Location: Wheat Health, Genetics, and Quality Research
2022 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 progress for project 2090-22000-020-000D, Enhancing Control of Stripe Rusts of Cereal Crops, which was certified in March 2022, and continues research from project 2090-22000-018-000D, Improving Control of Stripe Rusts of Wheat and Barley through Characterization of Pathogen Populations and Enhancement of Host Resistance.
Progress was made on the two objectives, all of which fall under National Program 303 Plant Diseases.
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 2021, and reported the results to the cereal community of researchers, developers, and growers. During the 2022 crop season, they accurately predicted stripe rust level in the winter and early spring, conducted field surveys, made recommendations for control of stripe rust, which successfully prevented major yield losses and saved growers millions of dollars in the Pacific Northwest. By collecting stripe rust samples in the Pacific Northwest and through collaborators in other regions, they obtained more than 300 stripe rust samples from more than ten states. Spores from these samples were recovered and multiplied on susceptible wheat 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 2021 samples, they identified 18 races of the wheat stripe rust pathogen and 9 races (including 1 new race) of the barley stripe rust pathogen and determined the distributions and frequencies of the races and virulence factors. From the 2022 collection, eleven 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 cultivars. Similar information has also been obtained for the barley stripe rust pathogen and barley resistance genes. Based on virulence patterns, distributions, and frequencies, 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, have continued characterized the wheat stripe rust collections from 2018 to 2022 in the United States after they published the results from the 1960s to 2017 using a set of simple sequence repeat (SSR) markers. In addition, they characterized the wheat stripe rust collection from eight countries from 2010 to 2018 in comparison with the U.S. population. In this study, they identified 433, including 333 new multi-locus genotypes (MLGs), from 567 isolates, which were clustered into 10 molecular groups (MGs). The MGs and country-wise populations differed in genetic diversity, heterozygosity, and correlation coefficient between the marker and virulence data. Many isolates from different countries, especially the isolates from Mexico, Ecuador, and the United States, were found to be identical or closely related MLGs, and some of the MGs were present in all countries, indicating pathogen migrations among different countries. Only low levels of differentiation were found by the pairwise comparisons of country populations. Identical and closely related MLGs identified from different countries indicated international migrations. The study provides information on the distributions of various genetic groups of the wheat stripe rust pathogen in different countries and evidence for the global migrations. The results are useful in understanding the pathogen evolution and in stressing the need for continual monitoring of the disease and pathogen populations at the global scale.
Under Objective 2, ARS scientists in Pullman, Washington, planted more than 20,000 wheat and barley entries in the fields near Pullman, Mount Vernon, Central Ferry, Washington, for screening the materials for resistance to stripe rust. Some of the nurseries were also planted in three additional locations. They have completed stripe rust response data for the nurseries planted in different 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. 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 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 19 fungicide treatments for control of stripe rust and 24 winter and 24 spring wheat varieties for response to fungicide application during the 2022 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 for individual varieties under different epidemic levels.
ARS scientists in Pullman, Washington, have continued identifying and mapping genes in wheat for resistance to stripe rust. They have completed phenotyping and genotyping three wheat germplasm panels including two winter wheat panels and one spring wheat panel (each panel consisting of 420 to 520 entries) for genome-wide association studies (GWAS) for identifying genes for resistance to stripe rust. They are currently analyzing the data to complete the studies. Continuing their studies for identifying and mapping stripe rust resistance in 40 winter wheat bi-parental mapping populations, they repeated the field experiments in both Pullman and Mount Vernon, Washington, for obtaining more sets of stripe rust phenotypic data of the selected mapping populations. They have completed a study of identifying a gene for high-temperature adult-plant (HTAP) resistance in a wheat near-isogenic line (NIL) for all-stage resistance gene Yr17 and published the results in Plant Disease in 2022. This study shows the usefulness of the wheat varieties carrying the Aegilops ventricosa translocation and the importance of combining all-stage resistance with HTAP resistance in developing wheat cultivars with durable resistance.
Accomplishments
1. Identification of secreted protein gene-based SNP markers associated with virulence phenotypes of the wheat stripe rust pathogen. The stripe rust pathogen is highly variable due to the capacity of virulent races to undergo rapid changes to circumvent resistance in wheat varieties. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in the pathogen so far. To identify molecular markers for avirulence genes, ARS scientists in Pullman, Washington, published a paper on identification of molecular markers associated with avirulence genes. They tested a well selected panel of 157 isolates representing 126 races with diverse virulence spectra using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis and identified 19 SP-SNP markers for significant associations with 12 avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.
2. Screened wheat and barley germplasm and release new wheat 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 multiple field locations and in the greenhouse with multiple races of the pathogen for response to stripe rust in 2022. They provided the data to various breeding programs for releasing new resistant varieties and to growers for selecting released resistant varieties to grow. Based on their stripe rust data in the recent years, they collaborated with various breeding programs in releasing and registering 12 new wheat varieties with resistance to stripe rust. Growing these new varieties will reduce potential risk of stripe rust.
3. 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 18 races of the wheat stripe rust pathogen and 9 races, including 1 new race of the barley stripe rust pathogen from the U.S. 2021 collections, and determined the frequencies and distributions of these races and virulence factors 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 releasing new varieties with adequate and durable resistance to stripe rust.
4. Determined population diversity, and global migration of the wheat stripe rust pathogen in nine countries. Molecular characterization of the stripe rust pathogen population is important for understanding the pathogen variation and migration. ARS scientists in Pullman, Washington, have recently published a paper on molecular characterization of the wheat stripe rust collections from nine countries. Using a set of simple sequence repeat (SSR) markers, they identified 433, including 333 new genotypes from 567 isolates received from nine countries including the United States and clustered them into 10 molecular groups (MGs). Through population genetic analyses, they determined population diversity in each country and identified pathogen migration between countries and continents. This study improves the understanding the variation and mechanisms of the pathogen evolution. The results are useful for managing wheat stripe rust in the global scale.
