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<p> Vegetable production is an important sector of the organic food industry in the Pacific Northwest USA. Significant acres of organic vegetable crops, particularly processing green pea and sweet corn, are grown in the semi-arid Columbia Basin of central Washington and north central Oregon, where Pythium damping-off can cause losses in early spring when cool and wet soil conditions are conducive to the disease. In this study, 37 certified organic fields were surveyed in the Columbia Basin for <i>Pythium</i> species, from which 305 isolates were baited and identified to 19 species. Pathogenicity tests of isolates of each species on pea in cool and wet soil conditions revealed isolates of 9 species were pathogenic, with differences in virulence among species and among isolates within species. <i>Pythium ultimum</i> (24.6% of the 305 isolates), <i>P. irregulare</i> group 1 (15.1%), and <i>P. abappressorium </i> (4.9%) were the most prevalent pathogenic species. Real-time PCR assays detected <i>P. ultimum</i>in 100% of the 37 fields compared to 78% for <i>P. abappressorium,</i> and 57% for <i>P. irregulare</i> group 1. </p><p> Given the lack of highly effective seed treatments for damping-off control in organic production, organic seed and drench treatments were evaluated in five pea field trials in the Columbia Basin, and two pea trials plus one sweet corn trial in maritime western Washington in 2011-12. Nordox seed treatment and seed priming demonstrated the greatest potential for damping-off control. Pea seed priming with 16 h of seed soaking + 10 h of air drying optimized priming for rapid emergence. In two field trials in 2012, combining Nordox seed treatment with seed priming using biochar as an alternative to air-drying, was promising for damping-off control. </p><p> Seed exudates produced during germination are measured using electrical conductivity (EC). The EC levels of 17 pea seed lots (six cultivars) significantly affected emergence and susceptibility to Pythium damping-off. A negative linear relationship was demonstrated between EC level and emergence, with a stronger regression at higher inoculum levels of <i>P. ultimum.</i> Measuring the EC of pea seed lots, and quantifying <i>Pythium</i> inoculum in soil using real-time PCR assays may enable organic pea growers to assess accurately the risk of damping-off.</p>

Fusarium head blight (FHB) of barley (Hordeum vulgare L.) is a devastating disease, caused by Fusarium graminearum (teleomorph: Gibberella zea), resulting in reduced yield and quality of grain by producing mycotoxins. The resistance in barley to FHB is quantitative and controlled by several genes, thus making it difficult to breed for resistance. In wheat (Triticum aestivum L.) and barley more than 100 quantitative trait loci (QTL) for resistance have been reported against FHB, but the mechanisms of resistance controlled by these QTL are unknown. Metabolic profiling technology was applied to better understand the mechanisms of resistance and to phenotype resistance in barley genotypes against FHB. The current study aimed to: 1) identified the resistance related (RR) metabolites by comparing resistance in barley cultivars Chevron and Stander against FHB, and determined antimicrobial properties of selected RR metabolites under in vitro conditions; 2)determined the effects of selected RR metabolites on inhibition of trichothecene biosynthesis by F. graminearum under in vitro conditions; 3) identified biomarker metabolites, in six barley genotypes ('Chevron', H5277-44, H5277-164, M92-513,M122, and 'Stander') varying in resistance to FHB, for potential biomarker selection to screen barley genotypes for resistance. Barley genotypes were mock-inoculated or pathogen-inoculated under greenhouse conditions; metabolites were extracted using aqueous methanol and analyzed using LCESI-LTQ-Orbitrap. XCMS and CAMERA algorithms were used to process the LC/MS output. Significant metabolites were classified as RR constitutive, and RR induced based on their greater abundance in resistant genotypes. Deoxynivalenol (DON) and its detoxified metabolite DON-3-O-glucoside (D3G), designated here as resistance indicator metabolites, were detected in both resistant and susceptible genotypes. The resistant cultivar Chevron had the least DON accumulation and high level of DON conversion to D3G. The selected RR metabolites varied in their ability to inhibit mycelial biomass and trichothecene synthesis by F. graminearum in vitro. The major potential biomarkers selected were: p-coumaric acid, sinapic acid, naringenin, naringenin-glucoside, kaempferol-glucosides, jasmonic acid, methyl jasmonate, and linolenic acid. In conclusion, we have demonstrated here that the mass spectrometry tool can be used to better understand the mechanisms of quantitative resistance in barley against biotic stress and to select potential biomarkers to screen for FHB resistance. / La fusariose de l'épi (FE) de l'orge est une maladie dévastatrice causée par Fusarium graminearum (Gibberella zea) et résultant en pertes de rendement et de qualité du grain dû à la production de mycotoxines. La résistance à la FE chez l'orge peut être quantifiée et est généralement contrôlée par plusieurs gènes, ce qui limite l'amélioration de ce trait par de simples croisements. Plus de 100 loci de caractères quantitatifs (LCQ) de résistance contre la FE ont été rapportés chez le blé et l'orge, mais les mécanismes de résistance contrôlés par ces LCQ sont inconnus. La technologie de profilage métabolique a été appliquée afin de mieux comprendre les mécanismes de résistance contre la FE et de 'phénotyper' la résistance de certains génotypes d'orge. Les objectifs de cette étude sont : 1) d'identifier les métabolites reliés à la résistance (RR) en comparant la résistance contre la FE descultivars Chevron et Stander et de déterminer les propriétés antimicrobiennes des métabolites RR sélectionnés in vitro; 2) de déterminer l'effet des métabolites RR sélectionnés sur l'inhibition de la biosynthèse du trichothécène par F. graminearum invitro; et 3) d'identifier des métabolites biomarqueurs chez six génotypes ('Chevron', H5277-44, H5277-164, M92-513, 'M122' et 'Stander') avec une résistance différente à la FE, afin de sélectionner des biomarqueurs permettant d'évaluer la résistance chez les génotypes d'orge. Les génotypes d'orge ont été inoculés avec de l'eau ou un pathogène enconditions de serre. Les métabolites ont été extraits avec du méthanol aqueux et analysés avec LC-ESI-LTQ-Orbitrap. Les algorithmes XCMS et CAMERA ont été utilisés pourtraiter le produit LC/MS. Des métabolites significatifs ont été classifiés en fonction de leur lien avec la résistance constitutive et exprimés en fonction de leur abondance qui est plus importante chez les génotypes résistants. Le déoxynivalénol (DON) et le glucoside DON-3-O, son métabolite détoxifié (D3G), désignés ici comme des métabolites indicateurs la résistance, ont été détectés dans les génotypes résistants et sensibles. Le cultivar résistant Chevron a produit le plus bas niveau de DON total et la plus grande proportion de DON converti en D3G. Les métabolites RR sélectionnés ont varié dans leur habileté à inhibiter la biomasse de mycélium et la synthèse du trichothécène par G. zeaein vitro. Les biomarqueurs potentiels qui ont été sélectionnés sont : l'acide p-coumarique, l'acide sinapique, la naringinine, le glucoside de naringinine, les glucosides de kaempférol, l'acide jasmonique, le jasmonate de méthyl et l'acide linolénique. En conclusion, nous avons démontré que la spectrométrie de masse peut être utilisée afin demieux comprendre les mécanismes de résistance quantitative chez l'orge contre le stress biotique et pour sélectionner des biomarqueurs potentiels permettant d'évaluer la résistance FE.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 68-02, Section: B, page: 0689. Adviser: Jerald K. Pataky. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

<p> Stem rust, caused by the macrocyclic fungal pathogen <i> P. graminis</i> (<i>Pg</i>), is one of the most devastating diseases of wheat and other small grains globally; and the emergence of new stem rust races virulent on deployed resistance genes brings urgency to the discovery of more durable sources of genetic resistance. Given its intrinsic durability and effectiveness across a broad range of pathogens, non-host resistance (NHR) presents a compelling strategy for achieving long-term rust control in wheat. However, NHR to <i>Pg</i> (<i>Pg</i>-NHR) remains largely unexplored as a protection strategy in wheat, in part due to the challenge of developing a genetically tractable system in which <i>Pg</i>-NHR segregates. In this dissertation, an investigation of <i>Pg</i>-NHR is undertaken via the pathogen's alternate (sexual) host, barberry (<i> Berberis</i> spp.). Within the highly diverse <i>Berberis</i> genus, numerous species function as alternate hosts to <i>Pg</i> but others are non-hosts. European barberry (<i>B. vulgaris</i> L.), for example, is susceptible to <i>Pg</i> infection but Japanese barberry (<i>B. thunbergii</i> DC.) is a non-host. In this study, the nothospecies <i>B. &times;ottawensis</i> C.K. Scheid, an inter-specific hybrid between <i>Pg</i>-susceptible <i>B. vulgaris</i> and <i>Pg</i>-resistant <i>B. thunbergii</i>, is explored as a possible means of mapping the gene(s) underlying the apparent <i> Pg</i>-NHR exhibited by <i>B. thunbergii</i>. The overall goal of this research is to contribute to the global search for novel sources of potentially durable stem rust resistance genes. </p><p> The first chapter describes a field study conducted in western Massachusetts, in which a natural population of <i>B. &times;ottawensis</i> was characterized to determine if the hybrid can be used to genetically dissect the <i>Pg</i>-NHR exhibited by <i>B. thunbergii</i>. A population of 63 <i>B. &times;ottawensis</i> individuals were clonally propagated, phenotyped for disease response to <i>Pg</i> via controlled inoculation using overwintered telia of <i>Pg</i> found on naturally infected <i>E. repens</i>, and genotyped using the <i>de novo </i> genotyping-by-sequencing (GBS) pipeline GBS-SNP-CROP. Controlled inoculation of a subset of 53 <i>B. &times;ottawensis</i> accessions, verified via GBS to be true, first-generation hybrids, revealed 51% susceptible, 33% resistant, and 16% intermediate phenotypes. Although such variation in disease response within a natural population of F₁ hybrids could be explained by non-nuclear (cytoplasmic) inheritance of resistance, a similar pattern of segregation was observed in a population of <i>B. &times;ottawensis </i> full-sibs, developed via controlled crosses. The results of this first chapter demonstrate not only that the <i>Pg</i>-NHR observed in <i>B. thunbergii</i> segregates among F₁ interspecific hybrids with <i>Pg</i>-susceptible <i>B. vulgaris</i> but that the resistance is likely nuclearly inherited. Therefore, at least in principle, the gene(s) underlying <i>Pg</i>-NHR in <i>B. thunbergii</i> should be mappable in an F₁ population derived from the controlled hybridization of the two parental species. </p><p> Building on the results of first chapter, the second chapter of this dissertation details the generation and use of a bi-parental <i>B. &times;ottawensis </i> mapping population to develop genetic linkage maps for both parental species and begin mapping the gene(s) underlying <i>Pg</i>-NHR in <i> B. thunbergii</i>. Using 162 full-sib F₁ hybrids and a total of 15,411 sequence variants (SNPs and indels) identified between the parents via GBS, genetic linkage maps with 1,757 and 706 markers were constructed for <i>B. thunbergii</i> accession 'BtUCONN1' and <i>B. vulgaris </i> accession 'Wagon Hill', respectively. In each map, the markers segregated into 14 linkage groups, in agreement with the 14 chromosomes present in these <i> Berberis</i> spp. The total lengths of the linkage maps were 1474 cM (<i>B. thunbergii</i>) and 1714 cM (<i>B. vulgaris</i>), with average distances between markers of 2.6 cM and 5.5 cM. QTL analysis for <i>Pg</i> resistance led to the identification of a single QTL, dubbed Q<i>Pg</i>r-3S, on the short arm of chromosome 3 of <i> B. thunbergii</i>. The peak LOD score of Q<i>Pg</i>r-3S is 28.2, and the QTL spans 13 cM, bounded by the distal SNP marker M411 and proximal SNP marker M969. To gain further insight into the Q<i>Pg</i>r-3S region, a chromosome-level 1.2 Gb draft genome for <i>B. thunbergii</i> was assembled using long PacBio reads and Hi-C data. By anchoring the <i> B. thunbergii</i> linkage map to the draft genome, the 13 cM Q<i> Pg</i>r-3S region was found to correspond to ~3.4 Mbp, represented by 10 contigs. Using a 189.3 Mb transcriptome assembled from a multiple tissue library of RNA-seq data, the Q<i>Pg</i>r-3S region was found to contain 99 genes. To help narrow this list to candidate genes of highest priority for subsequent investigation, a combination of approaches was taken. Specifically, annotation of the QTL region and differential gene expression analysis led to the identification of 12 candidate genes within the region. (Abstract shortened by ProQuest.) </p><p>

<p> Legume crops are significant agriculturally and environmentally for their ability to form symbiosis with specific soil bacteria capable of nitrogen fixation. Nitrogen fixation for a given legume in a given soil is limited by the availability of the plant&rsquo;s bacterial partners, and by variation in the effectiveness of those symbionts. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of nitrogen-fixing bacterial symbionts of the legume crop chickpea. This has been accomplished using culture-dependent and independent approaches to generate over 1,200 draft whole-genome assemblies at the level of bacterial populations, as well as 14 finished-quality genomes using the Pacific Biosciences platform. These strategies reveal that chickpea&rsquo;s symbionts across the globe are confined to the genus <i>Mesorhizobium </i>, but a diversity of taxa within the genus (chapter 1 and 3). Comparative phylogenomic analysis reveals that despite chickpea&rsquo;s symbionts within and across regions coming from different taxa, all share almost identical genes for symbiosis. PacBio genome-assemblies reveal that this is due to the horizontal transfer of a 500 kb chromosomal island known as a symbiosis island, between unrelated strains of the genus <i>Mesorhizobium </i>. Analyzing the symbiosis island at the population level reveals that the symbiosis island spreads repeatedly once introduced to a region, suggesting that strains well-adapted to a particular soil climate continue to dominate once the new host (chickpea) has been introduced, through repeated acquisition of the symbiosis island. This dataset provides additional insights into the functional and taxonomic diversity of other bacteria associated with chickpea nodules (chapter 2).</p><p>

When chilled, plants produce greater amounts of toxic oxygen compounds than they do under non-stressed conditions. These toxic oxygen compounds have the potential to cause severe damage to plants. Plants have evolved antioxidant systems which can scavenge these toxic oxygen compounds and thus allow for the avoidance of their detrimental effects. The purpose of this thesis was to characterize antioxidant capacities of differentially chilling sensitive lines of maize (Zea mays L.) in order to test the hypothesis that the most chilling sensitive lines would have less antioxidant capacity and, hence, less ability to scavenge damaging toxic oxygen compounds, than the more tolerant lines. Three objectives were set to test this hypothesis. The first objective was to select out relatively chilling sensitive and tolerant inbred maize based on their physiological responses to chilling. This first objective was successfully met by subjecting the inbred lines to laboratory chilling tests at the germination stage and early growth stages. Field trials which assessed physiological parameters at both the emergence and early growth phases were then carried out which confirmed laboratory results. The second objective of this thesis was to test if the selected chilling sensitive inbred maize lines had less antioxidant capacities than the tolerant. To this end, activities of the antioxidant enzymes catalase (CAT; EC 1.11.1.6), ascorbate peroxidase (ASPX; EC 1.11.1.11), superoxide dismutase (SOD; EC 1.15.1.1), monodehydroascorbate reductase (MDHAR; EC 1.6.5.4), and glutathione reductase (GR; EC 1.6.4.2), along with concentrations of the antioxidant compounds ascorbate, glutathione, $\beta$-carotene, and $\alpha$-tocopherol and levels of the general metabolic indicators of chilling stress (carbohydrates, chlorophyll, and soluble proteins) were assessed. These parameters were assessed at three developmental stages (first, third and fifth leaf stages) and under control (25$\sp\circ$C) and both short- and long-term chilling ($11\sp\circ$C) regimes. This second objective was successfully met. Significantly lower percent of control activities of the antioxidant enzymes ASPX, MDKAR, and CAT, were observed in the most chilling sensitive inbred line as compared to the tolerant at the first leaf stage of development. The third objective of this thesis was designed to determine if there were similar results for antioxidant capacities and metabolic indicator concentrations for the chilled hybrids as there were for the inbred maize lines. Thus, a complete diallel cross between the above selected inbreds was made, and the resulting hybrids then classified as relatively chilling sensitive or tolerant depending upon how they performed in the laboratory germination and early growth stage screening tests with confirmation in the field. The hybrids were grown until the third leaf stage under short-term chilling (11$\sp\circ$C) and assessed for activities of the antioxidant enzymes and concentrations of antioxidant compounds and metabolic stress indicators. This third objective was successfully met. The chilling sensitive maize hybrids were found to have lower, although not significantly so, percent of control activities of CAT, MDHAR, and ASPX than the chilling tolerant hybrids, paralleling the results of the parental inbreds. (Abstract shortened by UMI.)

Abstract not available.