Browsing by Subject "stem rust"

Now showing 1 - 7 of 7
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    Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici
    (Frontiers in Plant Science, 2016-02-24) Steffenson, Brian; Figueroa, Melania; Upadhyaya, Narayana M; Sperschneider, Jana; Park, Robert F; Szabo, Les J; Ellis, Jeff G; Dodds, Peter N
    The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
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    Effect of incubation time and temperature on the phenotypic expression of rpg4 to Puccinia graminis f. sp. tritici in barley
    (Canadian Journal of Plant Pathology, 1997-03-01) Sun, Yonglian; Steffenson, Brian
    To study the effect of incubation time and temperature on the phenotypic expression of rpg4, five barley genotypes with this resistance gene were infected with pathotype QCCJ of Puccinia graminis f. sp. tritici at the seedling stage, then subjected to various times of incubation at either 18-19°C or 27~28°C. Genotypes with rpg4 exhibited low (0, 0;, and 1), mesothetic (e.g. 3-210;, 120;3), and high (3,3) infection types at 18-19°C after initial incubation at 27-28°C for 0-28, 40-76, and 88 or more hours, respectively. A period of 88 or more hours of initial incubation at high temperature rendered the rpg4 resistance completely ineffective against this pathotype of P. g. f. sp. tritici. In contrast, high, mesothetic, and low infection types were found for the same genotypes at 27-28°C after initial incubation at 18-19°C for 0-40, 52-100, and 112 or more hours, respectively. The resistant infection types conferred by rpg4 are apparently established within the first 112 hours after the end of the infection period since subsequent shifts to higher temperature did not result in marked changes in the resistance response. These data indicate the critical importance of maintaining precise temperature control when assessing the infection phenotypes of barley genotypes carrying the stem rust resistance gene rpg4.
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    Genomic resources to study virulence and evolution of cereal rust fungi
    (2021-05) Henningsen, Eva
    Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) and crown rust caused by Pucciniacoronata f. sp. avenae (Pca) are global threats the production of wheat and oat, respectively. Fast evolving populations of both Pgt and Pca limit the efficacy of plant genetic resistance and constrain disease management strategies. Chapter 1 provides background information about both rust fungi and their biology, shares a comprehensive review of the available genome resources in the rusts, and highlights some advancements in rust research and how they can be utilized. Chapter 2 describes a study where my colleagues and I developed a pipeline for identifying candidate susceptibility genes for future study of stem rust virulence using comparative transcriptome-based and orthology-guided approaches. The analysis was targeted to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and reports several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. The approach was complemented with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes. This work could help further the understanding of the molecular mechanisms that lead to rust infection and disease susceptibility; this in turn could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. A significant contribution of this work is a pipeline that can be adapted to study virulence of other rust fungi. Finally, Chapter 3 describes a high-quality genome assembly of Pca isolate 203. The ultimate goal of the assembly is to provide the first fully haplotype-phased, chromosome level reference for Pca. To this end, PacBio long reads and Illumina short reads were obtained to create the initial draft assembly, while Hi-C reads were collected to order contigs and phase the genome. Contigs were assigned to haplotype bins using gene synteny initially, and these bins were aligned to the Pgt 21-0 A haplotype genome to evaluate the probable number of chromosomes and possible chromosome sizes. Future steps for completing the high-quality assembly include an iterative process to fix haplotype phase swaps through manual curation and scaffolding, final chromosome assignment, and annotation with RNAseq data. A collection of publications with my contributions is provided in the appendix section.
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    Reaction of barley seedlings with different stem rust resistance genes to Puccinia graminis f. sp. tritici and P. g. f. sp. secalis
    (Canadian Journal of Plant Pathology, 2005-03-01) Sun, Y; Steffenson, Brian
    Seedling tests are desirable for disease resistance screening in breeding programs because a large number of lines can be evaluated in a short period of time and with modest space requirements. This study was undertaken to identify pathotypes of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) and cultures of the rye stem rust pathogen (Puccinia graminis f. sp. secalis) that might be useful for detecting resistance genes in barley (Hordeum vulgare) at the seedling stage. Barley accessions with different resistance genes (Rpg1, Rpg2, Rpg3, rpg4, and rpgBH) were assessed for their infection types (ITs) to 13 pathotypes of P. graminis f. sp. tritici and two cultures of P. graminis f. sp. secalis at two temperature regimes (18–21 °C and 24–25 °C). The P. graminis f. sp. tritici pathotypes HKHJ and QCCJ were effective for specifically detecting Rpg1 and rpg4, respectively, and will facilitate resistance breeding efforts. No cultures were found to be effective for specifically detecting the resistance of Hietpas-5, PI 382313, or Black Hulless at the seedling stage. Some pathotypes or cultures did, however, produce low ITs on these sources and will therefore be useful for genetic studies involving crosses with susceptible barleys
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    Studies On Wheat Resistance To UG99
    (2010-10) Rouse, Matthew
    Wheat stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) has historically been a devastating disease of wheat. In 1998, a race of Pgt was detected in Uganda that is virulent to the majority of wheat cultivars being grown. This new race, commonly referred to as Ug99, was characterized as race TTKSK based upon the North American stem rust differentials. Race TTKSK has recently spread throughout eastern and southern Africa, and into the Middle East. Data suggest that Ug99 can alternatively be described as Pgt race PTKSK, based upon demonstrated avirulence to stem rust resistance gene Sr21. Accessions of wild relatives of wheat, Triticum monococcum, T. urartu, and Aegilops tauschii were screened with Pgt race TTKSK. Crosses among resistant and susceptible accessions of T. monococcum led to the characterization of two new stem rust resistance genes effective to Pgt-TTKSK. Preliminary screening of 700 accessions of spring wheat led to the identification of 88 accessions with resistance to Ug99. Examination of the genetics of resistance in one of these accessions, SD 1691, identified Sr28 as conferring a high level of resistance. Molecular markers linked to Sr28 were identified on chromosome arm 2BL. Examination of the genetics of resistance in Gabo 56 indicated the presence of a single dominant gene. This gene was temporarily designated as SrGabo56 and mapped on chromosome arm 2BL. Segregation of resistance in the progeny of the cross between SD 1691 and Gabo 56 indicated that Sr28 and SrGabo56 are linked. Characterization of the genetics of resistance to Pgt-TTKSK in synthetic wheat TA4152-37, resulted in the identification of Sr13 in TA4152-37. Molecular markers linked to Sr13 in hexaploid wheat were identified on chromosome arm 6AL. Overall, 3 new stem rust resistance genes effective to Pgt-TTKSK were identified. Molecular markers linked to SrGabo56, Sr13, and Sr28 were described. The identification of markers linked to multiple stem rust resistance genes will facilitate the combination of these genes in breeding lines. The identification of the new sources of resistance to Pgt-TTKSK will provide plant breeders with additional tools to protect wheat from this dangerous race.
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    Using R based image analysis to quantify rust on perennial ryegrass
    (2018-11) Heineck, Garett; Watkins, Eric; Jungers, Jacob; McNish, Ian
    Crown and stem rust caused by Puccinia coronata f. sp. lolii and Puccinia graminis subsp. graminicola are major diseases of perennial ryegrass (Lolium perenne L.) when grown for turfgrass, forage, and seed. Plant breeders and pathologists often quantify rust severity in the field using the modified Cobb scale, but this method is subjective, labor intensive, and dependent on the skill and experience of the scorer. Our objective was to develop a novel, open-source system that couples both ImageJ and R to quantify rust severity on simple RGB images.
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    Virulence of the stem rust fungus and non-host resistance against stem rust
    (2019-10) Li, Feng
    Wheat stem rust is a destructive disease caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), which poses a significant threat to global wheat production. A highly virulent Pgt strain known as Ug99 emerged in Uganda in 1998 overcame an important disease resistance gene Sr31. Ug99 can infect 90% of wheat cultivars worldwide. Part of the Ph.D. research included in this dissertation focuses on creating genomic resources to study Pgt and understanding the underlying genetic differences that explains virulence evolution. The research also aims to discover novel genes in mediating resistance or susceptibility against Pgt in the grass species, Brachypodium distachyon. In Chapter 1, I present a comprehensive literature review of our current state of knowledge of cereal rust fungi, particularly Pgt in light of the recent evolution of new broadly virulent races. I also discuss current genomic resources and approaches to study virulence evolution of rust fungi. Finally, I present an overview of genetic disease resistance and its mechanisms, as the main strategy to mitigate the effect of Pgt in wheat production. Chapter 2 describes the construction of the first de novo haplotype-phased genome assemblies of Pgt, including Ug99 and an Australian Pgt isolate 21-0. Importantly, a systematic comparison of both genomes shows that the Ug99 lineage emerged through a somatic hybridization event. This study also provides the first molecular demonstration that whole nuclear exchange at the vegetative stage contributes to the evolution of rust virulence in the field. One important goal within our scientific community is to develop novel and durable stem rust disease management strategies. Thus, another objective of my dissertation was to investigate non-host resistance against rust fungi to identify genes that may enable the development of these approaches. Using a reverse genetics approach, Chapter 3 describes a pipeline that merges phenotypic and genotypic screenings to identify rust defense-associated genes in Brachypodium distachyon, which serves as a non-host to several cereal rust fungi. Here, I utilized a collection of T-DNA insertional lines of B. distachyon to characterize genes of interest in Brachypodium-rust interactions. Two candidate genes, a WRKY transcription factor and a sugar transporter, were identified to play a role in non-host resistance. Finally, I also attach appendices that refer to my contributions to four other independent publications, including a research manuscript that defines the non-host status of B. distachyon to Puccinia coronate, the causal agent of oat crown rust; a research publication of the cloning of the first effector gene in Pgt; a review and perspectives on B. distachyon as a donor of resistance against cereal rusts and finally one pathogen profile of P. coronata. Overall, research presented in this dissertation has important implications for crop protection and advances the field of biology and genomics in rust fungi. By creating suitable genomic resources to study Pgt and enabling effector discovery, this dissertation is deemed to contribute to rust resistance gene stewardship and minimize wheat losses due to stem rust epidemics.