Browsing by Subject "oat crown rust"

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    Dissecting the oat crown rust pathosystem: identifying virulence factors and developing sources of adult plant resistance
    (2021-07) Nazareno, Eric
    This dissertation examines both sides of the crown rust pathosystem: the pathogen, Puccinia coronata f. sp. avenae, and the host, oat (Avena sativa L.). Oat is one of the most important cereals in the world, but its production is persistently constrained by crown rust. For decades, numerous studies have been conducted to understand the pathosystem but crown rust remains an important disease that devastates oat production. The quest to understand the molecular basis of the disease is far from over, but new resources make research advances possible. Chapter 1 and the review paper in Appendix 1 provide a general background about oat and crown rust. The chapter outlines the recent advances in oat and crown rust research that were not covered in the review paper. The review paper, on the other hand, presents details on the life cycle of the pathogen, economic importance, and disease management measures currently implemented for crown rust. Rusts are known to be “shifty” and the genetic variability of crown rust, in particular, has undermined efforts to control the disease. To help understand this variability, Chapter 2 presents a study on the evolution of virulence of crown rust populations over a 25-year period, with the use of the recently released crown rust genomes. In this chapter, I conducted a genome-wide association study (GWAS) to detect putative avirulence (Avr) genes using genotype data called against the 12SD80 and 12NC29 reference genomes. Several putative candidate Avr genes were identified through phenotyping with the oat differential lines, which also provided insights on the similarity of some of the Pc genes. This study may have meaningful impacts in developing molecular markers for diagnostics and tracking of pathogen movement and may provide a foundation for future work on crown rust race-typing based on genetic profiles. Chapters 3 to 5 focus on the other side of the pathosystem and present efforts on identifying and developing sources of oat adult plant resistance (APR). The apparent constant gain of pathogen virulence without fitness cost creates a shortage of resistance genes for crown rust breeding and compels us to deploy genes with broad-spectrum effects, in combination with race-specific genes. Chapter 3 describes a linkage mapping study of five recombinant inbred line (RIL) populations that identified two major quantitative trait loci (QTL) for APR on oat chromosome 4D and a minor QTL on chromosome 6C. In Chapter 4, four more RIL populations were mapped and an additional four unique QTL were discovered, one each on chromosomes 5D, 7C, 4D, and 7A. These are the first mapping studies that employed markers that are anchored to the OT3098 v1 oat reference genome. Moreover, qPCR markers linked to the QTL were developed for marker-assisted selection. Chapter 5 presents a pyramiding approach with the use of three sets of diallel crosses and attempts to generate effective combinations of all available QTL for APR. These involved the seven QTL mapped in Chapters 3 and 4 and a QTL on chromosome 4A from the MNBT lines. In the first set of crosses, up to three QTL were pyramided and lines with eight different combinations of at least two QTL were developed. These lines will be further tested in different years and locations and will be released as breeding germplasm to oat breeders. The QTL combinations have potential to extend the durability of crown rust resistance in the field. This work targets managing a “shifty” fungus, because after all, a variable pathogen calls for variable disease measures.
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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.