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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Research Project #432638

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

2017 Annual Report


1a. Objectives (from AD-416):
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.


1b. Approach (from AD-416):
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.


3. Progress Report:
This is the first report for this new project which replaced 2090-22000-015-00D, “Improved Control of Stripe Rust in Cereal Crops”. This report covers March 28 – September 30, 2017. For information covering October 1, 2016 – March 27, 2017, see the report for the previous project. Progress was made on the two objectives and four subobjectives, all of which fall under National Program 303 Plant Diseases. Under Subobjective 1A (Identify virulent races of stripe rust pathogens to determine effectiveness of resistance genes in wheat and barley), we completed all tests for identifying races from the stripe rust collections in the U.S. in 2016, and reported the results to the cereal community of researchers, developers, and growers. During the 2017 growing season, we have conducted field survey, made recommendations for control of stripe rust, and collected stripe rust samples in the Pacific Northwest. Through collaborators in other regions, we have received more than three hundred stripe rust samples from twenty states and will receive more as the season is progressing. These samples were used to inoculate susceptible wheat plants for recovering and increase 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 tested isolates, we have identified twelve races of the wheat stripe rust pathogen in this year so far. Based on these data, resistance genes Yr5 and Yr15, which are in many new wheat varieties, are still effective, which is useful for breeding for resistant varieties and control of stripe rust. The progress is according to schedule. Under Subobjective 1B (Develop molecular markers and characterize stripe rust pathogen populations to identify factors and mechanisms of pathogen dynamics for developing new management strategies), we have been continually re-sequencing the stripe rust fungal genome and using the sequences to develop molecular markers. In addition to the previously developed over hundred secreted protein gene single-nucleotide polymorphism (SP-SNP) markers, we have designed primers for two hundred SP-SNP markers. Using these markers and previously developed simple-sequence repeat (SSR) markers developed in our program and by others, we have characterized the stripe rust populations in the U.S. and some other countries. Using these markers, we characterized somatic recombinant isolates and determined somatic recombination as one of the major mechanisms for the stripe rust pathogen variation. We also used the markers, together with SNP markers generated from genotyping-by-sequencing (GBS), we characterized a sexual population of the wheat stripe rust pathogen generated under controlled conditions. In this study, we determined the base number of chromosomes and constructed the first genetic map for the stripe rust pathogen. We determined homozygous and heterozygous avirulence and virulence loci. The results improve the understanding of the stripe rust fungus pathogenicity and virulence variation, and provide the information about effectiveness and possibly durability of resistance genes. Under Subobjective 2A (Identify and map new genes for stripe rust resistance, and develop new germplasm for use in breeding programs), we have planted over ten mapping populations at Pullman and Mount Vernon, Washington, for phenotyping their stripe rust responses for mapping resistance genes. In addition, we planted populations from forty wheat crosses to advance the generation and obtain initial segregation data from stripe rust phenotypes. We have taken stripe rust notes two times at the Mount Vernon location and one time note at the Pullman location for the winter wheat and one time note for spring wheat at the Mount Vernon location. We have completed a study to identify and map stripe rust resistance genes in ‘Madsen’, a soft white winter wheat variety that has been widely grown in the Pacific Northwest since the early 1990s and is considered as a standard for high-level and durable high-temperature adult-plant (HTAP) resistance to stripe rust. We have mapped three genes for race-specific all-stage resistance and two genes for non-race specific HTAP resistance. The results are useful for understanding the mechanisms of durable resistance, and provide resources for developing new varieties with high-level durable resistance to stripe rust. Under Subobjective 2B (Screen breeding lines for supporting breeding programs to develop wheat and barley cultivars with adequate and durable resistance to stripe rust), we planted more than 35,000 entries of wheat, barley, and triticale near Pullman and Mount Vernon, Washington, and some of the nurseries were also planted in three additional locations. For the winter nurseries, we have completed note-taking twice at the Mount Vernon, Walla Walla, and Lind locations; and once at the Pullman location. For the spring nurseries, we have taken notes once at the Mount Vernon and Lind locations. Additional notes will be taken before the stripe rust season. The data will be provided to the breeding programs for releasing new varieties with stripe rust resistance.


4. Accomplishments
1. Developed new wheat germplasm lines with resistance to stripe rust. Growing resistant varieties is the most effective, economical, easy-to-use, and environmentally friendly approach to control stripe rust, and germplasm with well-characterized effective resistance genes are essential and more efficient for developing new resistant varieties. ARS scientists in Pullman, Washington, recently released twenty-nine new wheat germplasm lines (PI 679598 – PI 679626), of which fifteen have a single different resistance gene and fourteen each have a combination of two linked resistance genes. These lines also have improved agronomic traits compared to the original donors through multi-year selections in the fields. Use of these new germplasm lines will diversify stripe rust resistance genes used in the breeding programs, especially the lines with two linked genes that should increase the possibility of combining two different genes on the same chromosome into new wheat varieties with high-level, durable or long-lasting resistance.

2. Established a linkage map for the stripe rust fungus and mapped virulence genes to chromosomes. Because the stripe rust pathogen is an obligate biotrophic parasite and the sexual life cycle was not known until recently, genes for virulence have not been genetically studied and mapped. ARS scientists in Pullman, Washington, developed a sexual population through self-crossing a stripe rust isolate on alternate host barberry plants under controlled conditions. Through virulence phenotyping and molecular genotyping the population using genotyping-by-sequencing (GBS) markers, they determined the base number of six chromosomes for the stripe rust fungus and established a linkage map consisting six linkage groups. They determined the homozygosity of avirulence loci corresponding to nine resistance genes and a virulence locus corresponding to one resistance gene, and identified twenty-nine dominant virulence genes, of which seventeen were mapped to two of the chromosomes. The data and map are useful for further cloning virulence genes and studying their functions. The results are also useful for selecting resistance genes with corresponding homozygous avirulence genes to be used in breeding programs for high-level and possibly long-lasting resistance to stripe rust.

3. Re-sequenced the stripe rust pathogen genome, identified effectors, and developed molecular markers. Through collaboration with U.S. scientists in Broad Institute, Washington State University, and University of California, Davis, and Chinese scientists, ARS scientists in Pullman, Washington, previously sequenced seven stripe rust isolates using various techniques, but the sequences were either incomplete or poorly annotated due to the large and complex genome. They re-sequenced and annotated an additional seven isolates, which were carefully selected to have a relatively balanced ratio for virulence and avirulence allele frequencies for a maximum number of virulence loci. They improved the assembling and increased the number of genes annotated for the stripe rust pathogen, especially secreted protein or effector genes that are likely related to the fungal pathogenicity and virulence. Through comparing the sequence data of all fourteen isolates, they identified effector candidates significantly associated to five avirulence genes. This study improved the knowledge of the stripe rust genome and functional genomics. The data can be used to develop molecular markers for studying the pathogen populations, possibly tagging individual virulence genes, and studying the host-pathogen interactions.

4. Identified and mapped wheat genes for resistance to stripe rust. Growing resistant varieties is the most effective approach for control of stripe rust, but virulent races may circumvent high-level race-specific all-stage resistance and durable high-temperature adult-plant (HTAP) resistance may not provide adequate control. ARS scientists in Pullman, Washington, completed a study of mapping genes for stripe rust resistance in ‘Madsen’, a soft white winter wheat variety widely grown in the Pacific Northwest since the early 1990s and considered as a standard for high-level and durable HTAP resistance for breeding programs in the region. They identified three genes for race-specific all-stage resistance and two genes for non-race specific HTAP resistance, mapped these genes to specific chromosomal regions, and determined the effects of each gene and interactions among the genes under different environmental conditions. The study provides the genetic basis for durable resistance and resources of genes and linked markers for developing new wheat varieties with high-level and durable resistance to stripe rust.

5. Tested 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 2017 growing season, ARS scientists from Pullman, Washington, tested twenty-three fungicide treatments, including several new chemicals, for control of stripe rust on both winter and spring wheat crops. They also tested twenty-three winter wheat and fifteen spring wheat varieties, which were selected based on their acreage grown in the previous years in the Pacific Northwest, plus highly susceptible varieties as checks, to determine their yield losses caused by stripe rust and responses to fungicide application. The efficacies, rates, and timing of the chemicals 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 for the chemical developers to register new fungicides and for growers to have more choices of chemicals and to use an individual variety based integrated management system to control stripe rust.


Review Publications
Sthapit Kandel, J., Krishnan, V., Jiwan, D., Chen, X., Skinner, D.Z., See, D.R. 2017. Mapping genes for resistance to stripe rust in spring wheat landrace PI 480035. PLoS One. 12(5):e0177898.

Kumar, N., Randhawa, H.S., Higginbotham, R.W., Chen, X., Murray, T.D., Gill, K.S. 2017. Targeted and efficient transfer of multiple value-added genes into wheat varieties. Molecular Breeding. 37:68. doi:10.1007/s11032-017-0649-1.