Location: Wheat Health, Genetics, and Quality Research
2024 Annual Report
Objectives
This project will work to achieve the following objectives over the next five years:
1) Monitor and characterize stripe rust pathogen populations towards the development of appropriate measures to reduce damage on wheat and barley.
2) Enhance resistance in wheat and barley cultivars for effective stripe rust control.
Approach
For Objective 1 (Monitor and characterize stripe rust pathogen populations towards the development of appropriate measures to reduce damage on wheat and barley), we will use our models for the Pacific Northwest (PNW) to predict stripe rust epidemic levels. To monitor and mange stripe rust, we will conduct field survey and provide rust updates and recommendations to growers to implement appropriate control measures. To identify stripe rust races, rust samples will be collected from cereals (wheat, barley, rye, and triticale) and various grasses by collaborators and ourselves during surveys, and the isolates will be characterized for virulence using our standard protocols of our program. To identify population changes, we will use a standard set of 14 SSR markers to characterize stripe rust isolates. We will also identify SNP markers associated to avirulence genes and converted them into KASP markers. KASP markers with the highest value of correlation coefficient will be selected to establish a set of KASP markers for avirulence genes.
For Objective 2 (Enhance resistance in wheat and barley cultivars for effective stripe rust control), we will screen wheat, barley, and triticale lines from breeding programs throughout the U.S for developing new resistant varieties. To determine the stripe rust resistance levels, potential yield losses, and response to fungicide application of commercially grown varieties, each year we will evaluate 23 winter and 23 spring wheat varieties from the Pacific Northwest, plus a susceptible check in each nursery. The results of these tests will be used to guide growers for selecting resistance varieties and appropriately use of fungicides. For identifying new geremplasm and stripe rust resistance genes, we will complete the studies of mapping and identifying stripe rust resistance in three wheat panels using the genome-wide association study (GWAS) approach. We will also focus on mapping and identifying genes for resistance to stripe rust in the 40 crosses made from 40 winter wheat varieties crossed with susceptible AvS. We have identified 233 SNP markers associated to stripe rust resistance using a bulk-segregant approach for at least 70 individual genes in the 40 varieties. The SNP markers will be validated using the individual bi-parental mapping populations. The SNP markers for new resistance loci will be converted to KASP markers. New germplasm lines carrying new genes will be selected based on morphological plant types, stripe rust reactions, and molecular markers, and these lines will be deposited and registered in the ARS National Small Grain Collections.
Progress Report
This report documents FY 2024 progress for project 2090-22000-020-00D, "Enhancing Control of Stripe Rusts of Cereal Crops", which began in March 2022.
In support of Objective 1, ARS scientists in Pullman, Washington, completed all tests for identifying races from the stripe rust collections in the United States in 2023 and reported the results to the cereal community of researchers, developers, and growers. During the 2024 crop season, they accurately predicted the potential stripe rust level of the season as early as January and March, conducted field surveys and made recommendations for stripe rust management, which successfully prevented a potential major epidemic, reduced unnecessary use of fungicides, and saved growers’ multimillions of dollars in the Pacific Northwest (PNW). By collecting stripe rust samples in the PNW and through collaborators in other regions, they obtained more than 400 stripe rust samples from over 20 states so far. Spores from these samples were recovered and multiplied on susceptible wheat or barley plants in the greenhouse to establish isolates. 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 2023 samples, they identified 21 races of the wheat stripe rust pathogen and five races of the barley stripe rust pathogen and determined the distributions and frequencies of the races and virulence factors. From the 2024 collection, 15 races of the wheat stripe rust pathogen and four races of the barley stripe rust pathogen have been identified so far. Based on the virulence data of the races, resistance genes, such as Yr5, Yr15, and many other genes identified by this program and other programs in the world, have been determined to be effective against all populations of the wheat stripe rust pathogen in the United States, and these genes can be used in breeding programs for developing stripe rust resistant wheat varieties. Similar information has also been obtained for the barley stripe rust pathogen and barley resistance genes. Based on the virulence patterns, distributions, and frequencies of the identified races, they selected races for use in their wheat and barley germplasm screening research. The progress of race identification is on schedule.
For molecular characterization of the stripe rust pathogen populations, ARS scientists in Pullman, Washington, continued characterizing the U.S. wheat stripe rust isolates collected from 2018 to 2023 using a set of simple sequence repeat (SSR) markers and Kompetitive allele specific PCR (KASP) markers associated to virulence and fungicide-target gene mutants.
Under Objective 2, ARS scientists in Pullman, Washington, planted more than 16,000 wheat and barley entries in the fields near Pullman, Mount Vernon, and Central Ferry, Washington, for screening the materials for resistance to stripe rust. Some of the nurseries were also planted in additional locations in Walla Walla and Lind, Washington. ARS scientists completed collecting stripe rust response data for the nurseries planted in the different locations. They also 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 and levels of resistance to stripe rust as well as which entries are resistant and which ones are susceptible. ARS scientists provided the data to various breeding programs throughout the country for selecting resistant lines for releasing as new varieties. The test results of currently grown varieties are used to update stripe rust ratings for the wheat and barley varieties listed in Seed-Buying Guides to be selected by growers to grow. Growing resistant varieties will reduce the potential risk of stripe rust damage.
To provide precise recommendations for managing stripe rust based on the resistance levels of individual varieties, ARS scientists in Pullman, Washington, tested 16 fungicide treatments for control of stripe rust on both winter and spring wheat crops and 23 winter and 23 spring commercially grown wheat varieties, plus a susceptible check in each nursery, for yield losses and responses to fungicide application during the 2024 crop season. The efficacies of fungicides and responses of fungicide application verses non application of the commercially grown varieties should be useful for managing stripe rust based on individual varieties under different epidemic levels.
ARS scientists in Pullman, Washington, continued identifying and mapping new genes in barley and wheat for resistance to stripe rust. They also completed phenotyping a spring barley panel consisting of 320 entries that have been genotyped for genome-wide association studies (GWAS) for identifying genes for resistance to stripe rust. Their preliminary analysis identified 26 loci associated to stripe rust resistance, and they have been continually analyzing the 2024 phenotypic data to complete the study. For wheat, ARS scientists completed the phenotyping and genotyping experiments for two spring bi-parental populations and two winter biparental populations and have been continually analyzing the data. They completed a study for identifying and mapping a new gene conferring high-temperature adult-plant (HTAP) resistance in the wheat Yr8 near-isogenic line and demonstrated that the HTAP resistance gene is also originated from Aegilop comosa, and published the results in Plant Disease in 2024. ARS scientists in Pullman, Washington, in collaboration with researchers in Italy, Mexico, Morocco, Spain, and the University of Minnesota, carried out a genome-wide association study (GWAS) that identified five loci for stripe rust, nine loci for stem rust, and 34 loci for leaf rust resistance, from a collection of 230 tetraploid wheat lines with some of the loci conferring resistance to all three rusts, and published the results in Frontiers in Plant Science in 2024. Their identified genes and developed molecular markers for stripe rust resistance genes make the resistant germplasm and genes useful in breeding programs for developing new wheat varieties with stripe rust resistance.
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 21 races of the wheat stripe rust pathogen and five races of the barley stripe rust pathogen from the U.S. collection in 2023, and determined the frequencies and distributions of these races and virulence factors in the pathogen populations in various epidemic regions. The results can be 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 developing new varieties with adequate and durable resistance to stripe rust.
2. Screened wheat and barley germplasms and released new wheat and barley varieties for resistance to stripe rust. Developing resistant varieties is the most effective, economical, easy to use, and environmental-friendly approach to control stripe rust. ARS scientists in Pullman, Washington, screened more than 16,000 wheat and barley germplasm from breeding programs throughout the United States in multiple field locations and in the greenhouse with multiple races of the pathogen for response to stripe rust in 2024. They provided the data to various breeding programs for releasing new resistant varieties and to growers for selecting resistant varieties to grow. Based on their stripe rust data in recent years, they collaborated with various breeding programs in releasing and registering 10 new wheat varieties and one new barley variety with resistance to stripe rust. Growing these new varieties will reduce the risk of stripe rust and reduce the cost of using fungicides.
3. Identified and mapped new genes for resistance to stripe rust in wheat. Stripe rust is best controlled through developing and growing resistant varieties. ARS scientists in Pullman, Washington, completed studies on identification and molecular mapping of genes or quantitative trait loci (QTL) for stripe rust resistance in wheat germplasms. Through mutagenesis and molecular genotyping of a bi-parental mapping, they identified and mapped a new gene conferring high-temperature adult-plant (HTAP) resistance to stripe rust in a wheat line carrying Yr8 that has become ineffective to the current U.S. wheat stripe rust population and demonstrated that the non-race specific HTAP resistance was also originally from Aegilops comosa. The identified durable resistance gene and developed molecular markers are useful for breeding programs to develop new wheat varieties with durable stripe rust resistance.
4. Identified new fungicides for control of stripe rust and determined yield losses and fungicide responses of wheat varieties. Stripe rust can be controlled by planting resistant varieties and applying fungicides when needed. To develop an integrated strategy for effectively managing stripe rust, ARS scientists in Pullman, Washington, tested 16 fungicide treatments on susceptible varieties of both winter and spring wheats for their efficacies on control of stripe rust and determined yield losses caused by stripe rust and fungicide responses in reduction of yield losses of 23 winter and 23 spring wheat varieties used in production plus susceptible checks. The fungicide trials identified new effective fungicides and best timing of application, and the tests of commercially grown varieties determined yield losses caused by stripe rust and yield increases by applying a currently used effective fungicide for individual varieties. The results can be used by chemical companies to register new fungicides and growers to determine if fungicide application is needed based on varieties planted in their fields and which fungicide should be selected.
Review Publications
Chen, J., Wheeler, J., Marshall, J.M., Chen, X., Windes, S., Wilson, C., Su, M., Yimer, B., Schroeder, K., Jackson, C. 2024. Release of 'UI Gold' hard white spring wheat. Journal of Plant Registrations. 18(1):104-112. https://doi.org/10.1002/plr2.20309.
Zhou, A., Wang, J., Chen, X., Xia, M., Feng, Y., Ji, F., Huang, L., Kang, Z., Zhan, G. 2024. Virulence characterization of Puccinia striiformis f. sp. tritici in China using the Chinese and Yr single-gene differentials. Plant Disease. 108(3):671-683. https://doi.org/10.1094/PDIS-08-23-1524-RE.
Marone, D., Laido, G., Saccomanno, A., Petruzzino, G., Giaretta Azevedo, C.V., De Vita, P., Mastrangelo, A., Gadaleta, A., Ammar, K., Bassi, F.M., Wang, M., Chen, X., Rubiales, D., Matny, O., Steffenson, B.J., Pecchioni, N. 2024. Genome wide association study of common resistance to rust species in tetraploid wheat . Frontiers in Plant Science. 14. Article 1290643. https://doi.org/10.3389/fpls.2023.1290643.
Chen, X., Evans, C.K., Qin, R. 2024. Evaluation of Pacific Northwest winter wheat cultivars to fungicide application for control of stripe rust in 2023. Plant Disease Management Reports. 18. Article CF068.
Chen, X., Evans, C.K. 2024. Evaluation of Pacific Northwest spring wheat cultivars to fungicide application for control of stripe rust in 2023. Plant Disease Management Reports. 18. Article CF067.
Chen, C., Hu, Y., Li, X., Morris, C., Delwiche, S.R., Carter, A.H., Steber, C.M., Zhang, Z. 2023. An independent validation reveals the potential to predict Hagberg-Perten falling number using spectrometers. The Plant Phenome Journal. 6(1). Article e20070. https://doi.org/10.1002/ppj2.20070.
Chen, X., Wang, M., Evans, C.K. 2023. Development of resources for control of stripe rust on wheat and barley in the United States. International Congress of Plant Pathology Abstracts and Proceedings. 909:P41-024.
Wang, M., Chen, X. 2023. Virulence characterization of Puccinia striiformis causing stripe rusts on wheat and barley in the United States in 2022. American Phytopathological Society Annual Meeting. 113(11s):S3.170. https://apsjournals.apsnet.org/doi/epdf/10.1094/PHYTO-113-11-S3.1.
Bao, X., Hu, Y., Li, Y., Chen, X., Shang, H., Hu, X. 2023. The interaction of two Puccinia striiformis f. sp. tritici effectors modulates high-temperature seedling-plant resistance in wheat. Molecular Plant Pathology. 24(12):1522-1534. https://doi.org/10.1111/mpp.13390.
Li, Y., Wang, M., Hu, X., Chen, X. 2023. Identification of a locus for high-temperature adult-plant resistance to stripe rust in the wheat Yr8 near-isogenic line through mutagenesis and molecular mapping. Plant Disease. 108(5):1261-1269. https://doi.org/10.1094/PDIS-10-23-2037-RE.
