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United States Department of Agriculture

Agricultural Research Service

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Location: Wheat Genetics, Quality Physiology and Disease Research

2012 Annual Report

1a. Objectives (from AD-416):
The long term goal of this project is to reduce losses in wheat and barley yield and quality caused by stripe, leaf, and stem rusts, and assure stable,sustainable wheat and barley production while protecting the environment. Over the next five years we will focus on the following objectives: 1)determine factors influencing epidemic development and host-pathogen interactions for rusts, including to identify and monitor emerging races of stripe rust on a national basis and to improve rust prediction and integrated control; 2)evaluate germplasm and breeding lines of wheat and barley for resistance to rusts,including to support breeding programs in developing cultivars with adequate and durable resistance and to identify new sources and genes of effective resistance to stripe rust; and 3)determine the genomic structure and functional genes of the stripe rust pathogen and molecular mechanisms of plant-pathogen interactions.

1b. Approach (from AD-416):
The prevalence, severity, and distribution of rusts will be monitored through disease surveys in commercial fields, monitoring nurseries, and experimental plots of wheat and barley, as well as wild grasses. Stripe rust races will be identified by testing rust samples on wheat and barley differential genotypes. Rust epidemics will be predicted based on environmental and cropping system factors. Geographic regions where stripe rust can over-winter and over-summer will be mapped by analyzing climatic and cropping data. Disease forecasting models will be developed for various epidemic regions by analyzing historical weather and disease data and tested with rust survey data. Fungicide tests will be conducted to identify new effective fungicides. Germplasms and breeding lines of wheat and barley will be evaluated in greenhouses with selected races and in field plots under natural infections of rusts to support breeding programs. New sources and genes of effective resistance to stripe rust will be identified through germplasm evaluation, genetic studies, and molecular mapping. Molecular markers for resistance genes will be developed using resistance gene analog, microsatellite, and other marker techniques. The genomic structure and functional genes of the stripe rust pathogen and molecular mechanisms of plant-pathogen interactions will be determined through constructing physical and functional gene maps. Fingerprinting and end-sequencing bacterial artificial chromosome (BAC) clones will be conducted to construct the physical map, which will be filled with functional genes identified from cDNA clones of the pathogen. Functional genes will be identified by comparing the sequences of full-length cDNA clones to genes in GenBank databases. Molecular markers will be developed using sequences of functional genes and BAC-ends for studying population structures of the stripe rust pathogen. Genes of wheat and the stripe rust pathogen involved in the plant-pathogen interactions will be identified.

3. Progress Report:
This is the final report for the project 5348-22000-014-00D terminated in March 2012. From October 2011 to March 2012, all planned experiments were completed. During the 5 years of the project, progress was made on all three objectives and sub-objectives. Under Objective 1A, we established and improved the systems for characterizing virulence and identifying stripe rust races. We detected 27 to 41 races of wheat stripe rust and 5 to 11 races of barley stripe rust in each year; identified a total of 23 new races; and determined race frequencies, distribution, and dynamics of the races. The information was used to guide breeding programs to select genes for developing cultivars with effective stripe rust resistance. Under Objective 1B, we established monitoring programs for stripe rusts of wheat and barley, which have provided essential information for determining environmental and cropping factors affecting epidemics and for implementing effective disease control measures. We developed new models for predicting potential yield loss caused by stripe rust and used the models for guiding stripe rust management in the Pacific Northwest; and determined over-summer and over-winter regions for the stripe rust pathogen throughout the US. We tested new fungicides for control of stripe rust and almost every registered fungicide used for stripe rust control was resulted from our studies. We developed an integrated stripe rust management system based on cultivar resistance, weather conditions, and timing of fungicide applications. Using the system, potential yield loss of many million dollars caused by stripe rust was prevented every year. Under Objective 2A, we evaluated more than 20,000 wheat and barley lines for stripe rust resistance to support breeding programs. Almost every wheat or barley cultivar released in the U.S. was resulted from our tests and we co-registered 24 new wheat and barley cultivars in the last 5 years. Under Objective 2B, we identified and mapped numerous wheat and barley genes for stripe rust resistance, determined their chromosomal locations, and developed molecular markers, which included 12 wheat genes and 3 barley genes by our program and more than 10 genes together with other programs. We developed more than 70 new wheat lines with effective stripe rust resistance and improved plant types for breeding programs to use. Under Objective 3A, we constructed the first bacterial artificial chromosomal (BAC) library, cDNA library, physic map, and the first stripe rust genechip for the stripe rust pathogen. We generated the first whole genome sequence of the pathogen together with collaborators. Under Objective 3B, we identified the first group of important genes of the stripe rust pathogen and developed 34 molecular markers to characterize rust populations. Using the markers, we demonstrated that the stripe rust fungus is reproduced asexually and barberry does not play an important role in the stripe rust biology and epidemiology, but essential for stem rust. Using the microarray technology, we also identified defense genes in wheat for different types of resistance to stripe rust and rust genes involved in different interactions.

4. Accomplishments
1. Determined the high diversity of stripe rust on grasses. Various grass species can be infected by stripe rust, but the diversity of stripe rust populations on grasses and their relationships to wheat and barley stripe rusts are not clear. ARS scientists in Pullman, WA, completed a study to characterize stripe rust isolates collected from various grasses using virulence tests and molecular markers they developed. They found that both wheat and barley stripe rust forms can infect various grasses, and more importantly that a high proportion of the grass stripe rust collection appear to be hybrids between the wheat and barley stripe rust forms. These results demonstrated that grasses play an important role in generating genetic variations for the stripe rust pathogens and that the wheat and barley stripe rust forms can recombine through asexual reproduction on their common grass hosts.

2. Determined the asexual reproduction of the wheat stripe rust pathogen. The stripe rust pathogen evolves rapidly into different virulence races and molecular groups, but it was not clear whether the fungus can generate variations through sexual recombination on barberry plants like the stem rust pathogen under natural conditions. ARS scientists in Pullman, WA, completed a study to characterize wheat stripe rust collections from various regions of the US with an emphasis on the Palouse region in the Northwest, where barberry plants are present and play an essential role for stem rust epidemics. They found that the Palouse population of the wheat stripe rust pathogen, as well as those in the other regions, was completely reproduced asexually and no sexual reproduction was detected. These results are important for understanding the stripe rust biology and useful for developing disease management strategies focused on the crop and grass hosts of the pathogen.

3. Identified races of the stripe rust pathogens of wheat and barley and determined their frequencies and distributions. The stripe rust fungi evolve to new races and populations that often damage previously resistant cultivars. To monitor the pathogen virulence changes, ARS scientists in Pullman, WA, conducted research to determine races using wheat and barley differential varieties. From 391 stripe rust samples collected from 19 states in 2011, they detected 8 barley stripe rust races and 35 wheat stripe rust races of which 10 new races were identified; and determined their frequencies and distributions in the US. The race information is useful for guiding breeding programs to use effective resistance genes for developing resistant cultivars and growers to choose resistant varieties to grow.

4. Evaluated wheat and barley germplasms and breeding lines for resistance to stripe rust. For better control of cereal rusts, it is critical to develop breeding lines of wheat and barley with resistance. During the 2011-2012 winter and early spring of 2012, ARS scientists in Pullman, WA, completed greenhouse tests the 2011 variety trial nurseries and uniform regional nurseries with selected stripe on rust races in both seedling and adult-plant stages; completed all field and greenhouse test data analysis; and reported the data to collaborators and growers. The rust resistance and susceptibility data were used by various programs to identify resistant germplasm and select resistant lines for release of new cultivars. Relying on these rust resistance evaluations and resistance resources and molecular markers for resistance genes, more than 10 wheat cultivars with stripe rust resistance were pre-released, released, or registered by various breeding programs in late 2011 and early 2012.

5. Identified and mapped new genes for effective resistance to stripe rust. Growing cultivars with genetic resistance is the most effective, economical, and environmentally friendly approach for control of stripe rust, but there are not many available genes effective against all races of the stripe rust pathogen. It is essential to identify new genes for effective resistance. From October 2011 to March 2012, ARS scientists in Pullman, WA, officially named a gene, Yr52, in spring wheat germplasm ‘PI 183527’ originally from India, conferring a high level of high-temperature adult-plant resistance to stripe rust. This gene will be useful for breeding programs to develop resistant cultivars.

6. Tested fungicides for control of stripe rust. Although stripe rust can be effectively controlled by growing resistant cultivars, fungicides are needed for reducing damage in fields grown with susceptible cultivars or cultivars with a level of resistance not adequate under severe epidemic conditions. ARS scientists in Pullman, WA, completed the data analyses for the experiments conducted during the 2011 growing season and reported the data directly to collaborators and submitted the results for publishing in Plant Disease Management Reports. New fungicides that are more effective than the previously registered chemicals were identified and it was determined that under unusually long stripe rust epidemic conditions like in 2011, two or more applications of fungicides are needed to control the disease and maximize profits. The results were used by chemical companies to register new fungicides for control of stripe rust and were used for guiding growers for appropriate and on-time application of fungicides.

Review Publications
Xia, N., Zhan, G., Sun, Y., Lin, Z., Xu, L., Chen, X., Liu, B., Yu, Y., Wang, X., Huang, L., Kang, Z. 2010. TaNAC8, a novel NAC transcription factor gene in wheat, responds to stripe rust pathogen infection and abiotic stresses. Physiological and Molecular Plant Pathology. 74:394-402.

Nirmala, J., Drader, T., Chen, X., Steffenson, B., Kleinhofs, A. 2010. Stem rust spores elicit rapid RPG1 phosphorylation. Molecular Plant-Microbe Interactions. 23:135-1642.

Dong, Y., Yin, C., Hulbert, S., Chen, X., Kang, Z. 2010. Cloning and expression analysis of three secreted protein genes from wheat stripe rust fungus Puccinia striiformis f. sp. tritici. World Journal of Microbiology and Biotechnology. 27:1261-1265.

Riveland, N.R., Berg, J.E., Kephart, K.D., Wichman, D.M., Carlson, G.R., Kushnak, G.D., Stougaard, R.N., Eckhoff, J.L., Nash, D.L., Johnston, M., Grey, W.E., Jin, Y., Chen, X., Bruckner, P.L. 2011. Registration of ‘Decade’ wheat. Journal of Plant Registrations. 5:345-348.

Chen, J., Chu, C., Souza, E.J., Guttieri, M.J., Chen, X., Xu, S.S., Hole, D., Zemetra, R. 2011. Genome-wide identification of QTLs conferring high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici) in wheat. Molecular Breeding. DOI:10.1007/s11032-011-9590-x.

Zhang, H., Wang, C., Cheng, Y., Wang, X., Li, F., Han, Q., Xu, J., Chen, X., Huang, L., Wei, G., Kang, Z. 2011. Histological and molecular studies of the non-host interaction between wheat and Uromyces fabae. Planta. 234:979-991.

Lu, N., Chen, C., Chen, X., Wang, J., Zhan, G., Huang, L., Kang, Z. 2011. Spatial genetic diversity and interregional spread of Puccinia striiformis f. sp. tritici in the Northwest China. European Journal of Plant Pathology. 131:685-693.

Wang, M., Chen, X., Xu, L., Cheng, P., Bockelman, H.E. 2011. Registration of 70 Common Spring Wheat Germplasm Lines Resistant to Stripe Rust. Journal of Plant Registrations. 6:104-110.

Fang, T., Garland Campbell, K.A., Liu, Z., Chen, X., Wan, A., Li, S., Liu, Z., Cao, S., Chen, Y., Bowden, R.L., Carver, B., Yan, L. 2011. Stripe rust resistance in the wheat cultivar Jagger is due to YR17 plus a novel QTL. Crop Science. 51:2455-2465.

Zhang, G., Li, Y., Wang, X., Xia, N., Dong, Y., Zhang, Y., Guo, J., Wei, G., Huang, L., Chen, X., Kang, Z. 2012. Molecular cloning and characterization of two hypersensitive induced reaction genes from wheat infected by stripe rust pathogen. Biologia Plantarum. 55(4): 696-702.

Gao, Y., Sun, Q., Wang, R., Feng, J., Lin, F., Cui, N., Chen, X., Xu, S., Bai, Y., Xu, X. 2011. Inheritance of stripe rust resistance to predominant Chinese races in six spring wheat cultivars from the Pacific Northwest of the United States. Cereal Research Communications. 39:44-52.

Feng, H., Wang, X., Sun, Y., Wang, X., Chen, X., Guo, J., Duan, Y., Huang, L., Kang, Z. 2010. Cloning and characterization of a calcium binding EF-hand protein gene TaCab1 from wheat and its expression in response to Puccinia striiformis f. sp. tritici and abiotic stresses. Molecular Biology Reports. 38:3857-3866.

Huang, X., Chen, X., Coram, T., Wang, M., Kang, Z. 2011. Gene expression profiling of Puccinia striiformis f. sp. tritici during development reveals a highly dynamic transcriptome. Journal of Genetics and Genomics. 38:357-371.

Cantu, D., Govindarajulu, M., Wang, M., Chen, X., Kojima, K.K., Jurka, J., Michelmore, R.W., Dubcovsky, J. 2011. Next generation sequencing provides rapid access to the genome of wheat stripe rust. PLoS One. 6(8)e24230. doi:10.1371/journal.pone.0024230.

Last Modified: 2/23/2016
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