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

Location: Cereal Disease Lab

2022 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
This is the first progress report for project 5062-21220-025-000D "Surveillance, Pathogen Biology, and Host Resistance of Cereal Rusts" that replaced project 5062-21220-023-000D, "Cereal Rust: Pathogen Biology and Host Resistance". In the first three months of the new 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, thirty collections of the wheat leaf rust Puccinia triticina (Pt) have been received by scientists at the Cereal Disease Laboratory in mid-June. Thirty single uredinial isolates have been processed for race identification. To date, we have received 28 collections of the crown rust Puccinia coronata (Pc) from various regions of the United States (substantially reduced compared to previous years) and are in process of characterizing the fungal population for diversity. Two collections of the barley leaf rust Puccinia hordei (Ph) were received during April and May of 2022. Stem rust on wheat and barley have not been observed in the crop season of 2022. Fifteen oat stem rust samples were received from Louisiana and Florida, and race analyses are in progress. Preliminary results indicated that race TGN continues to be the dominant race in the oat stem rust population in the United States. A total of 42 stem rust wheat stem rust samples and 3 aecial samples from barberry have been received by an ARS lab located in Fort Detrick from international collaborators and are in the process of being increased. 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. One hundred and twenty-four isolates of the wheat leaf rust pathogen derived from a random mating population were tested for virulence in 24 lines of Thatcher wheat that is near isogenic for leaf rust resistance genes. The isolates were genotyped by sequencing. After filtering the genotype data, 103 isolates were used for genome-wide association analysis with an updated chromosome level-phased haplotype assembly of Pt. Preliminary results indicate single nucleotide polymorphism (SNP) significantly associated with virulence to wheat leaf rust resistance genes Lr3 and Lr26. Aecial infections of common barberry have been observed in 2022 and collected from southeastern Minnesota. Samples are currently being analyzed. Aecial samples were collected from barberry inoculated with telia of Puccinia graminis f. sp. secalis in the greenhouse. Isolates are being developed to analyze the virulence composition. 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, we described the genetics of seedling and field resistance of bread wheat to race TTRTF of the wheat stem rust pathogen using single-race field nurseries deployed in Ethiopia. Association analysis for resistance to TTRTF resulted in detection of 20 markers in 11 chromosomes; a marker associated with resistance at both seedling and adult plant stages was identified. Models with 2-4 quantitative trait loci (QTL) combinations reduced seedling and field disease severity by 12%-48% and 9%-17%, respectively. Wheat lines with the combination of stem rust resistance genes Sr26+Sr61 were continued in backcrossing to recurrent parents contributed by collaborating wheat breeders at the University of Minnesota, South Dakota State University, and North Dakota State University. Wheat lines with wheat leaf rust resistance gene Lr78 were continued to be backcrossed to recurrent parents contributed by collaborating wheat breeders at the University of Minnesota, South Dakota State University, and North Dakota State University. Over 1,800 oat breeding lines and genetic stocks with combination of seedling and/or adult plant resistance genes are being evaluated in the buckthorn crown rust nursery. The phenotypic data on these lines will be collected in the summer of 2022 as disease symptoms progress. A total of 2500 elite breeding lines and genetic stocks from public and private wheat breeding programs and research institutions in the United States were planted in the field stem rust nurseries last fall. These nurseries are currently being inoculated. Entries from the 2022 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 leaf rust in seedling tests. Leaf rust resistance genes were postulated based on the infection types caused by 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.

Accomplishments
1. Identification of wheat resistance loci effective to emerging wheat stem rust pathogen race TTRTF. Identification of wheat resistance loci effective against emerging wheat stem rust pathogen race TTRTF. Emerging races of the stem rust pathogen threaten wheat production. Race TTRTF of the wheat rust pathogen caused a stem rust epidemic in Sicily in 2016. ARS researchers in Saint Paul, Minnesota, identified quantitative trait loci (QTL) effective to TTRTF using field nurseries in Ethiopia inoculated with race TTRTF and seedling assays of a panel of bread wheat lines. Genome mapping association analysis for resistance to TTRTF resulted in detection of 20 QTL in 11 chromosomes. The QTL tagged by marker S1B_175439851 was associated with resistance at both seedling and adult plant stages. Wheat lines with 2-4 QTL combinations showed reduced seedling and field disease severity by 12%-48% and 9%-17%, respectively. Identification of resistance lines and QTL is expected to assist plant pathologists and breeders in selection towards improved resistance to TTRTF.

2. Identification of genetic markers associated with avirulence-effector genes in Puccinia triticina. Identification of genetic markers associated with genes important for virulence in the wheat leaf rust pathogen. Leaf rust 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. The leaf rust fungus is highly variable in virulence, with many different races occurring each year in the United States. The objective of this research was to find genetic markers in Pt that are associated with genes that control virulence that overcomes specific leaf rust resistance genes in wheat. ARS researchers in Saint Paul, Minnesota, tested a random mating population of Pt for virulence in 24 lines of Thatcher wheat that carry single genes for leaf rust resistance. A total of 103 Pt isolates were genotyped used for a genome wide association analysis. Genome sequence single DNA base changes (SNP) associated with virulence to leaf rust resistance genes Lr3 and Lr26 were detected. These genetic markers can be used by plant pathologists to find genes that are associated with virulence in Pt.

3. Development of chromosome-level fully phased genome assembly of oat crown rust. Development of a genome sequence assembly for the oat crown rust pathogen. Previous studies have clearly illustrated that oat crown rust has become drastically more virulent in the past decade accumulating more virulent genes in a single isolate. Thus, development of diagnostic virulence markers and robust surveillance activities with capacity for large volume of samples is particularly critical for this pathogen that is highly variable and virulent. ARS researchers in Saint Paul, Minnesota, completed a fully phased genome assembly with 18 complete chromosomes. This genome assembly will significantly enhance the ability of plant pathologists to discover diagnostic markers for pathogen virulence genes to enable a robust pathogen surveillance program.