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United States Department of Agriculture

Agricultural Research Service

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Location: Wheat Genetics, Quality Physiology and Disease Research

2009 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 2009, 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 appropriately applied fungicides to reduce yield losses. New models were developed to forecast potential stripe rust damage for the PNW and data analyses were finished to determine stripe rust over-wintering and over-summering regions in the US. We completed testing of 331 stripe rust samples obtained from 20 states in 2008 and we have finished about 50% of more than 300 samples in 2009 to identify races. From the 2008 samples, we identified 11 barley stripe rust races and 33 wheat stripe rust races, of which one new race was identified for each of the stripe rust forms. The information on predominant races is essential to breeding for resistance and disease management. To support breeding programs in the US, 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. Growing resistant cultivars in the majority of wheat fields prevented the potentially more than 20% yield losses in the PNW and other regions, which saved growers millions of dollars. Through our intensive testing, cultivars with adequate resistance to stripe rust have been developed. In 2009, we cooperated on the pre-release, final release, and registration of 16 wheat cultivars possessing stripe rust resistance with breeding programs in various states. To identify new genes for stripe rust resistance and develop molecular markers, we completed studies of identifying and mapping two new genes from world wheat germplasms 'PI181434' and 'PI480148' for effective resistance. We made progress on our genetic and molecular mapping studies, and developed new wheat germplasms with high level and durable high-temperature adult-plant (HTAP) resistance to stripe rust through marker-assisted pyramiding of genes previously identified from wheat cultivars 'Alpowa' and 'Express'. To understand molecular mechanisms of stripe rust resistance, we completed studies to identify unique and common defense genes and their biochemical pathways regulated by various stripe rust resistance genes using a custom wheat genechip. We obtained good molecular data to answer the questions why non-race specific HTAP resistance is durable and the other type of resistance is not durable. In cooperation with scientists in UC Davis and other ARS programs, we cloned the Yr36 gene and published the results in Science. We evaluated 15 fungicide treatments to control stripe rust. Better chemicals were identified. We also determined potential yield losses of 24 winter wheat cultivars popular in the PNW and their responses to fungicide. These results are useful for registering new fungicides and for growers to choose best fungicides when needed.

4. Accomplishments
1. Evaluated wheat and barley germplasm and breeding lines for resistance to stripe rust. For control of the rust diseases, it is critical to identify more resistant germplasm and to select resistant breeding lines of wheat and barley for resistance. In 2009, ARS scientists in Pullman, WA evaluated more than 15,000 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 16 wheat cultivars with stripe rust resistance were pre-released, released, or registered by public breeding programs in ARS, Washington, Idaho, Utah, Colorado, and Virginia, as well as new cultivars developed by private breeding programs. Thus leading to reduce yield loss from rust fungus.

2. Identified and mapped two new genes for effective resistance to stripe rust in wheat. Growing wheat 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. Using genetic and molecular mapping approaches, ARS scientists in Pullman, WA identified two new genes from world wheat germplasm that conferring resistance to all races of the wheat stripe rust pathogen identified so far in the U.S. These genes, their molecular markers, and better adapted wheat genotypes carrying the resistance genes will be useful for breeding programs to develop resistant cultivars.

3. Developed new wheat germplasms with high level and durable resistance to rust. Of the different types of resistance to stripe rust, race-specific all-stage resistance usually provides complete resistance, but can become ineffective when new virulent races develop in the rust population. High-temperature adult-plant (HTAP) resistance is non-race specific and durable, but usually does not provide complete control. To improve the level of such durable resistance, ARS scientists in Pullman, WA developed new wheat germplasm with high-levels of HTAP resistance through marker-assisted pyramiding of HTAP resistance genes previously identified from wheat cultivars 'Alpowa' and 'Express’, each having a moderate level of HTAP resistance controlled by different genes. The new wheat germplasm was much higher levels of the durable resistance than that of the parental cultivars. The germplasm will be more useful for breeding programs to develop cultivars with high level and durable resistance to stripe rust. The germplasm will be important to breeding programs developing rust resistant cultivars.

4. Identified common and unique defense genes regulate by various stripe rust resistance genes. For sustainable control to stripe rust, it is essential to know the molecular mechanisms to different types of resistance. ARS researchers in Pullman, WA constructed a custom wheat genechip to study the common and unique defense genes involved in all-stage resistance. This resistance is controlled by 8 genes with diverse functions. There are fewer common genes regulated by different High Temperature adult-plant(HTAP) resistance genes. There is slower and less dramatic change in defense gene expression upon pathogen infection than all-stage resistance. These results will be an aid in achieving sustainable control of stripe rust.

5. Determined frequencies and distributions of stripe rust races and determined mechanisms of virulence changes. The stripe rust fungus is able to evolve into new virulent races that can spread from one region to another to render certain resistant cultivars susceptible and therefore, it is critical to identify new races, determine frequencies and distributions of races, and determine the mechanisms of virulence variation. In 2009, ARS scientists in Pullman, WA completed the study to identify races for more than 330 samples from 20 states, compared the race data with those since 2000, and characterized stripe rust isolates with molecular markers and gene sequences. They identified 33 wheat stripe rust races and 11 barley stripe rust races including one new race in each group, and determined the race frequencies and distributions in various epidemiological regions as well as the whole country. They discovered three major waves of race changes occurred since 2000 and identified asexual hybridization as one of the major mechanisms for the fungal pathogen to change virulences. The results provide guidance for breeding programs to use right genes to develop resistant cultivars, the first molecular evidence for understanding the pathogen evolution, and possible rust genes as targets for developing more effective fungicides.

5. Significant Activities that Support Special Target Populations
Advises on disease control were provided to growers through seminars, field day talks, on-farm visits, phone conversation, and e-mails, which directly benefited growers and field consulting companies, many of which have small farms and business.

Review Publications
Li, Y., Niu, Y.C., Chen, X. 2008. Mapping a stripe rust resistance gene YrC591 in wheat variety C591 with SSR and AFLP marker. Theor. Appl. Genet. 118:339-346.

Fu, D., Uauy, C., Distelfeld, A., Blechl, A.E., Epstein, L., Chen, X., Sela, H., Fahima, T., Dubcovsky, J. 2009. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science. 323:1357-1360.

Lin, F., Chen, X. 2008. Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express. Theor. and Appl. Genet. 118:631-642.

Coram, T., Settles, M.L., Chen, X. 2009. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics 10:253.

Lin, F., Sun, Q., Xu, S., Chen, X., Zhang, L., Zhang, C., Xu, Y., Miao, Q., Qu, B., Li, N. 2009. Identification of wheat-Thinopyrum intermedium alien disomic addition lines conferring resistance to stripe rust. Canadian Journal of Plant Science 89:569-574.

Haley, S.D., Johnson, J.J., Westra, P.H., Peairs, F.B., Stromberger, J.A., Heaton, E.E., Seifert, S.A., Kottke, R.A., Rudolph, J.B., Bai, G., Bowden, R.L., Chen, M., Chen, X., Jin, Y., Kolmer, J.A., Seabourn, B.W. 2009. Registration of 'Thunder CL' Wheat. Journal of Plant Registration. 3(2):181-184.

Zhang, L., Lavery, L., Gill, U., Gill, K., Steffenson, B., Yan, G.P., Chen, X., Kleinhofs,, A. 2008. Loss of function of the barley Nad1 gene, encoding a cation/proton exchanging protein, results in necrosis and defense response to stem rust. Theor. Appl. Genet. 118:385-397.

Wang, X., Tang, C., Zhang, G., Li, Y., Wang, C., Liu, B., Qu, Z., Zhao, J., Han, Q., Huang, L., Chen, X., Kang, Z. 2009. cDNA-AFLP analysis reveals differential gene expression in compatible reaction of wheat challenged with Puccinia striiformis f. sp. tritici. BMC Genomics 10:289.

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.

Last Modified: 2/23/2016
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