Research Project: Surveillance, Pathogen Biology, and Host Resistance of Cereal Rusts

Location: Cereal Disease Lab

2023 Annual Report

Objectives
Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogen populations, and characterize foreign populations that threaten U.S. cereal production. • Sub-objective 1.A: Monitor, collect and characterize cereal rust pathogen populations in the U.S. for virulence that overcomes rust resistance genes in current cultivars. • Sub-objective 1.B: Characterize key exotic rust pathogen strains in advance of their introduction to the United States and contribute towards consortia for global pathogen surveillance through strategic partnerships and alliances. • Sub-objective 1.C: Development and/or improvement of molecular diagnostic tools for detection of cereal rust pathogen strains. Objective 2: Develop new genomic resources for cereal rust pathogens, identify links between pathogen phenotypes and genotypes, and improve understanding of the role of the sexual cycle in population dynamics. • Sub-objective 2.A: Develop genomic resources for population genetics and evolutionary studies of cereal rust pathogens. • Sub-objective 2.B: Identify linkages between phenotype and genotype of cereal rust fungi involved in pathogenicity and host resistance. • Sub-objective 2.C: Improve understanding of the roles of the sexual cycle in cereal rust fungal population dynamics. 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. • Sub-objective 3.C: Incorporate rust resistance into adapted germplasm.

Approach
Cereal rust fungi are dynamic leading to constant changes in the U.S. populations, which leads to the erosion of effective resistance in cereal crops. In addition, foreign isolates further threaten cereal production if they are introduced and established. Development of cereal cultivars with effective rust resistance will depend on the monitoring and characterization of virulence phenotypes of the rust pathogens with host differential lines containing single genes for rust resistance. Rust fungi have large, complex genomes and the uredinial stage is dikaryotic with two distinct haploid genomes. Genetic and genomic approaches will be used to (1) complete phased haploid genome assemblies for cereal rust fungi; (2) characterize population genetics of cereal rust pathogens; and (3) identify linkages between phenotype and genotype of cereal rust fungi involved in pathogenicity and host resistance. Surveys and identification of rust infections on Berberis and Mahonia species will be conducted to investigate the potential roles of alternate hosts in pathogen variations and disease epidemiology. Rust resistant cereal germplasm will be selected by testing wheat, oat, and barley lines from breeding programs throughout the U.S. for resistance to Pca, Pgt, P. hordei and P. triticina, using prevalent races, and races that have high virulence to rust resistance genes common in released cultivars and breeding lines. The identity of rust resistance genes in breeding lines will be postulated in seedling tests using specific races of these rust fungi. Adult plant resistance of breeding lines will be evaluated in field plots. Genetic loci that mediate rust resistance genes will be identified along with molecular markers that facilitate plant breeding via marker assisted selection. Advanced germplasm lines with combinations of rust resistance genes will be derived and distributed for use in cultivar development.

Progress Report
In the first full year of the project, we made progress in the following objectives: Objective 1: Monitor, collect, and characterize U.S. cereal rust pathogen populations, and characterize foreign populations that threaten U.S. cereal production. In 2022, 243 isolates of Puccinia triticina (Pt) were processed for race identification. A total of 37 races identified in the United States. The hot and dry weather reduced the number of collections received in 2022. Races MNPSD and MPPSD that are virulent to many winter wheat cultivars were the two most common races and were found throughout the Great Plains region. Race TNBJS that is virulent to many spring wheat cultivars, was detected in Minnesota and North Dakota, and was the third most common race. In 2023, 129 collections of leaf rust have been received to date. These, and additional collections, will be processed for race identification later in 2023-early 2024. In 2022, 48 collections of Puccinia coronata f. sp. avenae (Pca) from various regions of the United States were received yielding 101 single pustule isolates that were scored on the oat differential lines. In 2023, we have received 57 collections of Pca from the southern region of the United States yielding 145 single pustule isolates. To date, 10 of these isolates have been scored on the oat differential lines. The Pca population is highly diverse with many isolates being unique in virulence profile indicating defeat of all single gene seedling resistance loci identified in oat. A total of seven collections of Puccinia hordei (Ph), the barley leaf rust pathogen, were received during the months of April and May in 2023. Race QFCSC of the wheat stem rust pathogen was identified from wheat stem rust samples collected from Alabama, Louisiana, and South Dakota in the 2022 crop season, the dominant race in North America. The rye stem rust pathogen was identified from infected barley from California, Minnesota, North Dakota and New York. Five races of the oat stem rust pathogen, DBD, JBD, SGD, TGN and TJS, were identified from 15 oat stem rust samples collected from California, Florida, Louisiana, and Texas in 2022. Race TGN continued to be the dominant race in the oat stem rust population in the United States. From a total of 47 wheat stem rust samples received from Ethiopia, races TTKTT and TTKTT+ of the Ug99 race group (clade I), TTRTF (clade III), and TKKTF and TTKTF (clade IV) were identified. The most virulent race in the Ug99 race group, TTKTT+, was detected for the first time in Ethiopia. Stem rust infections on wheat have been observed in Louisiana, Oklahoma, and Kansas and stem rust infections on oat have been observed in Alabama, Louisiana, and Texas as recently as to June 6, 2023. Race analyses are in progress. The transfer of molecular diagnostics tools from a recently retired project SY to a newly hired project SY was completed. A total of 37 molecular diagnostic assays were performed to evaluate the phylogenetic origin of international Pg isolates from East Africa. Objective 2: Develop new genomic resources for cereal rust pathogens, identify links between pathogen phenotypes and genotypes, and improve understanding of the role of the sexual cycle in population dynamics. A total of 124 isolates of Pt derived from a random mating population were phenotyped for virulence to 24 Thatcher lines of wheat near-isogenic for single leaf rust resistance genes. The isolates were genotyped by sequencing (GBS). After filtering the genotype data, 103 isolates were used for genome wide association analysis (GWAS) with a phased chromosome level assembly genome of Pt. Single nucleotide polymorphisms (SNPs) significantly associated with virulence/avirulence to Lr10, Lr14a, Lr3ka, Lr11, Lr17, and Lr30 on a single chromosome in both haplotypes were detected. The genomic locations of the SNPs will be used to find secreted proteins that may be candidate genes that condition avirulence/virulence to leaf rust resistance genes in wheat. A fully phased assembly of the Pca genome, represented by 18 chromosomes in each haplotype, was published and made public. This genomic resource has allowed us to delve deeper into the diversity of oat crown rust pathogen and its variation leading to identification of candidate effector genes corresponding to plant resistance loci. The rye stem rust pathogen was identified from aecial infections of common barberry collected from southeastern Minnesota and central Wisconsin in 2022. Additional isolates from aecial samples from Minnesota are being developed and characterized using a new set of genetic stocks developed through this project. Preliminary results indicated that the rye stem rust pathogen possesses virulence to several of the major resistance genes used in wheat. Data transfer of genomic resources from a recently retired project SY to a recently hired project SY has been completed. In total, current in house Pg genomic resources include 13 PacBio HiFi and 120 Illumina sequenced isolates. Initial assemblies have been performed for all Pg isolates. 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. In this reporting period, the SrTm4 stem rust resistance gene was fine-mapped to within a 0.06 cM interval on chromosome 2A of wheat. Molecular markers tightly linked and predictive of this resistance gene were reported, which can facilitate the utilization of this recessively inherited stem rust resistance gene with effectiveness to several virulent stem rust pathogen strains. Analyses were completed and a report was drafted describing the genetics of stem rust resistance in wheat variety 'Linkert'. Wheat lines with the combination of disease resistance genes Sr2 and Fhb1 were distributed to collaborating wheat breeders at the University of Minnesota, South Dakota State University, and North Dakota State University. Entries from the 2023 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 the leaf rust pathogen 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 leaf rust (Lr) gene postulations were distributed to the organizers of each nursery. A total of 3,500 wheat breeding lines and genetic stocks were evaluated with multiple stem rust races, including Ug99 and other virulent stem rust pathogen races that caused epidemics. These lines were also tested in field nurseries in Saint Paul, Minnesota inoculated with a composite of domestic stem rust pathogen races. Rust reaction data were distributed to breeders via regional nursery coordinators. In 2023, a total of 730 spring wheat and 340 spring barley lines from 12 collaborating breeders were assessed for response to virulent strains of the stem rust pathogen (including Ug99) in the field in Kenya and Ethiopia. Lines with adult plant resistance to stem rust were identified. A line previously identified with adult plant resistance to Ug99 was released by North Dakota State University as 'ND-VitPro' and reported in the Journal of Plant Registrations. In 2022, over 2,000 oat breeding lines from various oat uniform nurseries and different breeding programs in the United States and Canada were evaluated for crown rust resistance in the buckthorn nursery and nearby field plots. Close to 300 diploid oat accessions from the United States and Canadian seed bank collections were obtained and evaluated for their phenotypic reaction to various crown rust isolates. We recently released two oat lines, each carrying a combination of 3 APR loci (Journal of Plant Registration, in review) under a Material Transfer Agreement (MTA) requiring that the combination of QTL be retained in any resulting varieties utilizing the appropriate PCR based markers. These lines have been rapidly adapted by the various breeding programs in the United States and Canada. A comprehensive literature review has been completed on known sources of resistance to barley stripe rust. Seed for resistant sources will be obtained and crossed to the universal susceptible barley accession Manchuria to develop a panel of near-isogenic lines.

Accomplishments
1. New wheat leaf rust disease resistance gene discovered. Protection of the U.S. wheat crop from diseases is necessary for production of high-quality wheat consumed by the American public and for the United States to continue to be a global leader in wheat exports. Leaf rust (Lr) caused by Puccinia triticina (Pt) is the most common disease of wheat in the United States, resulting in significant yield losses on an annual basis. ARS researchers in Saint Paul, Minnesota, discovered a new leaf rust resistance gene in wheat. This new gene gives resistance to all of the current races or biotypes of Pt that occur in the United States. This gene can be used by public and private wheat breeding organizations to develop new U.S. wheat cultivars that will be highly resistant to leaf rust.

2. Identification of wheat leaf rust pathogen DNA associated with virulence to wheat leaf rust resistance. Protection of the U.S. wheat crop from diseases is necessary for production of high-quality wheat consumed by the American public and for the United States to continue to be a global leader in wheat exports. Leaf rust (Lr) caused by Puccinia triticina (Pt), is the most common disease of wheat in the United States and worldwide, resulting in significant yield losses on an annual basis. ARS researchers in Saint Paul, Minnesota, conducted a study to find regions in DNA in Pt that are close to genes that give the fungus the ability to attack wheat. Using advanced DNA sequencing technology and new bioinformatics approaches, DNA regions that are close to genes that give the fungus that ability to attack wheat cultivars with six different leaf rust resistance genes were found. This data can be used to find genes that allow the rust fungus to attack wheat cultivars with many different resistance genes. This information may also be used to (1) develop new rust resistance genes that are resistant to all races of Pt using advanced biotechnology methods and (2) enable next-generation pathogen surveillance techniques that track virulence factors.

3. Identification of diverse wheat stem rust pathogen strains in Idaho. Protection of the U.S. wheat crop from diseases is necessary for production of high-quality wheat consumed by the American public and for the United States to continue to be a global leader in wheat exports. Emerging strains of the wheat stem rust pathogen threaten U.S wheat production. ARS researchers in Saint Paul, Minnesota, identified six wheat stem rust pathogen strains from a single sample from Idaho Falls in mid-July 2022. The virulence of these strains was unusual and included virulence to resistance genes currently used to protect U.S. wheat from strains of the stem rust pathogen. In addition, the samples came from the alternate host of stem rust, barberry, indicating the importance of monitoring the alternate host in disease surveillance. This finding impacted wheat breeders in the United States by directing efforts to select for stem rust resistance to additional strains of the stem rust pathogen now present in the United States.

4. New oat lines with durable oat crown rust resistance. Production of high-quality oats in the United States requires control of dangerous oat diseases. Oat crown rust is the most devastating disease of this crop leading to major yield losses on an annual basis, especially in organic production. The oat crown rust pathogen is highly variable and overcomes oat crown rust resistance genes when they are used singly. ARS researchers in Saint Paul, Minnesota, developed two oat lines, CDL 111 and CDL 167, carrying a combination of 3 adult plant resistance genes. These lines had low disease ratings compared to susceptible checks and exhibited good agronomic characteristics. These lines have been widely adopted by the oat breeding community with many requests for the germplasm, as evident from the number of Material Transfer Agreements (MTAs) to date. Oat breeders are using these lines as parents in their breeding programs to derive new oat cultivars with durable resistance to oat crown rust.

Review Publications
Nazareno, E.S., Fiedler, J.D., Miller, M.E., Figueroa, M., Kianian, S. 2022. A reference-anchored oat linkage map reveals quantitative trait loci conferring adult plant resistance to crown rust (Puccinia coronata f. sp. avenae). Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-022-04128-6.
Chemonges, M., Herselman, L., Pretorius, Z.A., Rouse, M.N., Mare, A., Boshoff, W.H. 2022. Mapping and validation of all-stage resistance to stem rust in four South African winter wheat cultivars. Euphytica. 219. Article 11. https://doi.org/10.1007/s10681-022-03143-4.
Negash, T., Edae, E.A., Tilahun, L., Anderson, J.A., Rouse, M.N., Bajgain, P. 2022. Genome-wide association mapping for field and seedling resistance to the emerging Puccinia graminis f. sp. tritici race TTRTF in wheat. The Plant Genome. 15(4). Article e20274. https://doi.org/10.1002/tpg2.20274.
Mehnaz, M., Dracatos, P., Dinh, H.X., Forest, K., Rouse, M.N., Park, R.F., Singh, D. 2022. A novel locus conferring resistance to Puccinia hordei maps to the genomic region corresponding to Rph14 on barley chromosome 2HS. Frontiers in Plant Science. 13. Article 980870. https://doi.org/10.3389/fpls.2022.980870.
Athiyannan, N., Long, Y., Kang, H., Chandramohan, S., Bhatt, D., Zhang, Q., Klindworth, D.L., Rouse, M.N., Friesen, T.L., MciIntosh, R., Zhang, P., Forrest, K., Hayden, M., Patpour, M., Hovmoller, M.S., Hickey, L.T., Ayliffe, M., Cai, X., Lagudah, E.S., Periyannan, S., Xu, S.S. 2022. Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat. Theoretical and Applied Genetics. 135: 2627-2639. https://doi.org/10.1007/s00122-022-04132-w.
Abdulridha, J., Min, A., Rouse, M.N., Kianian, S., Isler, V., Yang, C. 2023. Evaluation of stem rust disease in wheat fields by drone hyperspectral imaging. Sensors. 23(8). Article 4154. https://doi.org/10.3390/s23084154.
Gracia, N., Yin, L., Dukowic-Schulze, S., Milsted, C., Kianian, P.M., Kianian, S., Pawlowski, W.P., Chen, C. 2022. Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination. BMC Genomics. 23. Article 702. https://doi.org/10.1186/s12864-022-08922-w.
Henningsen, E.C., Hewitt, T., Dugyala, S., Nazareno, E., Gilbert, E., Li, F., Kianian, S., Steffenson, B.J., Dodds, P.N., Sperschneider, J., Figueroa, M. 2022. A chromosome-level, fully phased genome asssembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in cereal rusts. G3, Genes/Genomes/Genetics. 12(8). Article jkac149. https://doi.org/10.1093/g3journal/jkac149.
Carlson, C.H., Fiedler, J.D., Naraghi, S., Nazareno, E., Ardayfio, N., Mcmullen, M., Kianian, S. 2022. Archetypes of inflorescence: Genome-wide association networks of panicle morphometric, growth, and disease variables in a multiparent oat population. Genetics. https://doi.org/10.1093/genetics/iyac128.
Kolmer, J.A., Rouse, M.N. 2022. Adult plant leaf rust resistance QTL derived from wheat line CI13227 maps to chromosomes 2AL, 4BS, and 7AL. The Plant Genome. 15(3). Article e20215. https://doi.org/10.1002/tpg2.20215.
Nyamesorto, B., Zhang, H., Rouse, M.N., Wang, M., Chen, X., Huang, L. 2022. A transcriptomic-guided strategy used in identification of a wheat rust pathogen target and modification of the target enhanced host resistance to rust pathogens. Frontiers in Plant Science. 13. Article e962973. https://doi.org/10.3389/fpls.2022.962973.
Li, H., Luo, J., Zhang, W., Hua, L., Li, K., Wang, J., Xu, B., Yang, C., Wang, G., Rouse, M.N., Dubcovsky, J., Chen, S. 2023. High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust. Theoretical and Applied Genetics. 136. Article 120. https://doi.org/10.1007/s00122-023-04369-z.
Greatens, N.J., Klejeski, N., Szabo, L.J., Jin, Y., Olivera, P.D. 2023. First report of a rust fungus (Puccinia sp.) infecting lemongrass in Minnesota. Plant Disease. https://doi.org/10.1094/pdis-10-22-2314-pdn.