races from Ethiopia with novel virulence combinations, which may explain why the Ug99-resistant durum wheat cultivars were susceptible in Ethiopia. These two races are of concern because they are able to overcome two resistance genes (Sr9e and Sr13) that constitute major components of stem rust resistance in North American durum cultivars. In addition, one of the new races appears to be virulent to stem rust resistance, conferred by the 1AL.1RS translocation, used widely in winter wheat in the United States. This information on new virulent races of the wheat stem rust pathogen is of value to breeding programs in order to develop resistant varieties.


Review Publications
Kolmer, J.A. 2010. Genetics of Leaf Rust Resistance in the Soft Red Winter Wheat Cultivars Coker 9663 and Pioneer 26R61. Plant Disease. 94:628-632.

Baenziger, P.S., Graybosch, R.A., Nelson, L.A., Klein, R.N., Baltensperger, D.D., Xu, L., Wegulo, S.N., Watkins, J.E., Jin, Y., Kolmer, J.A., Hatchett, J.H., Chen, M., Bai, G. 2009. Registration of 'Camelot' Wheat. Journal of Plant Registrations. 3:256-263.

Griffey, C.A., Thomason, W.E., Pitman, R.M., Beahm, B.R., Paling, J.J., Chen, J., Fanelli, J.K., Kenner, J.C., Dunaway, D.W., Brooks, W.S., Vaughn, M.E., Hokanson, E.G., Behl, H.D., Corbin, R.A., Custis, J.T., Waldenmaier, C.M., Starner, D.E., Gulick, S.A., Ashburn, S.R., Whitt, D.L., Souza, E.J., Bockelman, H.E., Long, D.L., Jin, Y., Chen, X., Cambron, S.E. 2009. Registration of ‘USG 3555’ Wheat. Journal of Plant Registrations. 3(3):273-278.

Glynn, N.C., Dixon, L.J., Castlebury, L.A., Szabo, L.J., Comstock, J.C. 2010. PCR assays for the sugarcane rust pathogens Puccinia kuehnii and P. melanocephala and detection of a SNP associated with geographic distribution in P. kuehnii. Plant Pathology. 59:703-711.

Griffey, C.A., Thomason, W.E., Pitman, R.M., Beahm, B.R., Paling, J.J., Chen, J., Fanelli, J.K., Kenner, J.C., Dunaway, D.W., Brooks, W.S., Vaughn, M.E., Hokanson, E.G., Behl, H.D., Corbin, R.A., Custis, J.T., Waldenmaier, C.M., Starner, D.E., Gulick, S.A., Ashburn, S.R., Jones, E.H., Whitt, C.M., Souza, E.J., Bockelman, H.E., Long, D.L., Jin, Y., Chen, X., Cambron, S.E. 2009. Registration of ‘5205’ Wheat. Journal of Plant Registrations. 3(3):283-288.

Griffey, C.A., Thomason, W.E., Pitman, R.M., Beahm, B.R., Paling, J.J., Chen, J., Gundrum, P.G., Fanelli, J.K., Kenner, J.C., Dunaway, D.W., Brooks, W.S., Vaughn, M.E., Hokanson, E.G., Behl, H.D., Corbin, R.A., Hall, M.D., Liu, S., Custis, J.T., Waldenmaier, C.M., Starner, D.E., Gulick, S.A., Ashburn, S.R., Jones, E.H., Whitt, D.L., Bockelman, H.E., Souza, E.J., Brown Guedira, G.L., Kolmer, J.A., Long, D.L., Jin, Y., Chen, X., Cambron, S.E. 2010. Registration of ‘Shirley’ Wheat. Journal of Plant Registrations. 4:38-44.

Griffey, C.A., Thomason, W.E., Pitman, R.M., Beahm, B.R., Paling, J.J., Chen, J., Gundrum, P.G., Fanelli, J.K., Kenner, J.C., Dunaway, D.W., Brooks, W.S., Vaugh, M.E., Hokanson, E.G., Behl, H.D., Corbin, R.A., Hall, M.D., Liu, S., Custis, J.T., Waldenmaier, C.M., Starner, D.E., Gulick, S.A., Ashburn, S.R., Jones, E.H., Whitt, D.L., Bockelman, H.E., Souza, E.J., Brown Guedira, G.L., Kolmer, J.A., Long, D.L., Jin, Y., Chen, X., Cambron, S.E. 2010. Registration of ‘3434’ Wheat. Journal of Plant Registrations. 4:44-49.

Griffey, C.A., Thomason, W.E., Pitman, R.M., Beahm, B.R., Paling, J.J., Chen, J., Fanelli, J.K., Dunaway, D.W., Brooks, W.S., Vaughn, M.E., Hokanson, E.G., Behl, H.D., Corbin, R.A., Hall, M.D., Liu, S., Custis, J.T., Waldenmaier, C.M., Starner, D.E., Gulick, S.A., Ashburn, S.R., Whitt, D.L., Bockelman, H.E., Souza, E.J., Brown Guedira, G.L., Kolmer, J.A., Long, D.L., Jin, Y., Chen, X., Cambron, S.E. 2010. Registration of ‘Jamestown’ Wheat. Journal of Plant Registrations. 4:28-33.

Haley, S.D., Johnson, J.J., Peairs, F.B., Quick, J.S., Stromberger, J.A., Butler, J.D., Miller, H.R., Heaton, E.E., Rudolph, J.B., Seabourn, B.W., Bai, G., Jin, Y., Kolmer, J.A., Chen, X. 2008. Registration of 'Bill Brown' wheat. Journal of Plant Registrations. 2:218-223.

Jin, Y., Szabo, L.J., Carson, M.L. 2010. Century-old Mystery of Puccinia striiformis Life History Solved with the Identification of Berberis as an Alternate Host. Phytopathology. 100(5):432-435.

Xu, S.S., Jin, Y., Klindworth, D.L., Wang, R., Cai, X. 2009. Evaluation and Characterization of Seedling Resistances to Stem Rust Ug99 Races in Wheat-Alien Species Derivatives. Crop Science. 49:2167–2175.

Yu, G., Zhang, Q., Klindworth, D.L., Friesen, T.L., Knox, R., Jin, Y., Zhong, S., Cai, X., Xu, S.S. 2010. Molecular and Cytogenetic Characterization of Aegilops Speltoides Chromosome Segments Carrying Sr39 in the Original Translocation Stock and Derived Wheat Lines. Crop Science. 50:1393–1400.

Olson, E.L., Brown Guedira, G.L., Marshall, D.S., Jin, Y., Mergoum, M., Lowe, I., Dubcovsky, J. Genotyping of U.S. wheat germplasm for presence of stem rust resistance genes Sr24, Sr36 and Sr1RSAmigo. Crop Science. 50:668-675. 2010.

Anderson, J.A., Linkert, G.L., Busch, R.H., Kolmer, J.A., Jin, Y., Dill-Macky, R., Wiersma, J.V., Hareland, G.A., Mcvey, D.V. 2010. Registration of 'RB07' Wheat. Journal of Plant Registrations. 3:175-180.

Glover, K.D., Rudd, J.C., Devkota, R.N., Hall, R.G., Jin, Y., Osborne, L.E., Ingemansen, J.A., Richertsen, J.R., Baltensperger, D.D., Hareland, G.A. 2010. Registration of "Brick" Wheat. Journal of Plant Registrations. 4:22-27.

Maccaferri, M., Sanguineti, M.C., Mantovani, P., Demontis, A., Massi, A., Ammar, K., Kolmer, J.A., Czembor, J.H., Breiman, A., Tuberosa, R. 2010. Association Mapping of Leaf Rust Response in Durum Wheat. Molecular Breeding. 26:189-228.

Kolmer, J.A., Long, D.L., Hughes, M.E. 2010. Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2008. Plant Disease. 94:775-780.

Mantovani, P., Maccaferri, M., Tuberosa, R., Kolmer, J.A. 2010. Virulence Phenotypes and Molecular Genotypes of Puccinia triticina Isolates from Italy. Plant Disease. 94:420-424.

Ordonez, M.E., German, S.E., Kolmer, J.A. 2010. Genetic Differentiation within the Puccinia triticina Population in South America and Comparison with the North American Population Suggests Common Ancestry and Intercontinental Migration. Phytopathology. 100:376-383.

Steffenson, B.J., Jin, Y., Brueggeman, R.S., Kleinhofs, A., Sun, Y. 2009. Resistance to Stem Rust Pathotype TTKSK Maps to the Rgp4/Rpg5 Complex of Chromosome 5H of Barley. Phytopathology. 99:1135-1141.

Yu, L., Liu, S., Anderson, A., Singh, R., Jin, Y., Dubcovsky, J., Brown Guedira, G.L., Bhavani, S., A. Morgounov, He, Z., Heurta-Espino, J., Sorrells, M. 2010. Haplotype Diversity of Stem Rust Resistance Loci in Uncharacterized Wheat Lines. Molecular Breeding. 26:667-680.

Last Modified: 7/24/2014
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