2013 Annual Report
1a.Objectives (from AD-416):
Stripe rust is one of the most important diseases of wheat, causing significant crop losses every year throughout the world. Stripe rust of barley can cause significant yield loss in the western U.S. The long-term goal of this project is to reduce losses in wheat and barley yield and quality caused by stripe rust and assure stable, sustainable production while protecting the environment. Significant progress has been made in recent years in understanding virulence compositions of the pathogen population, identification of new sources of resistance, disease forecasting, and control of the disease using fungicides in recent years. However, more research is needed to monitor dynamic changes of virulent races, obtain better knowledge of resistance genes in elite germplasm, to identify more genes for effective resistance, and to develop molecular markers for use in the efficient incorporation of new genes into wheat and barley cultivars. For the next five years, we will conduct research to achieve the following objectives: 1). Use molecular markers and host plant responses to characterize and differentiate current and emergent virulent races of the stripe rust pathogens of wheat and barley. 2). Determine the distribution, nature, and effectiveness of host plant resistance genes amongst elite wheat and barley germplasm. 3). Identify and determine linkage relationships of new major and minor stripe rust resistance genes, and develop molecular markers for application in wheat and barley breeding efforts. Accomplishment of these objectives will lead to improved knowledge of the disease epidemiology, more resistance genes and germplasm, and more effective technology to achieve sustainable control of stripe rust.
1b.Approach (from AD-416):
Rust survey will be conducted in commercial fields, monitoring nurseries, trap plots, and experimental plots of wheat and barley, as well as wild grasses, during the plant growing-season. Rust samples will be collected by collaborators and us during rust survey. Stripe rust samples will be tested in our laboratory for race identification. New races will be tested on genetic stocks, breeding lines, and commercial cultivars to determine their danger potential. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers will be used to characterize races and populations of the stripe rust pathogens.
All germplasm and breeding nurseries of wheat and barley will be evaluated in two locations: Pullman (eastern Washington) and Mt. Vernon (western Washington) under natural infection of the stripe rust pathogens. Uniform regional nurseries and cultivar monitoring nurseries, which include currently grown cultivars and advanced breeding lines from all U.S. regions and important stripe rust resistance stocks, will be tested with selected races at seedling stage under the low temperature profile (4-20C) and at adult-plant stage under the high temperature profile (10-30C) for determine race-specific all-stage resistance and/or non-race-specific high-temperature adult-plant resistance in wheat and barley germplasm. Stripe rust resistance genes in elite germplasm will be determined or postulated by testing elite lines, together with single resistance gene lines, with a series of races that will be selected to distinguish important genes; analyzing the pedigrees of the elite lines; testing elite lines, together with known gene lines, with molecular markers associated with particular genes; and conducting genetic studies to identify and map new genes.
To identify and map new genes for effective resistance to stripe rust in wheat. Crosses have been made with resistant germplasm lines with a susceptible line. The recombinant inbred lines of these crosses will be phenotyped for stripe rust resistance in fields and also in the greenhouse with selected races and genotyped with resistance gene analog polymorphism (RGAP), SSR, and SNP markers. The phenotypic and genotypic data will be used to map the resistance gene(s) or QTL in each cross. New genes will be identified based on their resistant types, reactions to various races, and chromosomal locations in comparison with previously reported genes. Formerly 5348-22000-014-00D
Under Objective 1A, we conducted field surveys for monitoring stripe rust and other diseases during the 2012-2013 growing season since early November, 2012. Rust forecasts and updates were sent to growers and the cereal crop research community. Recommendations for appropriate control measures were provided to growers based on the forecasts, rust development, and weather conditions. As a result, early starting stripe rust with a potential to cause yield losses between 40 and 50% on susceptible cultivars, and up to 10% on average on commercially grown winter wheat and 5% on spring wheat cultivars was effectively controlled by applying fungicides at the time of herbicide application in the Pacific Northwest. We collected or received more than 500 stripe rust samples from 28 states. Race identification has been completed for all 430 recovered isolates of the 2012 samples and 50% of the 2013 samples. Under Objective 1B, DNA was extracted from the 2012 samples. The standard set of 20 simple sequence repeat (SSR) markers was used to characterize the 2010 to 2012 isolates. In addition, more than 130 single nucleotide polymorphism (SNP) markers were developed based on sequences of secreted protein genes and used to characterize 192 isolates for identifying markers associated to specific virulence genes. Under Objective 2, we evaluated more than 20,000 wheat and 3,000 barley lines for stripe rust resistance in the fields. We have completed data collections from all of the nurseries. The various regional uniform or variety trial nurseries were also tested in the greenhouse with selected stripe rust races. The field and greenhouse data will be used to determine if the individual lines have resistance and what types of resistance. The results will be used by breeding programs to eliminate susceptible lines and select resistant lines for releasing new cultivars. Under Objective 3, we advanced and evaluated progeny populations for several crosses for mapping new genes for stripe rust resistance in wheat. In 2013, we completed studies of mapping a gene in spring wheat ‘PI 178759’ and two genes in ‘PI 192252’ and more than 10 genes or quantitative trait loci in winter wheat ‘Druchamp’ for stripe rust resistance.
Evaluated wheat and barley germplasms and breeding lines for resistance to stripe rust. For better control of cereal rusts, it is critical to identify more germplasms and to select breeding lines of wheat and barley for resistance. During the 2013 growing season, ARS scientists from Pullman, Washington, evaluated more than 20,000 wheat and 3,000 barley lines for resistance to stripe rust in the field and hundreds were also tested in the greenhouse with selected stripe rust races. From the tests, resistant germplasms were selected for further characterizing the resistance types and identifying resistance genes. The data will be used by breeding programs to select lines for releasing new cultivars with effective resistance to stripe rust.
Identified Oregon grapes (Mahonia spp.) as alternate hosts for the stripe rust pathogen. The lack of alternate hosts for the stripe rust fungus to reproduce sexually is an obstacle for genetic characterization of important genes in the pathogen. In addition to the previous confirmation of barberry species as alternate hosts, ARS scientists from Pullman, Washington, identified Oregon grapes that can serve as alternate hosts for the stripe rust pathogen to reproduce sexually under controlled greenhouse conditions. Using the sexual reproduction system, they have established a segregating population for mapping virulence genes and studying other traits of the pathogen. Genetic and molecular studies using the system will integrate genome sequencing data with important traits, leading to a better understanding of the mechanisms of plant-rust pathogen interactions.
Characterized virulence and races of the stripe rust pathogens. The stripe rust fungi evolve to new races and populations that damage previously resistant cultivars and it is important to known races and their virulence patterns in the rust population for control of the diseases. To monitor the pathogen virulence and races, ARS scientists from Pullman, Washington, conducted research to determine races using wheat and barley differential varieties. From the 2012 stripe rust samples, they identified 23 races including two new races of the wheat stripe rust pathogen and 7 races of the barley stripe rust pathogen, and determined their frequencies and distributions in various epidemic regions in the U.S. From the 2013 samples, they have so far identified 12 wheat stripe rust races and 5 barley stripe rust races. The results are useful for growers to select resistant cultivars to grow and breeding programs to choose effective stripe rust resistance genes for developing new cultivars.
Tested fungicides for control of stripe rust. Although stripe rust can be effectively controlled by growing resistant cultivars, fungicides are still needed for reducing damage in fields grown with cultivars without an adequate level of resistance. During the 2013 growing season, ARS scientists from Pullman, Washington, tested 33 fungicide treatments, including several new chemicals, for control of stripe rust on both winter and spring wheat crops. The efficacies, rates and timing of the chemicals for stripe rust control were determined. The results will be useful for the chemical developers to register new fungicides and for growers to use in disease management.
Established a stripe rust website for disseminating scientific information and guiding disease management. Information about stripe rust is largely in journal publications, which is hard for growers and also scientists to find useful information. ARS scientists from Pullman, Washington, established a website (http://striperust.wsu.edu) specifically for stripe rust. The continually enriching website covers almost every aspect of the research and management of the disease. The website has become a major tool for disseminating information for control of the disease and resource for scientists and growers to search for useful information.
Identified and mapped a number of genes in wheat germplasm for resistance to stripe rust. Growing resistant cultivars is the most effective, economical, and environmentally friendly approach for control of stripe rust, but new genes for effective resistance are needed to diversify the resistance sources used in breeding programs to improve the durability of resistance in commercial cultivars. In 2013, ARS scientists from Pullman, Washington, completed the studies of identifying and mapping genes in spring wheat ‘PI 178759’ and ‘PI 192252’ and winter wheat ‘Druchamp’ for high-temperature adult-plant (HTAP) resistance to stripe rust. One gene was identified in PI 178759, two genes in PI 192252, and six quantitative trait loci for HTAP resistance plus five genes for all-stage resistance in Druchamp. These genes and closely linked markers are useful for breeding programs developing stripe rust resistant cultivars.
Xu, L.S., Wang, M., Chen, P., Kang, Z., Hulbert, S., Chen, X. 2012. Molecular mapping of Yr53, a new gene for stripe rust resistance in durum wheat accession PI 480148 and its transfer to common wheat. Theoretical and Applied Genetics. 126:523-533.
Zhao, L., Feng, J., Zhang, C., Xu, X., Chen, X., Sun, Q., Miao, Q., Xu, S., Lin, F. 2012. The dissection and SSR mapping of a high-temperature adult-plant stripe rust resistance gene in American spring wheat cultivar Alturas. European Journal of Plant Pathology. 134:281-288. Available: http://www.springerlink.com/content/t27110v866wg1141/fulltext.pdf.
Carter, A.H., Jones, S.S., Lyon, S.R., Balow, K.A., Shelton, G.B., Higginbotham, R.W., Chen, X., Engle, D.A., Baik, B., Guy, S.O., Murray, T.D., Morris, C.F. 2013. Registration of 'Otto' Wheat. Journal of Plant Registrations. 7(2). Avalable: doi: 10.3198/jpr2012.07.0013cr.
Campbell, J., Zhang, H., Giroux, M.J., Feiz, L., Jin, Y., Wang, M., Chen, X., Huang, L. 2012. A mutagenesis-derived broad-spectrum disease resistance locus in wheat. Theoretical and Applied Genetics. 125:391-404.
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., 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., 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.
Ren, R., Wang, M., Chen, X., Zhang, Z. 2012. Characterization and molecular mapping of Yr52 for high-temperature adult-plant resistance to stripe rust in spring wheat germplasm PI 183527. Theoretical and Applied Genetics. 125:847-857.
Wang, X., Tang, C., Huang, X., Li, F., Chen, X., Zhang, G., Sun, Y., Han, D., Kang, Z. 2012. Wheat BAX inhibitor-1 contributes to wheat resistance to Puccinia striiformis. Journal of Experimental Botany. 63:4571-4584. Available: http://jxb.oxfordjournals.org/.
Zhang, H., Wang, C., Cheng, Y., Chen, X., Han, Q., Huang, L., Wei, G., Kang, Z. 2012. Histological and cytological analyses of adult plant resistance to wheat stripe rust. Plant Cell Reports. 31:2121-2137. Available: http://www.springerlink.com/content/m170011277g6u777/fulltext.pdf.
Christopher, M.D., Liu, S., Hall, M.D., Marshall, D.S., Fountain, M.O., Johnson, J.W., Milus, E.A., Garland Campbell, K.A., Chen, X., Griffey, C.A. 2013. Identification and mapping of adult plant stripe rust resistance in soft red winter wheat VA00W-38. Crop Science. 53:871-879.
Xi, K., Chen, X., Capettini, F., Falconi, E., Yang, R.C., Helm, J.H., Holtz, M.D., Juskiw, P., Kumar, K., Nyachiro, J., Turkington, T.K. 2013. Multivariate analysis of stripe rust assessment and reactions of barley in multi-location nurseries. Canadian Journal of Plant Science. 93:209-219.
Dawit, W., Flath, K., Weber, W., Shumann, E., Roder, M.S., Chen, X. 2012. Postulation and mapping of seedling stripe rust resistance genes in Ethiopian bread wheat cultivars. Journal of Plant Pathology. 94:403-409.
Chen, X., Coram, T., Huang, X., Wang, M., Dolezal, A.L. 2011. Toward understanding molecular mechanisms of durable and non-durable resistance to stripe rust in wheat. Current Genomics. 14:111-126.
Christopher, M.D., Liu, S.Y., Hall, M.D., Marshall, D.S., Fountain, M.O., Johnson, J.W., Milus, E.A., Garland Campbell, K.A., Chen, X., Griffey, C.A. 2013. Identification and mapping of adult plant stripe rust resistance in soft red winter wheat cultivar ‘USG 3555’. Plant Breeding. 132:53-60.
Carlson, G.R., Berg, J.E., Kephart, K.D., Wichman, D.M., Lamb, P.F., Miller, J.H., Stougaard, R.N., Eckhoff, J.L., Riveland, N.R., Nash, D.L., Grey, W.E., Jin, Y., Kolmer, J.A., Chen, X., Bai, G., Bruckner, P.L. 2013. Registration of ‘Judee’ wheat. Journal of Plant Registrations. 7:191-194.
Carlson, G.R., Berg, J.E., Stougaard, R.N., Eckhoff, J.L., Lamb, P.F., Kephart, K.D., Wichman, D.M., Miller, J.H., Riveland, N.R., Nash, D.L., Grey, W.E., Jin, Y., Kolmer, J.A., Chen, X., Bai, G., Bruckner, P.L. 2013. Registration of ‘Bearpaw’ wheat. Journal of Plant Registrations. 7:180-183.
Huang, X., Ma, J., Chen, X., Wang, X., Ding, K., Han, D., Qu, Z., Huang, L.L., Kang, Z. 2012. Expressed sequence tags from a SSH cDNA library identified genes involved in adult-plant resistance to stripe rust in ‘Xingzi 9104’ wheat. Biomed Central (BMC) Plant Biology. 81:26-32.
Chen, X., Evans, C.K., Garner, J.P., Liu, Y. 2013. Evaluation of chemical seed treatments for control of stripe rust in winter wheat, 2012. Plant Disease Management Reports. 7:ST013.
Chen, X., Evans, C.K., Garner, J.P., Liu, Y. 2013. Evaluation of chemical seed treatments for control of stripe rust in spring wheat, 2012. Plant Disease Management Reports. 7:ST012.
Chen, X., Garner, J.P., Liu, Y. 2013. Evaluation of chemical seed treatments for control of stripe rust in wheat under controlled conditions. Plant Disease Management Reports. 7:ST003.
Chen, X., Evans, C.K., Garner, J.P., Liu, Y. 2013. Control of stripe rust of winter wheat with foliar fungicides. Plant Disease Management Reports. 7:CF032.
Chen, X., Evans, C.K., Garner, J.P., Liu, Y. 2013. Control of stripe rust of spring wheat with foliar fungicide. Plant Disease Management Reports. 7:CF031.