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United States Department of Agriculture

Agricultural Research Service

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2011 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. Formerly 5348-22000-010-00D (3/07).

3. Progress Report
In 2011, we conducted monitoring and forecasting for stripe rust and provided disease updates to growers in the Pacific Northwest (PNW). Through cooperators in other states, stripe rusts of wheat and barley were monitored throughout the US. As a result of our disease monitoring, accurate forecasting, timely alerts, and advices for disease management, wheat growers implemented appropriate applications of fungicides, which reduced potentially huge yield loss under the long, widespread and severe stripe rust epidemic. New models were tested to forecast stripe rust damage for the PNW and all data analyses were finished to identify regions in the U.S. where the fungus can survive summer and/or winter. We completed testing 412 stripe rust samples obtained from 24 states in 2010 and have finished about 50% of more than 400 samples in 2011 to identify races. From the 2010 samples, we detected 6 barley stripe rust races and 51 wheat stripe rust races, using a new set of 20 wheat lines each with a single resistance gene. Six new races were identified using the old set of 20 differential cultivars. The races identified with the new set of single-gene line differentials provide direct information for virulence and avirulence to resistance genes and the information on predominant races and distribution is essential to breeding for resistance and disease management. In 2011, we conducted experiments and surveys to determine importance of barberry plants as alternate hosts for stripe rust. Our preliminary results show that barberry plants are essential for stem rust, but not for stripe rust in the U.S. Pacific Northwest. To support breeding programs in the U.S., we tested more than 20,000 wheat and barley entries for stripe rust resistance. The data were provided to breeders for developing resistant cultivars and to growers for choosing resistant cultivars to grow. Through our intensive testing, cultivars with effective and durable resistance to stripe rust have been developed. In 2011, we cooperated on the pre-release, final release, and registration of more than 10 wheat cultivars possessing stripe rust resistance with breeding programs in various states. In 2011, we completed the study for identifying and mapping a new gene in the ‘Yr8 NIL’ and ‘Compair’ wheat lines for high-temperature adult-plant (HTAP) resistance; completed studies to identify and map three new genes in two world wheat germplasm lines (two for HTAP and one for all-stage resistance to stripe rust); and deposited 70 new germplasm lines to the USDA-ARS Small Grain Collections. We also made crosses with more than 100 winter wheat lines selected based on our evaluation of world germplasms to identify more genes for effective resistance to stripe rust. We evaluated 31 fungicide treatments to control stripe rust. Effective fungicides were identified. We determined yield losses of 24 winter and 16 spring wheat cultivars grown in the PNW and their responses to fungicides. The data will be useful for registering new fungicides and for advising growers to determine whether or not to use fungicides on cultivars they grow.

4. Accomplishments
1. Evaluated wheat and barley germplasms and breeding lines for resistance to stripe rust. For control of cereal rusts, it is critical to identify more germplasms and to select breeding lines of wheat and barley for resistance. In 2011, ARS scientists in Pullman, WA, evaluated more than 17,000 wheat and 5,000 barley entries for stripe rust resistance. From the evaluation studies, we identified new germplasm and advanced breeding lines with stripe rust resistance. The data and information of stripe rust evaluation were provided to breeding programs for eliminating potential susceptible cultivars, and developing new cultivars with adequate resistance. Through our rust resistance evaluation and providing 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 2011.

2. Developed new wheat germplasms with effective resistance to stripe rust. Resistant germplasm usually has undesirable plant types or agronomic traits, which may discourage breeders to use this material in breeding programs. In 2011, ARS scientists in Pullman, WA, completed a study to select wheat lines from our genetic and molecular mapping populations and registered 70 new germplasms. These lines have effective resistance to stripe rust, most likely controlled by different resistance genes, and also more desirable agronomic traits than their resistance donor source. This new germplasm is valuable for breeding programs to develop cultivars with a great diversity of effective resistance genes.

3. 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. In 2011, ARS scientists in Pullman, WA, completed the study to identify and map a gene in the ‘Yr8’ isogenic line and ‘Compare’ for durable high temperature adult plant (HTAP) resistance and completed the studies for identifying and mapping two genes for HTAP resistance in spring wheat germplasms ‘PI 178759’ and ‘PI 183527’. These genes will be useful for breeding programs to develop resistant cultivars.

4. Developed a new set of wheat differentials and identified new races of the stripe rust pathogen. The stripe rust fungus is able to evolve into new virulent races and races also can spread from one region to another to render race-specific resistant cultivars susceptibile. Therefore, it is critical to identify new races, determine frequencies and distributions of races. In 2011, ARS scientists in Pullman, WA, completed the study to identify races for 412 samples collected from 24 states in 2010. We identified 51 wheat stripe rust races including 6 new races identified with the old set of cultivar differentials and 6 barley stripe rust races; and determined the race frequencies and distributions in various epidemiological regions. The information of races identified with the new differential set is more useful in guiding breeding programs to use effective genes to develop resistant cultivars.

5. Determined regions where the stripe rust pathogen can survive winter and/or summer throughout the U.S. Because stripe rust epidemics in a region depend upon how close it is to regions where the pathogen can survive the winter and/or summer, it is important to identify rust survival regions. In 2011, we completed a study to identify potential summer and winter survival regions of the stripe rust pathogen by analyzing historical weather data and cropping systems for more than 450 locations covering the entire inland U.S. We determined geographic regions where the pathogen is able to survive the winter or summer. The new information closely related to the stripe rust epidemiology should be useful for control of the disease in various areas through deploying cultivars with different types and genes of resistance, cultural practice, and use of fungicides.

6. Developed molecular markers to studying genetic variation and evolution of the stripe rust pathogen. Developed molecular markers to study genetic variation and evolution of the stripe rust pathogen. For sustainable control of stripe rust, it is essential to monitor genetic changes occurring in populations and understand the evolutionary mechanisms of the pathogen. In 2011, ARS scientists in Pullman, WA, developed more than 30 EST-derived simple sequence repeats (SSR) markers through characterization of our cDNA libraries constructed from the pathogen spores. We used the markers to study the U.S. and world populations. The mostly co-dominant SSR markers are more useful for characterizing isolates and populations of the rust fungus that has two nuclei in their infectious spores and structures. We have been using the markers to determine stripe rust population changes in the U.S. and the markers will be used by rust scientists to monitor population changes and understand evolutionary mechanisms of the pathogen in the world.

Review Publications
Chen, X., Penman, L., Wan, A., Cheng, P. 2010. Virulence races of Puccinia striiformis f. sp. in 2006 and 2007 and development of wheat stripe rust and distributions, dynamics, and evolutionary relationships of races from 2000 to 2007 in the United States. Canadian Journal of Plant Pathology. 32:315-323.

Kokhmetova, A., Chen, X., Rsaliev, S. 2010. Identification of Puccinia striiformis f. sp. tritici, characterization of wheat cultivars for resistance, identification of resistant germplasm, and inheritance of resistance to stripe rust in Kazakhstan wheat cultivars. Asian and Australasian Journal of Plant Science and Biotechnology. (Special Issue 1):64-70.

Chen, J., Souza, E.J., Bosque-Perez,, N., Guttieri, M., Obrien, K., Windes, J., Guy, S., Brown, B., Chen, X., Zemetra, R. 2010. Registration of ‘UI Winchester’ wheat. Crop Science. 4:224-227.

Li, Q., Chen, X., Wang, M., Jing, J. 2010. Yr45, A new wheat gene for stripe rust resistance mapped on the long arm of chromosome 3D. Theoretical and Applied Genetics. 122:189-197.

Chen, X., Wood, D.A. 2011. Control of stripe rust of winter wheat with foliar fungicides, 2010. Plant Disease Management Reports. 5:CF004.

Sharma-Poudyal, D., Chen, X. 2011. Models for predicting potential yield loss of wheat caused by stripe rust in the US Pacific Northwest. Phytopathology. 101:544-554.

Lowe, I., Jankuloski, L., Chao, S., Chen, X., See, D.R., Dubcovsky, J. 2011. Mapping and validation of Yr48 and other QTL conferring partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theoretical and Applied Genetics. 123:143-157.

Last Modified: 2/23/2016
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