Dynamics of Zymoseptoria tritici Fungicide Resistance in the Willamette Valley of Oregon

The development of resistance to multiple fungicide classes is currently limiting disease management options for many pathogens, while the discovery of new fungicide classes has become less frequent. To address this pressing issue, a three-part study with different layers of complexity, objectives, and experimental approaches was conducted using the model fungicide resistance pathosystem: Zymoseptoria tritici. The virulence of azoxystrobin-resistant Zymoseptoria tritici was tested in greenhouse assays, and results indicated that azoxystrobin-resistant Z. tritici populations were less virulent. Results of a series of field inoculations with fungicide-resistant, fungicide-sensitive, and resistant/sensitive mixtures indicated that the competitive ability and fitness of azoxystrobin-resistant Z. tritici in vivo was influenced by environmental factors. A large-scale hierarchical survey of commercial wheat fields in the Willamette Valley of Oregon was executed to monitor seasonal changes and spatial variation of propiconazole- and azoxystrobin- resistant Z. tritici. An increase of azoxystrobin resistance was recorded over the two-year study. In contrast, propiconazole resistance stayed relatively stable over time. Both fungicide-resistant phenotypes were found to be spatially random, and the greatest amount of spatial variation occurred at the smallest hierarchical scale of the survey. Results of this research represent a broad effort to understand fitness trade-offs associated with mutations, as well as a more focused effort to understand local dynamics of Z. tritici fungicide resistance in the in the Willamette Valley of Oregon

Mapping QTL for root rot resistance, root traits, and morphological trait in a common bean recombinant inbred population

Root rot diseases of bean (Phaseolus vulgaris L.) are a problem wherever they are grown, and are a major constraint to dry edible and snap bean production. Root rot is a primary yield limitation of snap bean production in the US, especially within the top three snap bean producing states of Wisconsin, Oregon and New York. Bean root rot pathogens will be present by the end of the first season even when starting with clean ground. The decline in yield can be relatively slow, so growers might not notice or appreciate the hidden yield cost associated with root rot disease. Traditional methods for disease control such as fungicides, crop rotations, cover crops, seedbed preparations have been proven ineffective (either physically ineffective or economically unviable) against root rot. Therefore, genetic resistance is needed. In order to address the need for genetic resistance to root rot in snap beans, the highly root rot resistant line RR6950, a small seeded black indeterminate type IIIA accession of unknown origin, was crossed with OSU5446, a highly root rot susceptible determinate type I blue lake four-sieve breeding line to produce the RR138 recombinant inbred mapping population. In this study we evaluated the RR138 RI population in the F₆ generation for resistance to Fusarium solani root rot in Oregon and Aphanomyces euteiches root rot in Wisconsin. We also evaluated this population for morphological traits and root structural traits including pod height, pod width, pod length, pod wall thickness, strings, seed color, flower color, tap and basal root diameter, and root angle measurements. The RR138 population was also genotyped on the 10K BeanCAP Illumina Beadchip. The Single Nucleotide Polymorphism (SNP) data was used to assemble a high-density linkage map and Quantitative Trait Loci (QTL) for phenotypic data were evaluated. The linkage map produced from this study contained 1,689 SNPs across 1,196cM. The map was populated with 1 SNP for every 1.4cM, spanning across 11 linkage groups. Three QTL associated with A. euteiches root rot resistance were consistently expressed in 2011 and 2012 trials. A. euteiches QTL were found on Pv02, Pv04, and Pv06 and accounted for 7-17% of total genetic variation. Two QTL associated with F. solani were found in 2011 trial on Pv03 and Pv07, account for 9 and 22% of total genetic variation, respectively. We also found several QTL for morphological traits and root structural traits including QTL for pod fiber and pod height on Pv04, pod length on Pv01, strings on Pv01, taproot diameter on Pv05, and shallow basal root angle on Pv05, accounting for 21, 26, 12, 20, 11, and 19% of total genetic variation, respectively. QTL discovered from Oregon data for F. solani resistance did not cluster with QTL for A. euteiches root rot resistance. "SNP0928_7", was highly associated with F. solani resistance on Pv07 and "SNP0508_2", was highly associated with A. euteiches on Pv02. QTL and markers associated with QTL from this study will be of value to snap bean breeders developing root rot resistant lines with processing traits, and provide more information about targeting the mechanism of resistance

An improved method for measuring quantitative resistance to the wheat pathogen Zymoseptoria tritici using high-throughput automated image analysis

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions

Mapping Snap Bean Pod and Color Traits, in a Dry Bean x Snap Bean Recombinant Inbred Population

Snap bean (Phaseolus vulgaris L.) breeding programs are tasked with developing cultivars that meet the standards of the vegetable processing industry and ultimately that of the consumer, all the while matching or exceeding the field performance of existing cultivars. While traditional breeding methods have had a long history of meeting these requirements, genetic marker technology, combined with the knowledge of important quantitative trait loci (QTL), can accelerate breeding efforts. In contrast to dry bean, snap bean immature pods and seeds are consumed as a vegetable. Several pod traits are important in snap bean including: reduced pod wall fiber, absence of pod suture strings, and thickened, succulent pod walls. In addition, snap bean pods are selected for round pod cross section, and pods tend to be longer with cylindrical seed shape. Seed color is an important trait in snap bean, especially those used for processing, as processors prefer white-seeded cultivars. The objective of this study was to investigate the genetic control of traits important to snap bean producers and processors. RR6950, a small seeded brown indeterminate type IIIA dry bean accession, was crossed to the Oregon State University (OSU) breeding line OSU5446, a type I Blue Lake four-sieve breeding line to produce the RR138 F₄:₆ recombinant inbred (RI) mapping population. We evaluated the RR138 RI population for processing and morphological traits, especially those affecting pods. The RR138 population was genotyped with the BARCBean6K_3 Beadchip, and single nucleotide polymorphisms (SNPs) were used to assemble a linkage map, and identify QTL for pod traits. The linkage map produced from this study contained 1689 SNPs across 1196cM. The map was populated with an average of one SNP per 1.4 cM, spanning 11 linkage groups. Seed and flower color genes B and P were located on Pv02 and Pv07, respectively. A QTL for string:pod length (PL) ratio was found on Pv02 controlling 32% of total genetic variation. QTL for a suite of important processing traits including pod wall fiber, pod height, pod width, and pod wall thickness were found clustering on Pv04 and controlled 21%, 26%, 18%, and 16% of genetic variation for each of these respective traits. A QTL for PL was found on Pv09 controlling 5% of genetic variation.This is the publisher’s final pdf. The article is published by American Society for Horticultural Science and can be found at: http://journal.ashspublications.org/Keywords: QTL, quantitative trait locus, common bean, SNP, linkage mapping, single nucleotide polymorphis

Relationship between the Clinical Frailty Scale and short-term mortality in patients ≥ 80 years old acutely admitted to the ICU: a prospective cohort study.

BACKGROUND: The Clinical Frailty Scale (CFS) is frequently used to measure frailty in critically ill adults. There is wide variation in the approach to analysing the relationship between the CFS score and mortality after admission to the ICU. This study aimed to evaluate the influence of modelling approach on the association between the CFS score and short-term mortality and quantify the prognostic value of frailty in this context. METHODS: We analysed data from two multicentre prospective cohort studies which enrolled intensive care unit patients ≥ 80 years old in 26 countries. The primary outcome was mortality within 30-days from admission to the ICU. Logistic regression models for both ICU and 30-day mortality included the CFS score as either a categorical, continuous or dichotomous variable and were adjusted for patient's age, sex, reason for admission to the ICU, and admission Sequential Organ Failure Assessment score. RESULTS: The median age in the sample of 7487 consecutive patients was 84 years (IQR 81-87). The highest fraction of new prognostic information from frailty in the context of 30-day mortality was observed when the CFS score was treated as either a categorical variable using all original levels of frailty or a nonlinear continuous variable and was equal to 9% using these modelling approaches (p < 0.001). The relationship between the CFS score and mortality was nonlinear (p < 0.01). CONCLUSION: Knowledge about a patient's frailty status adds a substantial amount of new prognostic information at the moment of admission to the ICU. Arbitrary simplification of the CFS score into fewer groups than originally intended leads to a loss of information and should be avoided. Trial registration NCT03134807 (VIP1), NCT03370692 (VIP2)

Data from: Variable competitive effects of fungicide resistance in field experiments with a plant pathogenic fungus

Classic evolutionary theory suggests that mutations associated with antimicrobial and pesticide resistance result in a fitness cost in the absence of the selective antimicrobial agent or pesticide. There is experimental evidence to support fitness costs associated with resistance to anti-microbial compounds and pesticides across many biological disciplines, including human pathology, entomology, plant sciences, and plant pathology. However, researchers have also found examples of neutral and increased fitness associated with resistance, where the effect of a given resistance mutation depends on environmental and biological factors. We used Zymoseptoria tritici, a model evolutionary plant pathogenic fungus, to compare the competitive ability of fungicide-resistant isolates to fungicide-sensitive isolates. We conducted four large-scale inoculated winter wheat experiments at Oregon State University agriculture experiment stations. We found a significant change in the frequency of fungicide resistance over time in all four experiments. The direction and magnitude of these changes, however, differed by experimental location, year of experiment, and inoculum resistance treatment (fungicide-resistant, resistant/sensitive mixture, and fungicide-sensitive). These results suggest that the competitive ability of resistant isolates relative to sensitive isolates varied depending upon environmental conditions, including the initial frequency of resistant individuals in the population

Disease-Induced Assemblage of the Rhizosphere Fungal Community in Successive Plantings of Wheat

Plant is one of the primary drivers of microbial communities in the rhizosphere. The consistent presence of the same plant species over time such as monocropping in agriculture can drive significant changes in plant-associated microbiomes. Most of the studies with monocropping have focused on bacteria, which are involved in the natural suppression of a number of soilborne diseases, including Rhizoctonia root rot and take-all. However, few studies have examined how monocropping and root rot pathogens jointly affect the structure of fungal communities in the rhizosphere. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings infected with the fungal pathogen Rhizoctonia solani AG8 were characterized using MiSeq sequencing targeting the internal transcribed spacer 1 region of the ribosomal RNA gene. Sequence analyses revealed that distinct fungal groups clustered by planting cycles with or without strain AG8 inoculation but infection with strain AG8 enhanced the separation of fungal communities. Clusters of fungal communities were also observed in strain-AG8-infected and noninfected rhizospheres, whereas there was no difference in fungal communities between the rhizospheres with the least root disease and those with the worst root disease. Planting cycles significantly reduced fungal α diversity. The most abundant fungal genus was Mortierella which increased in relative abundance with planting cycles in strain-AG8-infected samples. In contrast, fungal genera that included Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea were reduced in relative abundance with successive plantings and strain AG8 infection. Together, this study revealed how fungal communities change with successive wheat growth under the pressure of a soilborne fungal pathogen

Hyperspectral reflectance data of wheat in situ and lab scans infected with soilborne wheat mosaic virus

Hyperspectral images were taken in a lab setting from wheat leaves and in situ from agricultural wheat fields and disease nursery. The goal of this research was to find infection of soilborne wheat mosaic virus in wheat for early detection using digital imagery, i.e., either hyperspectral or multispectral.Keyword: soilborne wheat mosaic viru

Reaction of winter wheat and barley cultivars to Fusarium pseudograminearum‐inoculated fields in the dryland Pacific Northwest, USA

Abstract Fusarium crown rot (FCR) of winter wheat (Triticum aestivum L.), caused by Fusarium pseudograminearm and Fusarium culmorum, is a yield‐limiting disease in arid wheat‐producing areas of the inland Pacific Northwest. Foliar fungicide applications and currently available seed treatments do not control FCR. Alternative crops that provide a rotational benefit to reduce disease are not economically feasible. Major‐gene resistance is unavailable, but there is preliminary evidence that some wheat and barley (Hordeum vulgare L.) cultivars are more resistant than others. We followed up on preliminary work by growing 14 varieties of winter wheat, planted with in‐furrow FCR inoculum, in 2018 and 2019 in Morrow County, Oregon—one of the world's driest wheat producing regions. Two barley cultivars were added to the experiment during the second year of research. Evaluations of cultivar resistance were made by conducting aboveground visual assessments by counting whiteheads, prematurely senesced wheat heads that are indicative of FCR infection. Whitehead count information was correlated with yield and grain volume weight data. Maximum whitehead counts were measured in plots of the FCR‐susceptible check cultivar ‘Stephens’. There was no evidence of a cultivar‐specific relationship between whitehead count and corresponding values for yield and grain volume weight. There was limited evidence that some cultivars have the capacity to compensate for effects of disease