Research Project: Improving Control of Stripe Rusts of Wheat and Barley through Characterization of Pathogen Populations and Enhancement of Host Resistance

Location: Wheat Health, Genetics, and Quality Research

2018 Annual Report

Objectives
Stripe rust is one of the most important diseases of wheat throughout the U.S. and stripe rust of barley causes significant yield losses in western U.S. Significant progress has been made in understanding biology of the pathogen, virulence compositions of the pathogen population, identification of new sources of resistance, disease forecasting, and control of the disease using fungicides. However, research is needed to develop more effective strategies for sustainable control of stripe rusts. Therefore, this project has the following objectives for the next five years: Objective 1: Monitor and characterize stripe rust pathogen populations for providing essential information to growers for implementing appropriate measures to reduce damage on wheat and barley. Subobjective 1A: Identify virulent races of stripe rust pathogens to determine effectiveness of resistance genes in wheat and barley. Subobjective 1B: Develop molecular markers and characterize stripe rust pathogen populations to identify factors and mechanisms of pathogen dynamics for developing new management strategies. Objective 2: Enhance resistance in wheat and barley cultivars for sustainable control of stripe rusts. Subobjective 2A: Identify and map new genes for stripe rust resistance, and develop new germplasm for use in breeding programs. Subobjective 2B: Screen breeding lines for supporting breeding programs to develop wheat and barley cultivars with adequate and durable resistance to stripe rust. Accomplishment of these objectives will lead to improved knowledge of the disease epidemiology for developing more effective control strategies, more resistance genes and resistant germplasm to be used by breeders to develop stripe rust resistant wheat and barley cultivars, and more effective technology to be used by wheat and barley growers to achieve sustainable control of stripe rust.

Approach
Monitoring the prevalence, severity, and distribution of stripe rust and identify races of the pathogens, commercial fields, monitoring nurseries, trap plots, and experimental plots of wheat and barley, as well as wild grasses, will be surveyed during the plant growing-season. Recommendations will be made based on stripe rust forecasts and survey data to control stripe rust on a yearly basis. Rust samples will be collected by collaborators and ourselves during surveys and data-recording of commercial fields, experimental plots, and monitoring nurseries. Stripe rust samples will be tested in our laboratory for race identification. New races will be tested on genetic stocks, commercial cultivars, and breeding lines to determine their impact on germplasm and production of wheat and barley. Isolates of stripe rust pathogens will also be characterized using various molecular markers to determine population structure changes. To identify new genes for resistance to stripe rust in wheat, the mapping populations, which have been and will be developed in our laboratory, will be phenotyped for response to stripe rust in fields and/or greenhouse and genotyped using different approaches and marker techniques such as simple sequence repeat (SSR), single-nucleotide polymorphism (SNP), and /or genotyping by sequencing (GBS) markers. Linkage maps will be constructed with the genotype data using software Mapmaker and JoinMap. Genes conferring qualitative resistance will be mapped using the phenotypic and genotypic data using JoinMap or MapDisto, and quantitative trait locus (QTL) mapping will be conducted using the composite interval mapping program in the WinQTL Cartographer software. Relationships of genes or QTL to previous reported stripe rust genes will be determined based on chromosomal locations of tightly linked markers, type of resistance and race spectra, and origins of the resistance gene donors. Allelism tests will be conducted with crosses made between lines with potentially new gene with previously reported genes in the same chromosomal arms to confirm the new genes. A homozygous line carrying a identified new gene with improved plant type and agronomic traits will be selected from the progeny population using both rust testing and molecular markers. Lines with combinations of two genes in a same chromosome will be selected and confirmed using phenotypic and marker data. The new germplasm lines will be provided to breeding programs for developing resistant cultivars. To support breeding programs for developing cultivars with stripe rust resistance, wheat and barley nurseries will be evaluated in two locations: Pullman (eastern Washington) and Mount Vernon (western Washington) under natural infection of the stripe rust pathogens. Variety trials and uniform regional nurseries will also be tested in seedling and adult-plant stages with selected races of the stripe rust pathogen under controlled greenhouse conditions. The data will be provided to breeding programs for releasing new cultivars with adequate level and potentially durable stripe rust resistance.

Progress Report
Progress was made on the two objectives and four sub-objectives, all of which fall under National Program 303 Plant Diseases. Sub-objective 1A: All tests for identifying races from the stripe rust collections in the U.S. in 2017 were completed and results reported to the cereal community (researchers, developers, and growers). During the 2018 growing season, field surveys were conducted, and recommendations made for control of stripe rust. Stripe rust samples were collected in the Pacific Northwest. Through collaborators in other regions, more than 220 stripe rust samples from 14 states were received and more are expected as the season progresses. These samples were used to inoculate susceptible wheat plants for recovering and increasing spores. Each isolate was tested on the set of wheat or barley differentials for identifying races of the wheat or barley stripe rust pathogen. From the 2017 samples, 64 races were identified (including 31 new races) of the wheat stripe rust pathogen and 14 races (including 5 new races) of the barley stripe rust pathogen. The distribution and frequency of the races and virulence factors were determined. From the 2018 collection, so far eleven races (including three new races) of the wheat stripe rust pathogen have been identified. Based on the virulence data of the races, resistance genes, such as Yr5, Yr15, and others, were identified as effective against all populations of the wheat stripe rust pathogen in the United States and can be used in breeding programs for developing stripe rust resistant wheat cultivars. Similar information has also been obtained for the barley stripe rust pathogen and barley resistance genes. The progress is according to schedule. Sub-objective 1B: The genomes of more stripe rust isolates were re-sequenced. The genome sequences were used to develop molecular markers and characterize the stripe rust population. In addition to the previously developed simple sequence repeat (SSR) and single-nucleotide polymorphism SNP markers, we designed more than 700 SNP markers based on secreted protein (SP) genes for identifying virulence genes. Eighteen SSR markers have been identified as a core set of markers and used to characterize the historical U.S. collections of the wheat and barley stripe rust pathogens since 1968. Tests and data analysis were completed for the collections from 1968-2009, the marker tests for the collections from 2010 to 2015, and DNA extraction from the collections of 2016 and 2017. Marker tests for the 2016 and 2017 collection are being conducted. Based on the marker data, several events of stripe rust pathogen introduction and different population structures in various epidemiological regions have been identified. Through whole genome sequencing, genomic differences between the wheat and barley stripe rust pathogens were identified and the genomic mechanisms for the pathogen evolution determined. The genomic differences can be used to develop specific markers for more clearly differentiating the wheat and barley stripe rust forms and determining mechanisms for understanding why wheat is generally resistant to the barley stripe rust form and barley is generally resistant to the wheat form. Using the advanced sequencing technique, more than 120 isolates generated through sexual reproduction of a wheat stripe rust isolate on barberry, an alternate host plant for the stripe rust fungus, were sequenced. The quality of these sequences was much better than their previously sequenced sexual population due to using this improved and cost-effective technology. Based on the virulence phenotype and sequence genotype data of the sexual population, improved linkage groups representing different chromosomes were developed. Virulence genes were mapped and candidate genes identified for virulence. Sub-objective 2A: Twelve wheat mapping populations were planted at Pullman and Mount Vernon, Washington, for phenotyping stripe rust responses to map resistance genes in these crosses. Bulk F4 generations of both winter and spring types from 40 crosses made by crossing 40 winter wheat varieties to a susceptible spring wheat variety to advance the generation were also planted. Stripe rust responses have been recorded and 200 heads have been tagged to develop a segregating population for each cross. The same will be done for the spring type population for each cross in July. These populations will be used for further stripe rust phenotyping and marker genotyping to identify and map new stripe rust resistance genes and develop new germplasm with resistance genes. In addition, more than 800 winter and 900 spring U.S. wheat varieties for stripe rust phenotyping were plated in the fields and the winter wheat data completed. The collection of stripe rust data of all spring nurseries will be completed in July. These two panels of wheat germplasm have also been tested with selected stripe rust races in the greenhouse. DNA has been extracted from each variety and will be used in molecular marker genotyping. The stripe rust phenotype and marker genotype data will be used to identify and map stripe rust resistance genes in various wheat varieties. A study has been completed to identify and map genes for high-level and durable high-temperature adult-plant (HTAP) resistance to stripe rust in Pacific Northwest soft white winter wheat variety ‘Skiles’. In this study, six genes were identified on wheat chromosomes 3BS, 4BL, 1BL, 5AL, 6B and 7DL. The first two genes had major effects and were detected in all environments and the latter four genes had minor effects. Molecular markers of these genes were used in selection of breeding lines carrying the resistance genes for developing new varieties. A study for pyramiding stripe rust resistance genes Yr15 and Yr64 was completed. These two genes each were previously identified from different wheat varieties conferring resistance to all tested stripe rust races and mapped to a single chromosome arm (1BS). In this study, new wheat lines with the combination of the two genes closely linked in 1BS were developed and validated. These new wheat lines are more efficient than the original donor wheat lines for incorporating the tightly linked effective resistance genes together into new wheat varieties. Sub-objective 2B: More than 35,000 wheat and barley entries were planted in the fields near Pullman and Mount Vernon, Washington, for screening of resistance to stripe rust. Some of the nurseries in three additional locations were also planted. For the winter nurseries, note-taking at the Mount Vernon, Walla Walla, Lind, and Pullman locations has been completed. For the spring nurseries, note-taking at Lind and Walla Walla has been completed. The second note-taking at Mount Vernon will be completed before the end of June and at Pullman in July. The seedling and adult-plant tests of the various regional winter nurseries has been completed and testing the various spring regional nurseries with selected races in the greenhouse has begun. The data will be provided to various breeding programs throughout the country for releasing new wheat and barley varieties with stripe rust resistance.

Accomplishments
1. Developed new wheat germplasm lines with pyramided genes on the same chromosome arm for resistance to stripe rust. Growing resistant varieties is the most effective, economical, easy-to-use, and environmentally friendly approach to control stripe rust, and developing resistant germplasm is essential for improving stripe rust resistance in commercial varieties. ARS scientists in Pullman, Washington developed and validated wheat lines carrying Yr15 and Yr64 by crossing the donor lines, selecting from the progeny lines through phenotyping and marker-assisted selection, and validating the selected lines with more molecular markers. Both Yr15 and Yr64, previously mapped to the short arm of chromosome 1B, provide resistance to all tested races of the wheat stripe rust pathogen. The new lines also have improved agronomic traits compared to the original donors through multi-year selections in the fields and marker validation for their increased chromosomal segments from the recurrent parent. Due to their tight linkage in the new germplasm lines, the two effective genes will be kept together when the lines are crossed with elite wheat varieties. Use of the two-gene lines will be more efficient than the original single-gene lines for developing new wheat varieties with the two genes or combining with additional genes for high-level, durable resistance to stripe rust.

2. Mapping the stripe rust resistance genes in winter wheat variety Skiles. Stripe rust is best controlled through growing resistant varieties, and genes with tightly linked molecular markers are needed for breeding programs to develop new varieties with durable and high-level resistance. ARS scientists in Pullman, Washington, mapped six genes for the high-level, non-race specific high-temperature, adult-plant (HTAP) resistance in Pacific Northwest winter wheat variety Skiles and determined their different effect levels and interactions to growth stage and temperature. This work demonstrates the effective approach of combining several genes to achieve an adequate level of durable type resistance. They developed markers for the resistance genes using the new Komptitive allele-specific PCR (KASP) technique and validated the usefulness of the markers by testing breeding lines. The genes identified in this study can be used in breeding programs for developing new stripe rust resistant varieties. The developed markers can be used in marker-assisted selection to make breeding for stripe rust resistance more efficient.

3. Identifying new races of the stripe rust pathogen. The stripe rust pathogen evolves rapidly to produce new races that may damage previously resistant varieties, thus, it is essential to determine races and their virulence patterns in the rust population. From the 2016 stripe rust samples collected from 20 states of the U.S. plus Ontario, Canada, ARS scientists in Pullman, Washington, identified 64 races including 31 new races of the wheat stripe rust pathogen and 14 races including 5 new races of the barley stripe rust pathogen. They determined the frequencies and distributions of these races and individual virulence factors in various states and epidemic regions. Based on the results, isolates representing predominant and different groups of races were selected for screening wheat and barley germplasm for developing new varieties with effective resistance to stripe rust. The results will be used for guiding breeding programs to select effective genes in developing new varieties and for implementing management strategies through selecting resistant varieties to grow and applying fungicides when necessary.

4. Testing fungicides for control of stripe rust and wheat varieties for response to fungicide application. Although stripe rust can be effectively controlled by growing resistant varieties, fungicides are still needed for reducing damage in fields grown with varieties without an adequate level of resistance. During the 2018 growing season, ARS scientists from Pullman, Washington, tested thirty-one fungicide treatments, including new chemicals, for control of stripe rust on both winter and spring wheat crops. They also tested twenty-three winter wheat and twenty-three spring wheat varieties, which were selected based on their acreage grown in previous years in the Pacific Northwest, plus a highly susceptible variety as a check for each crop, to determine their yield losses caused by stripe rust and responses to fungicide application. The efficacies, rates, and timing of the fungicides for stripe rust control and potential yield loss to stripe rust and yield increase to fungicide application for each variety were determined. The results will be used by chemical developers to register new fungicides and for growers to have more choices of chemicals. The data of fungicide efficacy and variety potential yield loss are the essential components for the integrated stripe rust management strategy based on individual varieties.

Review Publications
Chen, X., Kang, Z. 2017. Introduction: History of research, symptoms, taxonomy of the pathogen, host range, distribution, and impact of stripe rust. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.1-33.
Wan, A., Wang, X., Kang, Z., Chen, X. 2017. Variability of the stripe rust pathogen. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.35-154.
Kang, Z., Tang, C., Zhao, J., Cheng, Y., Liu, J., Guo, J., Wang, X., Chen, X. 2017. Wheat-Puccinia striiformis interactions. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.155-282.
Chen, X. 2017. Stripe rust epidemiology. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.283-352.
Wang, M., Chen, X. 2017. Stripe rust resistance. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.353-558.
Chen, X., Kang, Z. 2017. Integrated control of stripe rust. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p.559-599.
Chen, X., Kang, Z. 2017. Stripe rust research and control: Conclusions and perspectives. In: Chen, X., Kang, Z., editors. Stripe Rust. Dordrect, The Netherlands: Springer Science. p. 601-630.
Liu, T., Wan, A., Liu, D., Chen, X. 2017. Changes of races and virulence genes of Pucccinia striiformis f. sp. tritici, the wheat stripe rust pathogen, in the United States from 1968 to 2009. Plant Disease. 101(8):1522-1532.
Wang, J., Tao, F., Tian, W., Chen, X., Xu, X., Hu, X. 2017. Wheat WRKY transcription factor genes TaWRKY49 and TaWRKY62 confer differential high temperature seedling-plant resistance to Puccinia striiformis f. sp. tritici. PLoS One. https://doi.org/10.1371/journal.pone.0181963.
Muleta, K.T., Rouse, M.N., Rynearson, S., Chen, X., Buta, B.G., Pumphrey, M. 2017. Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-017-1082-7.
Carter, A.H., Jones, S.S., Balow, K.A., Shelton, G.B., Burke, A.B., Higginbotham, R.W., Chen, X., Engle, D.A., Murray, T.D., Morris, C.F. 2017. Registration of ‘Jasper’ soft white winter wheat. Journal of Plant Registrations. 11(3):263-268.
Carter, A.H., Jones, S.S., Lyon, S.R., Balow, K.A., Shelton, G.B., Burke, A.B., Higginbotham, R.W., Schillinger, W.F., Chen, X., Engle, D.A., Morris, C.F. 2017. Registration of ‘Sequoia’ hard red winter wheat. Journal of Plant Registrations. 11(3):269-274.
Carter, A.H., Kidwell, K.K., Balow, K.A., Burke, A.B., Shelton, G.B., Higginbotham, R.W., Demacon, V., Lewien, M.J., Chen, X., Engle, D.A., Morris, C.F. 2017. Registration of 'Earl’ wheat. Journal of Plant Registrations. 11(3):275-280.
Muleta, K.T., Bulli, P., Zhang, Z., Chen, X., Pumphrey, M. 2017. Unlocking diversity in germplasm collections by genomic selection: a case study based on quantitative adult plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in spring wheat. The Plant Genome. https://doi:103835/plantgenome2016.12.0124.
Wu, J., Wang, Q., Chen, X., Liu, S., Li, H., Zen, Q., Mu, J., Dai, M., Han, D., Kang, Z. 2017. Development and validation of SNP markers for QTL underlying resistance to stripe rust in common wheat P10057. Plant Disease. 101(12):2079-2087.
Dong, Z., Hegarty, J.M., Zhang, J., Zhang, W., Chao, S., Chen, X., Zhou, Y., Dubcovsky, J. 2017. Validation and characterization of a QTL for adult plant resistance to stripe rust on wheat chromosome arm 6BS (Yr78). Journal of Theoretical and Applied Genetics. 130(10):2127-2137.
Liu, W., Maccaferri, M., Chen, X., Pumphrey, M., Laghetti, G., Pignone, D., Tuberosa, R. 2017. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum). Theoretical and Applied Genetics. 130(11):2249-2270.
Xia, C., Wang, M., Cornejo, O.E., Jiwan, D.A., See, D.R., Chen, X. 2017. Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms and identify candidate avirulence genes in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. BMC Genomics. https://doi:10.3389/fmicb.2017.02394.
Wu, J., Wang, Q., Xu, L., Chen, X., Li, B., Mu, J., Zen, Q., Huang, L., Han, D., Kang, Z. 2018. Combining SNP genotyping array with bulked segregant analysis to map a gene controlling adult-plant resistance to stripe rust in wheat line 03031-1-5 H62. Phytopathology. 108(1):103-113.
Yuan, C., Wang, M., Skinner, D.Z., See, D.R., Xia, C., Guo, X., Chen, X. 2018. Inheritance of virulence, construction of a linkage map, and mapping virulence genes in puccinia striiformis f. sp. tritici by virulence and molecular characterization of a sexual population through genotyping-by-sequencing. Phytopathology. 108(1):133-141.
Kidwell, K.K., Pumphrey, M.O., Kuehner, J.S., Shelton, G.B., Demacon, V.L., Rynearson, S., Chen, X., Guy, S.O., Engle, D.A., Baik, B., Morris, C.F., Bosque-Perez, N.A. 2018. Registration of 'Glee' hard red spring wheat. Journal of Plant Registrations. 12(1):60-65.
Chen, J., Wheeler, J., Zhao, W., Klassen, N., O'Brien, K., Marshall, J.M., Jackson, C., Schroeder, K., Chen, X., Higginbotham, R. 2018. Registration of ‘UI Sparrow’ wheat. Journal of Plant Registrations. 12(1):79-84.
Belcher, A.R., Cuesta-Marcos, A., Smith, K.P., Mundt, C.C., Chen, X., Hayes, P.M. 2018. Barley stripe rust resistance QTL identified in facultative winter 6-rowed malt barley breeding programs by genome-wide association studies. Crop Science. 58(1):103-119.
Godoy, J., Rynearson, S., Chen, X., Pumphrey, M. 2018. Genome-wide association mapping of loci for resistance to stripe rust in North American elite spring wheat germplasm. Phytopathology. 108(2):234-245.
Wang, L., Zheng, D., Zuo, S., Chen, X., Zhuang, H., Huang, L., Kang, Z., Zhao, J. 2018. Inheritance and linkage of virulence genes in chinese predominant race CYR32 of the wheat stripe rust pathogen Puccinia striiformis f. sp. tritici. Frontiers in Plant Science. https://doi:10.3389/fpls.2018.00120.
Tao, F., Wang, J., Guo, Z., Hu, J., Xu, X., Yang, J., Chen, X., Hu, X. 2018. Large-scale transcriptomic analysis of wheat high-temperature seedling plant resistance to Puccinia striiformis f. sp. tritici revealed non-race-specific resistance. New Phytologist. https://doi:10.3389/fpls.2018.00240.
Chen, X., Evans, C.K., Sprott, J.A., Liu, Y. 2018. Evaluation of foliar fungicide treatments for control of stripe rust on winter wheat in 2017. Plant Disease Management Reports. https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2018/CF073.pdf.
Chen, X., Evans, C.K., Sprott, J.A., Liu, Y. 2018. Evaluation of foliar fungicide treatments for control of stripe rust on spring wheat in 2017. Plant Disease Management Reports. https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2018/CF074.pdf.
Chen, X., Evans, C.K., Sprott, J.A., Liu, Y. 2018. Evaluation of Pacific Northwest winter wheat cultivars to fungicide application for control of stripe rust in 2017. Plant Disease Management Reports. https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2018/CF075.pdf.
Chen, X., Evans, C.K., Sprott, J.A., Liu, Y. 2018. Evaluation of Pacific Northwest spring wheat cultivars to fungicide application for control of stripe rust in 2017. Plant Disease Management Reports. https://www.plantmanagementnetwork.org/pub/trial/pdmr/reports/2018/CF076.pdf.
Kidwell, K.K., Kuehner, J.S., Marshall, J., Shelton, G.B., Demacon, V.L., Rynearson, S., Chen, X., Guy, S.O., Engle, D.A., Baik, B.K., Morris, C.F., Pumphrey, M.O. 2018. Registration of ‘Dayn’ hard white spring wheat. Journal of Plant Registrations. 12(2):222-227.
Feng, J., Wang, M., See, D.R., Chao, S., Zheng, Y., Chen, X. 2018. Characterization of gene Yr79 and four additional QTL for all-stage and high-temperature adult-plant resistance to stripe rust in spring wheat PI 182103. Theoretical and Applied Genetics. 108(6):737-747.
Farrakh, S., Wang, M., Chen, X. 2018. Pathogenesis-related protein genes involved in race-specific all-stage resistance and non-race specific high-temperature adult-plant resistance to Puccinia striiformis f. sp. tritici in wheat. Journal of Integrative Agriculture. https://doi:10.1016/S2095-3119(17)61853-7.
Liu, L., Wang, M., Feng, J., See, D.R., Chao, S., Chen, X. 2018. Combination of all-stage and high-temperature adult-plant resistance QTL confers high level, durable resistance to stripe rust in winter wheat cultivar Madsen. Theoretical and Applied Genetics. https://doi 10.1007/s00122-018-3116-4.
Xia, C., Wang, M., Yin, C., Cornejo, O.E., Hulbert, S., Chen, X. 2018. Resource announcement: Genome sequences for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei). Molecular Plant-Microbe Interactions. https://doi.org/10.1094/MPMI-04-18-0107-A.