Location: Wheat Health, Genetics, and Quality Research
2022 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
This is the final report for project 2090-22000-018-000D, “Improving Control of Stripe Rusts of Wheat and Barley through Characterization of Pathogen Populations and Enhancement of Host Resistance,” which has been replaced by new project 2090-22000-020-000D, “Enhancing Control of Stripe Rusts of Cereal Crops.” For additional information, please review the new project report.
The studies for the two objectives and four sub-objectives were completed, all of which fall under National Program 303 Plant Diseases.
Under Sub-objective 1A, ARS scientists in Pullman, Washington, completed all tests for identifying races from the stripe rust collections in the United States in 2017-2021. During the five-year period, they collected and received from collaborators a total of 1684 stripe rust samples throughout the United States and identified 32 different races on average every year and a total of 15 new races and determined the distributions and frequencies of the races and virulence factors in each year’s populations of the wheat and barley stripe rust pathogens. Using selected races presenting predominant races and different race groups, they tested wheat and barley genetic stocks and commercially grown varieties to identify genes and germplasm effective against the stripe rust pathogen populations. They reported the results to the cereal community of researchers, developers, and growers every year, which have been used by breeders for developing new wheat and barley varieties and by growers to implementing measures for managing stripe rusts.
Under Sub-objective 1B, ARS scientists in Pullman, Washington, developed a set of simple sequence repeat (SSR) markers and used the markers in a series of studies to characterize stripe rust collections of the United States from 1968 to 2021, as well as the stripe rust collections from other countries. In the study of the wheat stripe rust collections in the United States from 1968 to 2009, they identified 614 multi-locus genotypes (MLGs) from 1083 tested isolates. From 2,247 isolates of the wheat stripe rust collections from 2010 to 2017 in the United States, they identified 1,454 MLGs. Through comparison of the populations in these two studies covering the wheat stripe rust collections from 1968 to 2017, they clustered the populations of 49 years into three major molecular groups (MGs) and 10 sub-MGs. They determined the diversity, dynamics, and differentiation of the populations over the years and across different epidemiologic regions. Similarly, they studied genetic changes of the barley stripe rust populations in the United States from 1993 to 2017 and characterized wheat stripe rust collections from 20 countries from 2006 to 2018. Through various population genetic analyses, they identified multiple inter-regional and international migrations of the stripe rust pathogen in the United States and the world, multiple introduction events in the United States, and determined mechanisms underlying the population changes and factors influencing the pathogen population dynamics. They sequenced more than 130 stripe rust isolates and established best genomes, secretomes, and genetic linkages for the stripe rust pathogen. They developed more than 800 single-nucleotide polymorphism (SNP) markers based on secreted protein (SP) genes and identified more than 50 SP-SNP markers associated to avirulence genes in the stripe rust pathogen.
Under Sub-objective 2A, ARS scientists in Pullman, Washington, conducted a series of studies for identifying and mapping genes in wheat and barley for resistance to stripe rust using both bi-parental and genome-wide association study (GWAS) approaches. From 2017 to 2021, they published 43 papers from their studies and collaborative studies for this sub-objective. Using recombinant inbred line and doubled haploid line populations from crosses, they identified and mapped five (including one new) genes or quantitative trait loci (QTL) in the Pacific Northwest (PNW) winter wheat variety Madsen, six (including one new) QTL in PNW winter wheat variety Skiles, five (including two new) QTL in PNW winter wheat variety Eltan, five genes (including permanently named new gene Yr79) in spring wheat germplasm PI 182103, seven (including four new) QTL in spring wheat germplasm PI 181410, and three QTL in spring wheat germplasm PI 197734 for different types of stripe rust resistance, especially durable high-temperature, adult-plant resistance. Using the GWAS approach, they identified and mapped 51 (including at least 10 new) genes or QTL from a winter wheat panel of 857 entries and 37 (including 10 new) genes or QTL from a spring wheat panel of 616 entries of U.S. wheat cultivars and germplasm. Through collaborations with scientists in Washington State University, University of California Davis, Montana State University, North Dakota State University, and ARS at Fargo, North Dakota, ARS at St. Paul, Minnesota, Texas A&M University, Oregon State University, Northwest Agricultural & Forestry (A&F) University and Sichuan Agricultural University of China, and Tel Aviv University in Israel, they identified and mapped hundreds of genes or QTL for resistance to stripe rust from diverse panels of germplasm, including 3,605 common wheat, 846 durum wheat, 176 emmer wheat, and 480 wild emmer wheat entries. They collaborated with scientists in the University of Idaho, Shandong Agricultural University, and Northwest A&F University and cloned stripe rust resistance gene YrAS2388R, which is an ancestral NB-LRR gene with duplicated 3’ untranslated regions (UTRs), and several WRKY transcription factor and NB-LRR genes involved in temperature-sensitive resistance to stripe rust in wheat varieties. To efficiently transfer new effective genes for stripe rust resistance into new wheat varieties, ARS scientists in Pullman, Washington, developed and registered 29 new wheat lines, including 15 lines each carrying two genes on the same chromosome arms. To discover genes for resistance to stripe rust in barley, ARS scientists in Pullman, Washington, collaborated with ARS scientists in Aberdeen, Idaho, and mapped six QTL for stripe rust resistance in two bi-parental mapping populations, and with scientists in Oregon State University in mapping 14 (including five new) QTL from 300 lines of facultative winter 6-row barley. The new germplasm, genes and markers identified or developed in these studies have been used in breeding programs of the United States and other countries for developing new wheat and barley varieties with resistance to stripe rust.
Under Sub-objective 2B, ARS scientists in Pullman, Washington, planted more than 20,000 wheat and barley entries in each of the five years in the fields near Pullman and Mount Vernon, Washington, for screening the materials for resistance to stripe rust. Some of the nurseries were also planted in three additional locations. They also have tested the wheat and barley variety trial nurseries and uniform nurseries from various wheat and barley production regions of the United States in both seedling and adult-plant stages with selected races of the stripe rust pathogen in the greenhouse. The tests in both field and greenhouse allow identifying different types of resistance to stripe rust as well as different levels of resistance. They have provided the data to various breeding programs throughout the country for selecting resistant lines for releasing as new varieties. From 2017 to 2021, ARS scientists in Pullman, Washington, collaborated with breeders of ARS and universities in Colorado, Georgia, Idaho, Montana, Kansas, Virginia, and Washington, in the registrations of 40 new wheat varieties with stripe rust resistance. Wheat varieties released by breeders in many other states and private companies, such as BASF, Bayer, Limagrain, Monsanto, and Syngenta were also through the stripe rust evaluations conducted by the ARS scientists in Pullman, Washington. The test results of currently grown varieties are used to update stripe rust reactions for the varieties listed in Seed-Buying Guides to be selected by growers to grow. Growing resistant varieties has greatly reduced the potential yield losses caused by stripe rust.
Accomplishments
1. Identified races of the wheat and barley stripe rust pathogens. The wheat and barley stripe rust pathogens evolve rapidly to produce new races that can overcome resistance in currently grown varieties, and the information of races with their virulence factors is essential for breeding programs to use effective genes for developing new varieties with adequate and durable resistance. ARS scientists in Pullman, Washington, identified 32 different races on average every year and a total of 15 new races from 1,684 stripe rust samples collected from 2017 to 2021 throughout the United States. They determined the distributions and frequencies of the races and virulence factors in each year’s populations of the wheat and barley stripe rust pathogens. The results are used by breeders to select effective resistance genes for developing new varieties and by pathologists to select important races for screening wheat and barley germplasm for releasing new varieties with adequate and durable resistance to stripe rust.
2. Improved understanding of stripe rust pathogen variation and disease epidemiology. Genome sequencing and molecular characterization of the stripe rust pathogen populations are important for understanding the pathogen variation and epidemiology of the disease. ARS scientists in Pullman, Washington, have published a series of papers on genome sequencing and molecular characterization of the wheat and barley stripe rust collections in the United States and many other countries. They established high-quality genomes for the stripe rust pathogen, developed molecular markers based on the sequence variations, characterized stripe rust collections of natural populations from the United States and many other countries as well as experimental populations of the pathogen generated through sexual reproduction and mutagenesis under controlled conditions using the molecular markers. Through various whole genome and population analyses, they established high-quality genomes, linkage groups, and genetic resources of the stripe rust pathogen; determined population diversity, dynamics, differentiation, and evolutionary mechanisms of the wheat and barley stripe rust pathogens, which have greatly improved the understanding the pathogen variation.
3. Identified and mapped new genes for stripe rust resistance and developed new wheat germplasm. Stripe rust is best controlled through developing and growing resistant varieties. ARS scientists in Pullman, Washington, published 43 papers from their studies and collaborative studies on identification and molecular mapping of genes or quantitative trait loci (QTL) for stripe rust resistance in wheat and barley from 2017 to 2021. Through stripe rust phenotyping and molecular genotyping various bi-parental mapping populations and panels for genome-wide association studies (GWAS), they identified and mapped hundreds of genes or QTL (including at least 100 new genes) for stripe rust resistance in 22 bi-parental populations and 18 GWAS panels including more than 5,000 wheat entries and 20 (including five new) genes or QTL for stripe rust resistance from two bi-parental populations and 300 barley entries. They developed and registered 29 new wheat lines, including 15 lines each carrying two genes on the same chromosome arms. The identified and developed stripe rust resistant germplasm lines, effective genes, and linked molecular markers have been used by many breeding programs for developing new wheat and barley varieties.
4. Screened wheat and barley germplasm and released new varieties for resistance to stripe rust. Developing resistant varieties is the most effective, easy-to use, and environmental-friendly approach to control stripe rust. ARS scientists in Pullman, Washington, screened more than 20,000 wheat and barley germplasm from breeding programs throughout the United States in the field and in the greenhouse for response to stripe rust every year from 2017 to 2021. They provided the data to various breeding programs for releasing new resistant varieties and to growers for selecting released resistant varieties to grow. During the five years, they collaborated with breeding programs of ARS and universities in Colorado, Georgia, Idaho, Montana, Kansas, Virginia, and Washington in the registration of 40 new wheat varieties and one new barley variety with resistance to stripe rust. Wheat and barley varieties released by breeders in many other states and private companies, such as BASF, Bayer, Limagrain, Monsanto, and Syngenta were also through the stripe rust evaluations conducted by the ARS scientists in Pullman, Washington. Growing new stripe rust resistant varieties has reduced potential yield losses caused by wheat stripe rust from 34% to 8% in the Pacific Northwest and similar percentage in the other regions and will continue reduce potential yield losses and the use of fungicides.
Review Publications
Bai, Q., Wan, A., Wang, M., See, D.R., Chen, X. 2021. Molecular characterization of wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) collections from nine countries. International Journal of Molecular Sciences. 22(17). Article 9457. https://doi.org/10.3390/ijms22179457.
Wang, J.H., Wang, J.J., Li, J., Shang, H.S., Chen, X., Hu, X.P. 2021. The RLK protein TaCRK10 activates wheat high-temperature seedling-plant resistance to stripe rust through interacting with TaH2A.1. Plant Journal. 108(5):1241-1255. https://doi.org/10.1111/tpj.15513.
Aoun, M., Chen, X., Somo, M., Xu, S.S., Li, X., Elias, E.M. 2021. Novel stripe rust all-stage resistance loci edentified in a worldwide collection of durum wheat using genome-wide association mapping. The Plant Genome. 14. Article e20136. https://doi.org/10.1002/tpg2.20136.
Yao, F., Guan, F., Duan, L., Long, L., Tang, H., Jiang, Y., Li, H., Jiang, Q., Wang, J., Qi, P., Kang, H., Li, W., Ma, J., Pu, Z., Deng, M., Wei, Y., Zheng, Y., Chen, X., Chen, G. 2021. Genome-wide association analysis of stable stripe rust resistance loci in a Chinese wheat landrace panel using the 660K SNP array. Frontiers in Plant Science. 12. Article 783830. https://doi.org/10.3389/fpls.2021.783830.
Merrick, L.F., Lozada, D.N., Chen, X., Carter, A.H. 2022. Classification and regression models for genomic selection of skewed phenotypes: A case for disease resistance in winter wheat (Triticum aestivum L.). Frontiers in Genetics. 13. Article 835781. https://doi.org/10.3389/fgene.2022.835781.
Tene, M., Adhikari, E., Cobo, N., Jordan, K.W., Matny, O., del Blanco, I.A., Roter, J., Ezrati, S., Govta, L., Manisterski, J., Yehuda, P.B., Chen, X., Steffenson, B., Akhunov, E., Sela, H. 2022. GWAS for stripe rust resistance in wild emmer wheat (Triticum dicoccoides) population: Obstacles and solutions. Crops. 2(1):42-61. https://doi.org/10.3390/crops2010005.
