Location: Cereal Disease Lab2022 Annual Report
Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogens. Sub-objective 1.A. Monitor, collect, and characterize cereal rust pathogen populations in the U.S. for virulence to rust resistance genes in current cultivars. Sub-objective 1.B. Determine levels of genetic variation in Puccinia triticina, P. graminis and P. coronata populations. Sub-objective 1.C. Refine phylogenetics and systematics of P. graminis from Mahonia and other native Berberis spp. in North America. Objective 2: Further develop genomic resources of cereal rust pathogens and identify fungal genes involved in pathogenicity and development. Sub-objective 2.A. Identify effectors of P. graminis f. sp. tritici involved in fungal pathogenicity and host resistance. Sub-objective 2.B. Develop genomic resources and tools for more detailed analysis of P. coronata. Objective 3: Improve host resistance in cereal crops to rust pathogens through investigations in sources and genetics of rust resistance, characterization of various germplasm, and incorporation into adapted germplasm. Sub-objective 3.A. Evaluate wheat, oat and barley germplasm from U.S. breeding programs for rust resistance. Sub-objective 3.B. Identify and characterize new sources of rust resistance in wheat, barley, and oat; and incorporate into adapted germplasm.
Cereal rust fungi (Puccinia coronata, P. graminis, and P. triticina) are dynamic leading to constant changes in the U.S. population and erosion of effective rust resistance in cereal crops. In addition, introduction of foreign isolates, such as Ug99, further threaten cereal production. Development of cereal cultivars with effective rust resistance and management strategies of these diseases depend on monitoring, collection, virulence phenotyping, and genotypic characterization of cereal rust pathogen populations. Rust resistant cereal germplasm will be selected by testing wheat, oat, and barley lines from breeding programs throughout the U.S. and other sources for resistance to these pathogens using the prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. Testing with selected isolates of the cereal rust pathogens and host genetics studies will identify the rust resistance genes in breeding lines and germplasm. Advanced germplasm lines with combinations of rust resistance genes will be selected and released for further use in cultivar development. Rust fungi produce a large arsenal of effector proteins in order to infect and colonize the plant host. Genetic and genomic approaches will be used to identify and characterize effector genes from P. graminis and P. coronata.
This is the final progress report for project 5062-21220-023-000D "Cereal Rust: Pathogen Biology and Host Resistance". Progress is summarized in this report for the entire period of the project from April 2017 through March 2022. A total of 524 United States collections of Puccinia coronata f. sp. avenae (Pca; the oat crown rust pathogen) were received and over 515 isolates of oat crown rust were derived for race identification. The Pca population is highly diverse with many isolates being unique in virulence profile. A total of 163 isolates of the barley leaf rust pathogen (Puccinia hordei) derived from 103 United States field collections were tested for virulence on host differential sets. Differential responses were observed to barley leaf rust resistance genes Rph3, Rph5, Rph6, Rph7, Rph9, Rph10, Rph11, Rph12, Rph13, and Rph14. Virulence was not detected to Rph15. Regional patterns of virulence were observed where virulence to Rph3 was most common in the East Coast and Texas, whereas virulence to Rph5 was most prevalent in the Midwest and the Pacific Northwest, virulence to Rph7 was most common in the East Coast, and virulence to Rph13 was most common in the Pacific Northwest. A total of 1,426 single pustule isolates of P. triticina (the wheat leaf rust pathogen) from the United States were tested for race identification. Twenty-four to 65 different races of P. triticina were found annually. In the Great Plains, the most common races had virulence to Lr39. Races with virulence to Lr21 were at the highest frequency in the spring wheat region. In the southeastern states the most common races had virulence to Lr11, Lr26, and Lr18. Regional variations in virulence could be attributed to regional deployment of the corresponding resistance genes. A total of 831 isolates of P. triticina from 11 major worldwide wheat producing regions were genotyped using 23 SSR marker loci. Similarly, a total of 550 isolates of P. triticina from the worldwide collections were also genotyped using genotyping by sequencing (GBS). SSR and GBS results were congruent. Genotype data combined with race phenotype data indicated that P. triticina populations worldwide are genetically highly diverse and that migration of races-genotypes between major continental regions has occurred in the past and more recently. The population in Europe was the most diverse for genotype groups and the population in China was the most genetically distinct. Some of the GBS groups were found in more than one continental region, which strongly indicated migration between continental regions. Isolates within groups were highly related for race-virulence phenotype, which also indicated that clonal reproduction is most common in the worldwide populations. A total of 158 isolates of P. triticina from the United States from 2011 to 2018 were genotyped using 17,000 GBS SNPs. Over 95% of isolates were found in two widely distributed groups that differ for virulence to leaf rust resistance genes Lr17, Lr3bg, LrB, and Lr28. Many races in both groups are virulent to Lr39, which is in many hard red winter wheat cultivars. Data indicated the widespread movement of clonally reproducing P. triticina in North America. Approximately 350 stem rust samples from wheat, barley, oats and aecial samples from barberry obtained across United States were processed for race identification. 32 races of P. graminis f. sp. tritici (Pgt; the wheat stem rust pathogen) were identified. Race QFCSC was the dominant race east of the Rocky Mountains. Diverse races were found from samples collected from the Pacific Northwest, indicating the sexual cycle is playing an active role in generating pathogen variation. Five races of P. graminis f. sp. avenae (the oat stem rust pathogen), TGB, TGN, TJN, TJJ and TJS were found across the United States, and races TJS and TGN were most common. Several isolates of P. graminis f. sp. secalis (the rye stem rust pathogen) were identified from barley nurseries in California and stem rust sentinel plots in the Lower Rio Grande valley. A total of 1,394 stem rust samples from 20 countries (with a focus on eastern Africa) were received. Race analyses led to the identifications of 298 races of Pgt that possess diverse and novel virulence combinations that pose threats to wheat production. From analyzing international samples, several active sexual populations of Pgt were discovered. These populations were likely the origins of several important stem rust epidemic races, included novel significant virulences, and were identified as targets for future monitoring. A total of 1,913 United States and foreign Pgt isolates/collections were genotyped. These samples were from all continents except Australia and Antarctica. Common genotypes were observed across geographic regions, indicating broad movement between continental regions. Pgt isolates/collections were identified within particular race group clades. Diagnostic marker assays were developed to discriminate the nine most common race groups within the United States to predict race phenotypes of uncharacterized Pgt collections. Updates on the cereal rust diseases were distributed annually by 10 bi-weekly bulletins that were also posted on the ARS website. Collections of rust from the surveys were processed for race identity and the results were distributed through an interactive map hosted at the ARS website in Saint Paul, Minnesota and by posting the results on the website. Objective 2: Further develop genomic resources of cereal rust pathogens and identify fungal genes involved in pathogenicity and development. Historical oat crown rust isolate 203, which caused severe epidemics in the 1940s in the United States, was sequenced by both PacBio and Hi-C, resulting in a fully phased assembly of the genome represented by 18 chromosomes in each haplotype. This genomic resource allows more accurate identification of crown rust genomic regions associated with virulence and plant interaction. Progress on identifying Pgt (Puccinia graminis f. sp. tritici, the wheat stem rust pathogen) effectors was made by sequencing additional isolates within an F2 biparental population of Pgt, and by sequencing isolates from sexual populations. A total of 120 of such Pgt isolates were sequenced in 2017-2022 for the purpose of mapping effectors. Objective 3: Improve host resistance in cereal crops to rust pathogens through investigations in sources and genetics of rust resistance, characterization of various germplasm, and incorporation into adapted germplasm. A total of 3,540 oat breeding lines from different programs in the United States and Canada were evaluated for crown rust resistance in field plots. Additional 404 advanced oat breeding lines from the regional programs were analyzed for crown rust reaction. A total of 1,543 lines from USDA, ARS, Aberdeen were also evaluated for adult plant resistance to oat crown rust in the buckthorn nursery. Analysis of nine different oat recombinant inbred line populations has yielded several strong QTL loci explaining from 30% to 50% of phenotypic variance for adult plant crown rust resistance. Easy to use molecular markers have been developed flanking these QTL regions. Several lines carrying a combination of these QTL regions (up to 4) were developed. Entries from the 2017-2021 Northern Regional Performance, Southern Regional Performance, Uniform Southern Soft Red Winter Wheat, Uniform Eastern Soft White Winter Wheat, and Uniform Southern Soft Red Winter Wheat nurseries were tested with 11 races of P. triticina in seedling tests. The leaf rust resistance genes were postulated on the basis of the infection types to the different races, and in conjunction with the molecular marker data. The data and Lr gene postulations were distributed to the organizers of each nursery. The durable adult plant leaf rust resistance genes Lr74, Lr77 and Lr78 were identified and mapped. These genes contributed to long-lasting leaf rust resistance in cultivars that possessed these genes. The spring wheat AC Taber was determined to have the adult plant resistance gene Lr13 on chromosome 2BS and Lr74. The soft red winter wheat line CI13227 was determined to have quantitative trait loci for adult plant resistance on chromosomes 2AL, 4BS, and 7AL. The broadly-effective seedling leaf rust resistance gene Lr64 was mapped to chromosome 6AL. An additional broadly-effective leaf rust resistance gene was mapped to chromosome 1DS. Molecular markers were developed for Lr64, the gene on 1DS, the two genes in AC Taber and the three QTLs from CI13227 that can be used to select for long lasting leaf rust resistance. A total of 12,500 elite breeding lines and genetic stocks from public/private wheat breeding programs and research institutions in the United States were screened with nine domestic and several selected foreign Pgt races at the seedling stage and with five domestic races in field stem rust nursery. Resistance genes, especially those effective against Ug99 and other foreign races with significant virulence combinations, were postulated. The screening of 1,397 spring barley and 9,283 spring wheat public and private breeding lines, respectively, was coordinated by ARS scientists in Saint Paul, Minnesota for screening at Ug99 field nurseries in Ethiopia and Kenya. Data allowed for the selection of United States wheat and barley cultivars with Ug99 resistance. Combinations of linked stem rust resistance genes were back-crossed into adapted hard red spring wheat lines suggested by collaborating breeders and distributed to breeders for including in their breeding programs. Specifically, a linkage blocks Sr9h+Sr28, Sr15+Sr22 , and Sr2+Fhb1 were introgressed. This is the final progress report for this project which terminated March 2022. For additional information, see report for the replacement project, 5062-21220-025-000D, "Surveillance, Pathogen Biology, and Host Resistance of Cereal Rusts".
1. Sequence identification of six variants of wheat stem rust resistance gene Sr9 each providing resistance to different stem rust pathogen strains. Wheat stem rust caused by Puccinia graminis f. sp. tritici is an emerging threat to wheat production because of the detection of virulent strains such as Ug99. Wheat resistance genes effective to emerging strains are needed to develop wheat varieties with durable stem rust resistance. ARS researchers in Saint Paul, Minnesota identified a total of six variants in the Sr9 wheat stem rust resistance gene in collaboration with scientists from CSIRO and the University of Sydney. Gene modification techniques were used to confirm that four of the variants were changes in a highly related coiled-coil nucleotide-binding site leucine-rich repeat (CC-NB-LRR) type immune receptor that conferred resistance to a unique spectrum of wheat stem rust pathogen isolates. The identification of these alleles will enable them to be combined with other effective genes in wheat breeding, while the high similarity between these proteins will greatly assist in the understanding of structure/function for the design of new resistance specificities so that plant pathologists and breeders can develop new resistance to protect U.S. wheat from stem rust losses.
2. Identification of quantitative trait loci (QTL) for durable leaf rust resistance in wheat. Leaf rust caused by Puccinia triticina, is the most common disease of wheat in the United States and worldwide, resulting in significant yield losses on an annual basis. The leaf rust fungus is highly variable for virulence, with many different races occurring each year in the United States. As a result, obtaining durable leaf rust resistance in wheat cultivars has been difficult to achieve. ARS researchers in Saint Paul, Minnesota determined the chromosome location of genes in the soft red winter wheat breeding line CI13227 that has had long lasting resistance to leaf rust. A population of wheat derived from crossbreeding CI13227 with a susceptible spring wheat, Thatcher, were genotyped with DNA markers and tested for leaf rust resistance as adult plants in field plots over five years. Analysis of the genotyping and resistance data indicated that the chromosomal locations (QTL) for leaf rust resistance in CI13227 were present on chromosomes 2AL, 4BS, and 7AL. DNA based markers were developed that will allow wheat breeders and plant pathologists to select germplasm that carries these resistance genes.
3. Determining the location of a leaf rust resistance gene on chromosome 1DS of wheat. Leaf rust caused by Puccinia triticina, is the most common disease of wheat in the United States and worldwide, resulting in significant yield losses on an annual basis. The leaf rust fungus is highly variable for virulence, with many different races occurring each year in the United States. As a result, many of the previously characterized and mapped leaf rust resistance genes no longer provide any effective resistance to the current P. triticina population in the United States. ARS researchers in Saint Paul, Minnesota determined that a potentially new leaf rust resistance gene was present on chromosome 1DS. This gene provides resistance to the current P. triticina population in the United States. Nine DNA markers were used to map this gene that can also be used by wheat breeders and plant pathologists to select wheat germplasm with the gene.
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