Browsing by Subject "Plant pathology"
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Item Detection, diagnostics, and characterization of virus-like organisms and conformational disease-like proteins in plants(2016-10) Bratsch, Sara AnnThe projects in this thesis all investigated virus-like organisms in agronomically important plants. Chapter one consists of reports describing viruses identified in new hosts or locations. Tobacco rattle virus (TRV) was identified in symptomatic Phryma leptostachya L, a native perennial, from plants in an uncultivated habitat and suggests that TRV may be endemic to North America. Since TRV is the causal organism of corky ringspot of potato this study raises the possibility that native perennial plants could serve as a potential reservoir to cause disease in potato. Canna yellow mottle virus was isolated for the first time from symptomatic Canna indica in Kenya. Cut flowers are a major agronomic crop of Kenya and growers should plant only virus indexed plants to limit losses from virus infection. Orchid fleck virus was confirmed by microscopy and sequence analysis for the first time in the United States in Phalaenopsis hybrida. Asymptomatic P. hybrida tested by one step reverse transcription polymerase chain reaction (RT-PCR) did not yield the expected product while a two step RT-PCR, creating cDNA first, yielded the expected product. This indicates the one step RT-PCR diagnostic test can yield false negatives for asymptomatic plants. Chapter two describes the production of polyclonal antibodies for the detection of Orchid fleck virus (OFV). OFV is a mite transmitted virus and has been reported word wide. The previous project identified a need for a reliable, inexpensive method to detect OFV in plants use for propagation, breeding, conservatories, or virus indexing projects. Polyclonal antibodies were produced in rabbits against Escherichia coli expressed OFV phosphoprotein and matrix protein. The resulting antiserums were assayed in PTA-ELISA and DAS-ELISA. OFV phosphoprotein antisera in PTA-ELISA readily differentiated between healthy and OFV infected orchid (Phalaenopsis hybrida) tissue. OFV matrix antisera in PTA-ELISA detected bacterially-expressed protein but did not differentiate between healthy or OFV infected tissue. The OFV phosphoprotein antiserum can be used by in PTA-ELISA to reliably detect OFV. Chapter three describes the molecular and biological characterization of a new Nepovirus causing a leaf mottling disease in Petunia hybrida. The sequence of the majority of the genome was determined by next generation sequencing and the sequence of remainder of the genome was obtained using a 5’ RACE amplification and RT-PCR using poly-A tail and virus specific primers. Due to phylogenetic relationship and sufficient genome dissimilarity to characterized viruses I propose the name of Petunia Chlorotic Mottle Virus for a new Nepovirus. The fourth chapter describes characterization of filamentous virus-like particles in members of the Asteraceae plant family including sunflower, chrysanthemum, coneflower, gerbera daisy, and zinnia. The filaments were 7-10 nanometers in diameter and could exceed 3,000 nm in length. The N-terminal sequences of the major proteins associated with purified filaments from several species were nearly identical and shared homology with the kunitz soybean trypsin inhibitor (KTI) family of proteins. CID MS/MS sequencing of the major proteins of purified sunflower filaments also shared homology with a KTI sequence. A Western blot using antiserum prepared against recombinant sunflower KTI protein labeled the observable protein bands from sunflower filaments. Filaments composed of a major protein of KTI have been found across the Asteraceae family but have not been observed in dandelion, thistle, or lettuce.Item Evaluating the Effects of Antagonistic Interactions on Pathogen Inhibition by Streptomyces Isolates from a Disease Suppressive Soil(2021-02) Pereyra, MatthewDiseases of plants threaten global food security and increase the cost of producing food and fiber. Synthetic pesticides have proven effective at suppressing many plant diseases but can require repeated applications at significant expense and cause harm to humans and the environment. Disease suppressive soils often support naturally-occurring soil microbial communities that inhibit plant pathogens and could be used to develop biocontrol or other plant disease management methods. However, high frequencies of resource competition and antagonistic interactions among naturally-occurring pathogen-suppressive populations represent a challenge for reproducing effective microbial disease suppression in agricultural settings. This work sought to further understanding of how the complex network of interactions that occur within disease suppressive soil microbial communities influences pathogen suppression by evaluating pairwise interactions of community members in vitro. Specifically, I characterized inhibition and nutrient competition among community members and their relationships to pathogen inhibition. Among a random collection of 75 Streptomyces isolates from the rhizosphere soil of potato plants grown in a naturally-occurring scab-suppressive soil in Grand Rapids, MN, 34 isolates were able to inhibit pathogenic Streptomyces scabies strain S87. I hypothesized that isolates would have decreased pathogen inhibition when grown in vitro with an inhibitory partner isolate relative to when grown alone. Similarly, isolates were hypothesized to have decreased pathogen inhibition when grown with highly nutrient competitive partners relative to when grown alone. However, when pathogen-inhibiting isolates were grown in pairs there were no consistent effects of partner inhibition or nutrient competition on pathogen inhibition. These results suggest that antagonistic and resource competitive interactions, while potentially important to the long-term establishment of disease suppressive soil microbiomes, may have limited effects on direct inhibition of pathogens. Moreover, this work suggests that successful biological control of plant diseases may not be limited solely to non-antagonistic inoculant mixtures.Item Genetics of Rust Resistance in a Wheat Nested Association Mapping Population(2017-10) Manan, FazalWheat is an important food crop in many parts of the world, but its genetic diversity has been eroded due to intense selection in breeding programs. To increase genetic diversity in the Minnesota wheat breeding program, a nested association mapping population was developed by crossing 25 exotic accessions selected from the USDA-ARS Spring Wheat Core Collection with RB07, a Minnesota cultivar selected as the common parent because it has wide adaptation in the region. Virulent races of the stem rust (Puccinia graminis f. sp. tritici, Pgt), leaf rust (P. triticina, Pt), and stripe rust (P. striiformis f. sp. tritici, Pst) pathogens threaten the wheat crop in the region. Thus, the objective of this thesis was to elucidate the genetics of rust resistance in select families of the Minnesota Nested Association Mapping Population (MNAMP) based on qualitative (chi-square tests of Mendelian gene models) and quantitative (quantitative trait loci (QTL) mapping with 66,685 single nucleotide polymorphic markers) genetic analyses. Four families segregated for resistance to the widely virulent Pgt races of TTKSK, TRTTF, and TTKST. One to five Mendelian genes and five to 19 QTL conferred stem rust resistance in individual families. One family segregated for resistance to Pt race TFBGQ with Lr21 virulence. One Mendelian gene and two QTL controlled resistance to this pathogen race. Three families segregated for resistance to the Pst races PSTv-37 and PSTv-40. Three to five Mendelian genes and two to 12 QTL conferred resistance to these races in individual families. Rust resistant progeny identified from the MNAMP will be useful for enhancing the resistance of wheat to the three rust diseases.Item Global biogeography and local adaptation of Streptomyces(2013-10) Schlatter, Daniel CameronStreptomyces play crucial roles in key ecosystem processes including nutrient and plant disease suppression in natural and agricultural systems. Moreover, Streptomyces are major producers of clinically relevant antibiotic compounds. Despite the importance of Streptomyces in natural, agricultural, and clinical settings, we have a limited understanding of Streptomyces ecology and evolutionary biology in natural habitats. Here we characterize the function diversity and biogeography of Streptomyces to shed light on the roles of local adaptation and coevolution in structuring soil Streptomyces communities. Specifically, this work focuses on patterns of antibiotic inhibition, antibiotic resistance, resource use, and phylogeny among sympatric and allopatric Streptomyces communities from across the globe. This work documents the extensive functional diversity of Streptomyces antibiotic inhibitory, resistance, and resource use phenotypes and provides strong evidence that local adaptation, coevolution, and resource competition are crucial drivers of antibiotic inhibition and resistance among Streptomyces.Item Identification, transmission, and genomic characterization of four new viruses of cultivated roses(2012-12) Mollov, Dimitre StefanovBetween the period 2005 and 2008 four previously undescribed viruses infecting cultivated roses were identified and fully characterized in Minnesota. These four viruses were transmitted by grafting from infected to healthy roses and found to be the likely causal agents of the diseases that they were associated with. Viruses were provisionally named after the characteristic symptoms in infected plants as follows: Rose yellow vein virus (RYVV), Rose yellow mosaic virus (RoYMV), Rosa rugosa leaf distortion virus (RrLDV), and Rose yellow leaf virus (RoYLV). Based on virion and genome properties it was determined that RYVV is a member of the family Caulimoviridae , RoYMV is a member of the family Potyviridae , and RrLDV and RoYLV are members of the family Tombusviridae . Phylogenetic analyses suggest that these four viruses belong to distinct new genera in their respective taxonomic families. The whole genomic sequence of each virus was deposited in GenBank under the accession numbers: RYVV JX028536; RoYMV NC_019031; RrLDV KC166238; and RoYLV, KC166239. Reliable diagnostic protocols were developed for each virus by PCR for RYVV detection, RT-PCR, immunosorbent electron microscopy (ISEM), and indirect enzyme-linked immunosorbent assay (ELISA) for RoYMV detection, and RT-PCR for both RrLDV and RoYMV detection.Item Identifying novel sources of resistance to the soybean cyst nematode.(2012-01) Lian, LianSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most serious yieldlimiting pathogen on soybean [Glycine max (L.) Merr.]. Utilizing genetic resistance is an effective method to control SCN. Most commercial SCN-resistant cultivars in the North Central USA are developed from two sources of resistance, PI 88788 and Peking. However, frequent use of a limited number of resistance sources has shifted virulence phenotypes of SCN populations (HG Types) and the new types seem to overcome originally resistant cultivars. The main purpose of this study is to search for new sources of SCN resistance that are different from Peking or PI 88788 and to identify genetic regions that are associated with novel resistance loci. Since Peking is not resistant to HG Type 1- (race 14) and PI 88788 is not resistant to HG Type 2- (race 1), 17 soybean cultivars and accessions that were reported resistant to HG Type 1- or/and HG Type 2- were tested against 13 different nematode populations including race 1, race 2, race 3, race 4 and race 14. Most of the lines tested had high or moderate resistance to race 1, race 2 and race 3 populations and can serve as an alternative resistance sources to PI 88788. However, most of the lines were susceptible to race 4 and the two race 14 nematode populations. Only PI 633736 has a high level of resistance to all the nematode populations used. PI 417091, PI 404166, PI 567516C, PI 629013 have moderate or high resistance to race 4 and at least one of the two race 14 populations. The different resistance spectrums of those lines indicate that there should be novel genes in PI resistance spectrums of those lines indicate that there should be novel genes in PI 633736, PI 417091, PI 404166, PI 567516C and PI 629013 that are different from Peking and PI 88788. QTLs conferring resistance to an HG Type 2.5.7 population (race 1) were sought with 92 MN0095 × PI 567516C F2:3 families from greenhouse (Experiment 1) and 92 F2:3 families from field (Experiment 2) using 1536 SNP markers. Altogether, 5 QTLs were declared for Experiment 1 and Experiment 2, including 2 significant QTLs (genome-wide type I error =0.05) and 3 suggestive QTLs (LOD > 3). The two significant QTLs were detected on chromosome 10 and chromosome 19 and the three suggestive QTLs were detected on chromosome 8, chromosome 18, and chromosome 20. The QTL with the highest LOD score, located on chromosome 10 was detected in both Experiment 1 and Experiment 2 and was recently reported by another group. This QTL has not been identified in other sources of SCN resistance. This QTL has significant additive effect, and explained 22.2% and 22.4% total variance in Experiment 1 and Experiment 2, respectively. The QTLs on chromosome 19 was detected only in Experiment 1. It had significant dominance effect, and explained 12.7% of total variance. The suggestive QTL mapped on chromosome 18 in Experiment 2 was at or near the rhg1 locus. Haplotype analysis of rhg1 and Rhg4 genes for the 17 resistant soybean germplasm lines revealed that PI 567516C and Peking share the same rhg1 allele. Markers closest to rhg1 and the QTL on chromosome 10 might be considered for use in marker assisted selection.Item Interaction of temperature, soil moisture, seed treatment, cultivar, and soybean cyst nematode in root rot of soybean.(2011-04) Meyer, Paul WellsThe root rot complex comprised of Fusarium species, Rhizoctonia solani, Phytophthora sojae, and Pythium species is a major contributor to yield loss in soybean. Due to its wide distribution, Fusarium solani is possibly the most important contributor to losses caused by this complex in Minnesota. Heterodera glycines, commonly known as soybean cyst nematode (SCN), is the most destructive soilborne pathogen of soybean. Yield losses to Fusarium root rot and SCN for 2005 in Minnesota were estimated to be 85,000 tons and 250,000 tons, respectively. The etiology of seed, seedling, and root rots of soybean in Minnesota is poorly understood, and the interactions between the major root infecting pathogens of soybean are even less well understood. Root rot of soybean during germination and emergence is a major cause of stand establishment problems. Seed treatment fungicides have provided inconsistent control of pre-emergence seed, seedling, and root rot during field trials in Minnesota, and cultivars resistant to native isolates of F. solani are not available. Previous studies have investigated the interaction between SCN and Fusarium virguliforme, but not between SCN and F. solani. This is important, since SCN is prevalent in agricultural soils in Minnesota. My objectives were to (1) determine the relationship between soil temperature and moisture in root infection by Fusarium spp., Pythium spp., P. sojae, and Rhizoctonia spp. in natural soil samples taken from soybean fields in Minnesota, (2) determine the frequency of root infection as a function of seed treatment and sampling time after planting in natural soil, and the soil temperature and moisture conditions at which seed treatments are effective (or not effective), (3) determine the predominant native Fusarium species infecting soybean in Minnesota soil as a function of temperature and soil moisture, (4) screen soybean varieties in maturity group 2 and earlier for partial resistance to Fusarium spp. naturally present in soil, and for partial resistance to an isolate of F. solani artificially inoculated in sterile sand, and (5) determine the effect of soybean taproot infection by an isolate of F. solani on secondary root tip infection by SCN, and vice versa.Item Investigations on stem rust resistance genes in barley.(2011-01) Chai, YuanAbstract summary not availableItem New resistance in old places: resistance to the Ug99 race group of Puccinia graminis f. sp. tritici in wheat intra/inter-generic hybrids and historic germplasm(2015-01) Kielsmeier-Cook, JoshuaWheat stem rust caused by the rust fungus, Puccinia graminis f. sp. tritici, threatens global wheat (Triticum aestivum) production. New races originating in Eastern Africa have overcome many existing stem rust resistance genes. The W. J. Sando collection of wheat intra/inter-generic hybrids is a valuable source of stem rust resistance. The entire collection was characterized for seedling stem rust resistance to 8 races of the stem rust pathogen and cytogenetic analysis was performed on select lines. Several accessions are postulated to contain new sources of resistance. Full screening results are displayed in Supplementary Table S1 and the pedigrees of 29 resistant lines are displayed in Supplementary Table S2. South African accession PI 410954 displayed strong resistance to stem rust race TTKSK at the seedling stage and under field conditions. The source of new resistance was located and material suitable for integration into modern spring wheat breeding programs was produced.Item The oat-crown rust pathosystem: an interaction of a plant, a pathogen, and time(2020-12) McNish, IanPlant diseases are often described as the interaction of a plant, a pathogen, and the environment. For a disease to develop, there must be a susceptible plant, a virulent pathogen, and an environment amenable to disease. This concept is useful to explain the presence or absence of a disease, but many important questions and ideas in plant pathology, plant genomics, plant phenomics, and plant cultivar development are also dependent on time. A pathogen population changes over time, by a process of selection, to defeat the resistances deployed in crop cultivars. The genetic architecture of disease resistance changes as a plant grows from a seedling to an adult plant, matures, and dies. The visual and spectral signature of plant stress and disease also changes as the plant grows and the disease develops. Finally, plant breeders attempt to limit the damage diseases cause by quickly improving plant populations and deploying disease resistant plant cultivars. The dimension of time has been well-explored in some areas of plant science such as gene expression, but time is often overlooked in plant breeding, quantitative genetics, and phenomics. Crown rust, caused by the fungal pathogen Puccinia coronata f. sp. avenae Erikss. (Pca), is a dynamic and devastating disease of cultivated oat (Avena sativa L.). In this research, I found that the North American Pca population has gained many virulences over the past thirty years and that the Pca isolates collected in recent years are capable of defeating a surprisingly high number of crown rust resistance genes. I found that the genetic architecture of crown rust resistance changed throughout the growing season. Many resistance loci were detected briefly, sometimes just for a couple of days, and few loci were detected at many points in time. I found that the spectral signature of disease and plant stress changed throughout the season and that the predictive value of the collected data was greatest for adult plants before senescence. Finally, I found that quantitative resistance to crown rust could be rapidly improved in an oat population, but the race-specificity of that resistance was difficult to determine. If plant breeders understand how time influences the composition of pathogen populations, the observations they make, the analyses they perform, and the technologies they develop, then they will be more capable of improving complex plant traits like disease resistance.Item Population structure of Puccinia graminis f. sp. tritici in the United States.(2012-05) Stoxen, SamAbstract summary not available.