Plant Sciences Doctoral Work

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Browsing Plant Sciences Doctoral Work by browse.metadata.program "Plant Pathology"

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    Characterization of Genetic Resistance to Sclerotinia sclerotiorum and Epidemiology of the Disease in Brassica napus L.
    (North Dakota State University, 2020) Shahoveisi, Fereshteh
    This dissertation contains three research chapters conducted on Sclerotinia stem rot (SSR) of canola (Brassica napus L.). This disease is caused by the fungus Sclerotinia sclerotiorum and is considered endemic in canola-producing areas of North Dakota. The first research chapter presents results of a study that evaluated the role of eight phenotyping scoring systems and nine variant calling and filtering methods in detection of QTL associated with response to SSR. The study, conducted on two doubled-haploid mapping populations, showed that using multiple phenotypic data sets derived from lesion length and plant mortality and imputing missing genotypic data increased the number of QTL detected without negatively affecting the effect (R2) of QTL. Nineteen QTL were detected on chromosomes A02, A07, A09, C01, and C03 in this study. The second research chapter presents results of a work that assessed the role of temperature regimes and wetness duration on S. sclerotiorum ascospore germination and ascosporic infection efficiency. This study showed that optimum ascospore germination occurred at 21 °C while it significantly decreased at 10 and 30 °C. Infection efficacy experiments indicated that extreme temperatures and interrupting wet periods were detrimental for the disease development. A logistic regression model with 75% accuracy was developed for the disease perdition. The third research chapter presents results of a study that evaluated the role of temperature on mycelial growth of 19 S. sclerotiorum isolates collected from different geographical regions and on SSR development on plant introduction (PI) lines with different levels of resistance. Mycelial growth and disease development peaked at 25 °C. While lesion expansion on resistant cultivars and the susceptible check was negatively affected at 30 °C, the disease developed significantly on the PI with a high level of susceptibility. Results of these studies provide insights into integrated management strategies of SSR.
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    Evaluation of Management Tools for Stripe Rust in Hard Red Spring Wheat and Assessment of Virulence Phenotypes and Aggressiveness in Puccinia striiformis Isolates
    (North Dakota State University, 2019) Evin, Bryn Anndi
    Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an economically important foliar disease of wheat (Triticum aestivum). In the last decade, losses from stripe rust in North Dakota (ND) have increased, peaking at 5% in 2015. Three research studies were conducted to address questions on the pathogen, varietal resistance, and integrated management. The objective of the first study was to (i) identify virulent phenotypes of Pst isolates collected from ND from 2015 to 2017 and assign races, and (ii) determine the effect of temperature on in vitro urediniospore germination, latency, and lesion spread. Across the three years, five races were detected with PSTv 37 being the most common. The highest urediniospore germination occurred at 12oC followed by 16oC. Pst isolates had shorter latency at 21oC and larger lesion spread at 16oC. The objective of the second study was to evaluate seedling resistance and adult plant resistance in the North Dakota State University spring wheat breeding program using races PSTv 37 and PSTv 52. Results from seedling experiments indicated only four and two lines were resistant to PSTv 52 and PSTv 37, respectively. Adult plant resistance experiments were unsuccessful in 2019, and will be conducted again in the future. The objective of the third study was to develop fungicide timing recommendations for wheat rust (stripe and leaf) based on varietal resistance and time of disease onset. Rust developed in five of the eight field trials, and timing of disease onset was categorized by growth stage (tillering, flag leaf, or early-flowering). Results indicated fungicide application timing was influenced by timing of disease onset and varietal resistance. When rust was detected at the tillering growth stage on the susceptible variety, the best time to apply a fungicide was at Feekes 9. When rust was detected at flag leaf or beyond on a susceptible variety, a fungicide application at Feekes 10.51 provided the adequate disease reduction and protection of yield. Results from these research studies provide a better understanding of Pst, determined seedling resistance in the breeding program, and provides field data to refine management recommendations for wheat rusts in ND.
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    Further Characterization of Pathogen Virulence and Genetic Mapping of New Virulence Genes in Pyrenophora tritici-repentis, the Causal Agent of Tan Spot of Wheat
    (North Dakota State University, 2020) Guo, Jingwei
    The ascomycete Pyrenophora tritici-repentis (Ptr) causes tan spot of wheat, a devastating foliar disease on both common wheat (Triticum aestivum L., 2n=6x=42, AABBDD) and durum (T. turgidum ssp. durum L., 2n=4x=28, AABB). Ptr is known to produce three necrotrophic effectors (NEs), namely Ptr ToxA, Ptr ToxB and Ptr ToxC, to cause disease by interacting with corresponding host sensitivity genes. However, many studies in the last twenty years have suggested that Ptr produces additional virulence factors. My Ph.D. research focused on further identification and genetic mapping of new virulence genes in Ptr. In Chapter 2, a bi-parental fungal population was developed from a cross between two genetically modified heterothallic fungal strains followed by genotyping, phenotyping and QTL mapping. Two QTLs were identified with one being major and the other being minor, which confer virulence of 86-124 toward a Ptr ToxA-insensitive wheat line. In addition, the multiple copy gene ToxB was mapped to two genetically independent loci with one having five copies and the other having a single copy. In Chapter 3, I further characterized virulence of some Ptr isolates obtained from Chapter 2 that do not produce any known NEs. These isolates should be classified as race 4 but were found to still cause disease on many common wheat and durum cultivars. Using a common wheat host population, I identified several QTLs associated with the reaction to these isolates, which are different from three known host sensitivity gene loci. In Chapter 4, several natural race 4 isolates collected in North Dakota were shown to cause no or little disease on common wheat genotypes but cause disease on durum and other tetraploid wheat. Using a segregating population, I identified several new QTL associated with disease caused by these race 4 isolates, suggesting the presence of new virulence factors in these isolates. My Ph.D. research greatly advanced the understanding of the genetics of host-pathogen interaction in wheat tan spot and provided important information to wheat breeding programs aiming to improve tan spot resistance.
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    Managing Soybean Cyst Nematode by Utilizing Cover Crops and Resistant Sources from Early Maturing Soybean Accessions
    (North Dakota State University, 2020) Acharya, Krishna
    Greenhouse and microplot studies were conducted for understanding the effects of cover crop species/cultivars for hosts and population reduction of soybean cyst nematode (SCN; Heterodera glycines) from the fields of North Dakota. Moreover, early-maturing soybean [Glycine max (L.)] accessions from different countries of origin were screened for resistance against two common SCN populations for finding new sources of resistance. Thirty-eight cover crop species/cultivars were evaluated for their hosting ability of two SCN populations (SCN103 and SCN2W) from two fields of North Dakota in greenhouse experiments. The majority of the tested crops were non-hosts for both SCN populations. However, a few of them, such as Austrian winter pea (Pisum sativum L.), crimson clover (Trifolium incarnatum L. cv. Dixie), crambe (Crambe abyssinica, cv. BelAnn), field pea, cvs. Aragorn and Cooper, hairy vetch (Vicia villosa Roth), turnip (Brassica rapa L. cv. Purple top), and white lupine (Lupinus albus L.) were poor-hosts/hosts of both SCN populations. Furthermore, thirteen of them were tested for the SCN population reduction either or both in the greenhouse and microplot experiments. Out of 13, at least four crops, such as annual ryegrass (Lolium multiflorum L.), brown mustard (Brassica juncea L. cv. Kodiak), daikon radish (Raphanus sativus L.), and turnip cv. Pointer showed more than 50% population reduction compared with initial population densitiy, consistently in the greenhouse or microplot experiments. The resistance screening of 152 early-maturing soybean accessions showed that a majority of the accessions were susceptible/moderately susceptible to both SCN populations (SCN HG type 0 and 2.5.7), while a few (n=18) showed good resistance responses to both or either of the SCN populations. The cover crops, which were non-hosts/poor-hosts and have a greater ability for the SCN population reduction have great potential to be included in an integrated SCN management strategy. The novel resistant accessions identified in this study have the potential to be used in soybean breeding for developing SCN-resistant cultivars after confirming their resistance response and identifying the resistance genes/loci. The results obtained from this study helps in developing a sustainable SCN management strategy in the northern Great Plains.
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    The Molecular Basis of Demethylation Inhibitor Fungicide Resistance in Cercospora beticola and the Role of Seed Inoculum in Cercospora Leaf Spot Disease of Sugar Beet
    (North Dakota State University, 2020) Spanner, Rebecca Ellen
    Cercospora leaf spot (CLS) is the most destructive foliar disease of sugar beet worldwide. CLS is caused by the filamentous fungus Cercospora beticola. Disease management currently relies upon timely application of fungicides, but reliance on certain chemical classes has led to the development of resistance in multiple C. beticola populations. One such class is the demethylation inhibitor (DMI) fungicides of which the genetic basis of resistance has been unclear. Therefore, the first objective of this PhD research was to perform a genome-wide association study on 190 C. beticola isolates to identify mutations associated with tetraconazole (a common DMI) fungicide resistance. Whole genome resequencing identified multiple novel loci associated with sensitivity to tetraconazole including a pleiotropic drug resistance ATP-binding cassette transporter, a regulator of G-protein signaling domain (RGD) protein, a DYRK protein kinase and mutations within and upstream of the gene encoding the DMI target Cytochrome P450 51 (CYP51). This demonstrated the genetic complexity in resistance to DMIs and suggested the involvement of cellular signaling and multidrug resistance as well as target site mutations. The second objective of this research was to investigate the potential of seedborne C. beticola to initiate CLS disease in sugar beet. We showed that viable C. beticola was present in commercial sugar beet seed lots and could function as primary inoculum to cause CLS symptoms in seedlings. All strains identified were resistance to QoI fungicide chemistries and most were also resistant to DMI fungicides. Detection of C. beticola DNA in xylem sap suggested that the fungus may be systemically colonizing the plant via the vascular system. Long-read nanopore sequencing detected other potential pathogenic fungi in seed DNA (e.g. Fusarium and Alternaria spp.) that may also act as primary inoculum sources for important sugar beet diseases. This PhD research has improved our understanding of the development of DMI fungicide resistance in C. beticola, as well as highlighted the importance of seed inoculum in the manifestation of CLS in sugar beet, both of which could improve CLS disease management in the future.
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    Sensitivity of Alternaria Species to Ten Single-Site Mode of Action Fungicides
    (North Dakota State University, 2020) Rodriguez, Sarah Marie Budde
    Early blight caused by Alternaria solani and brown spot caused by the small-spored Alternaria spp., Alternaria alternata, Alternaria arborescens, and Alternaria tenuissima are observed annually in midwestern potato production areas. The use of foliar fungicides remains a primary management strategy. However, Alternaria spp. have developed reduced-sensitivity and/or resistance to many single-site fungicides such as quinone outside inhibitor (QoI), succinate dehydrogenase inhibitor (SDHI), and anilinopyrimidines (AP) fungicides in recent years. Boscalid, fluopyram, solatenol, and adepidyn are EPA-registered SDHI fungicides applied commercially to a variety of crops including potato. High intrinsic activity was observed in fluopyram, solatenol and adepidyn to A. solani isolates. Adepidyn and solatenol reduced disease severity caused by A. solani in field evaluations. Molecular characterization of 2018 A. solani field isolates determined that the frequency of the D123E and H134R SDH mutations increased. In contrast, the H278R/Y and H133R SDH mutations were found at low frequency. Adepidyn demonstrated the highest intrinsic activity against the small-spored Alternaria spp. but high intrinsic activity was also observed with boscalid, fluopyram, and solatenol. In vivo experiments demonstrated that adepidyn, solatenol, and fluopyram were more effective at managing A. arborescens and A. tenuissima than boscalid. Under greenhouse conditions, adepidyn and solatenol reduced brown spot severity caused by A. alternata to a greater extent than did fluopyram and boscalid. Results of these studies determined that accurate pathogen identification of small-spored Alternaria spp. may be important for brown spot management. Fludioxonil and cyprodinil exhibited a higher efficacy against of A. solani isolates when compared to pyrimethanil in greenhouse assays. Fludioxonil and cyprodinil were also highly efficacious against the Alternaria spp. evaluated and appear to be a good addition into fungicide rotation programs for early blight and brown spot management. Anilinopyrimidine (AP) (pyrimethanil and cyprodinil) and phenylpyrrole (PP) (fludioxonil) fungicides have demonstrated high intrinsic activity against other pathogens. Determining the efficacy of these fungicides on Alternaria spp. is important to the potato industry.
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    Understanding Host Resistance and Pathogen Biology in the Wheat-Fusarium graminearum Pathosystem
    (North Dakota State University, 2020) Poudel, Bikash
    Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.