A Fresh Look at Grape Powdery Mildew (Erysiphe necator) A and B Genotypes Revealed Frequent Mixed Infections and Only B Genotypes in Flag Shoot Samples

Erysiphe necator populations, causing powdery mildew of grapes, have a complex genetic structure. Two genotypes, A and B, were identified in most vineyards across the world on the basis of fixed single nucleotide polymorphisms (SNPs) in several DNA regions. It was hypothesized that A populations overwinter as mycelia in grapevine buds, giving rise to so-called flag shoots in spring, and are more sensitive to fungicides than B populations, which overwinter as ascospores and become widespread later in the season. Other studies concluded that the biological significance of these genotypes is unclear. In the spring of 2015, there was a unique opportunity to collect E. necator samples from flag shoots in Hungary. The same grapevines were sampled in summer and autumn as well. A total of 182 samples were genotyped on the basis of beta-tubulin (TUB2), nuclear ribosomal DNA (nrDNA) intergenic spacer (IGS), and internal transcribed spacer (ITS) sequences. Genotypes of 56 samples collected in 2009-2011 were used for comparison. Genotype A was not detected at all in spring, and was present in only 19 samples in total, mixed with genotype B, and sometimes with another frequently found genotype, designated as B2. These results did not support the hypothesis about temporal isolation of the two genotypes and indicated that these are randomly distributed in vineyards

The effect of biochar on plant diseases: what should we learn while designing biochar substrates?

The increasing demand for soilless substrates and rising environmental concerns about the use of non-renewable resources such as peat has led to the search for alternative constituents of growing mixtures for containerized plants. In this report we reviewed the works concerning biochar as constituent of growing media, targeting its influence on plant growth and plant disease. Biochar mostly has positive or neutral influences on plant growth compared with peat media when present in concentrations higher than 25% (v:v). However, studies of biochar influence on plant disease reveals that while lower concentrations (≤1%) of biochar often suppressed several diseases, higher concentrations (≥3%) were mostly ineffective or induced plant disease. For use as horticultural peat replacement, it is recommended that biochar feedstocks and concentrations be standardized and the potential effect of biochar on plant disease be considered, so that growers can rely on consistent and reproducible biochars for desired effects

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Delayed Development of Resistance to QoI Fungicide in <i>Venturia inaequalis</i> in Israeli Apple Orchards and Improved Apple Scab Management Using Fungicide Mixtures

Quinone outside inhibitors (QoI) fungicides group were introduced for commercial use against apple scab (Venturia inaequalis) in Israel in 1997. Unlike other regions in the world, in which resistance of V. inaequalis to QoI fungicides was observed within 3–5 years of use, in Israel it only occurred after 14 years of use. Field trials conducted between 2007 and 2017 showed a significant reduction in susceptibility to QoIs in northern Israel only since 2011. The delay in the development of resistance is related to limited fungicidal sprays resulting from unfavorable conditions for the pathogen. Of the 28 isolates collected from infected leaves or fruits of commercial orchards in northern Israel, 27 were resistant to the QoI fungicide Kresoxim-methyl. Amplification of the CYTB gene and sequencing of the G143A mutation region confirmed the resistance of all 27 isolates to QoIs. Resistance is demonstrated in the orchard, in vitro and molecular-based study, which forced the growers to avoid using QoIs against apple scab. We show that foliar applications of tank mixtures of systemic fungicides plus captan or prepacked fungicidal mixtures improved efficacy and can be used as a strategic approach in fungicide resistance management, including in orchards in which resistance to QoIs has been detected

The Impact of Information Relevancy and Interactivity on Intensivists’ Trust in a Machine Learning–Based Bacteremia Prediction System: Simulation Study

Abstract BackgroundThe exponential growth in computing power and the increasing digitization of information have substantially advanced the machine learning (ML) research field. However, ML algorithms are often considered “black boxes,” and this fosters distrust. In medical domains, in which mistakes can result in fatal outcomes, practitioners may be especially reluctant to trust ML algorithms. ObjectiveThe aim of this study is to explore the effect of user-interface design features on intensivists’ trust in an ML-based clinical decision support system. MethodsA total of 47 physicians from critical care specialties were presented with 3 patient cases of bacteremia in the setting of an ML-based simulation system. Three conditions of the simulation were tested according to combinations of information relevancy and interactivity. Participants’ trust in the system was assessed by their agreement with the system’s prediction and a postexperiment questionnaire. Linear regression models were applied to measure the effects. ResultsParticipants’ agreement with the system’s prediction did not differ according to the experimental conditions. However, in the postexperiment questionnaire, higher information relevancy ratings and interactivity ratings were associated with higher perceived trust in the system (PP ConclusionsInformation relevancy and interactivity features should be considered in the design of the user interface of ML-based clinical decision support systems to enhance intensivists’ trust. This study sheds light on the connection between information relevancy, interactivity, and trust in human-ML interaction, specifically in the intensive care unit environment

Editorial: Plant pathogen life-history traits and adaptation to environmental constraints

International audienc

Mixtures of Macro and Micronutrients Control Grape Powdery Mildew and Alter Berry Metabolites

Powdery mildew caused by the fungus Erysiphe necator is a major grape disease worldwide. It attacks foliage and berries and reduces yield and wine quality. Fungicides are mainly used for combating the disease. Fungicide resistance and the global requisite to reduce pesticide deployment encourage the use of environment-friendly alternatives for disease management. Our field experiments showed that the foliar application of the potassium phosphate fertilizer Top-KP+ (1-50-33 NPK) reduced disease incidence on leaves and clusters by 15–65% and severity by 75–90%, compared to untreated vines. Top-KP+ mixed with Nanovatz (containing the micronutrients boron (B) and zinc (Zn)) or with TruPhos Platinum (a mixture containing N, P2O5, K2O, Zn, B, Mg, Fe, Mn, Cu, Mo, and CO) further reduced disease incidence by 30–90% and disease severity by 85–95%. These fertilizers were as effective as the fungicide tebuconazole. Tank mixtures of fertilizers and tebuconazole further enhanced control efficacy in the vineyards. The modes of action of fertilizers in disease control were elucidated via tests with grape seedlings, microscopy, and berry metabolomics. Fertilizers applied preventively to the foliage of grape seedlings inhibited powdery mildew development. Application onto existing mildew colonies plasmolyzed mycelia and conidia and arrested the development of the disease. Berries treated with fertilizers or with a fungicide showed a significant increase in anti-fungal and antioxidant metabolites. Twenty-two metabolites, including non-protein amino acids and carbohydrates, known for their anti-fungal and bioactive effects, were significantly upregulated in grapes treated with fertilizers as compared to grapes treated with a fungicide, suggesting possible indirect activity against the pathogen. Esters and organic acids that contribute to wine quality were also upregulated. We conclude that integrating macro and micronutrients in spray programs in commercial vineyards shall control powdery mildew, reduce fungicide deployment, delay the buildup of fungicide resistance, and may improve wine quality

Ecological Genetic Divergence of the Fungal Pathogen Didymella rabiei on Sympatric Wild and Domesticated Cicer spp. (Chickpea)

For millennia, chickpea ( Cicer arietinum ) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei . We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes

Fusarium Wilt of Coriander: Root Cause Analysis and Varietal Tolerance Development

Since 2012, growers of coriander, Coriandrum sativum L., in Israel have been suffering from summer wilting that can result in entire fields collapsing. The current study aimed to determine the cause of the phenomenon and find a genetic solution to the problem. The disease was reproduced in a growth chamber using naturally-infested soil from a commercial field. Wilt became apparent within two weeks, and after ten weeks, all plants died compared to plants in sterilized soil from the same source. Fusarium oxysporum was isolated from infected plants, and Koch’s postulates were completed. Sequence analysis of the Elongation Factor (EF1α) encoding gene of the pathogen had a 99.54% match to F. oxysporum f. sp. coriandrii. Several coriander varieties were screened for resistance or tolerance to the disease. In four independent experiments, only the cultivar ‘Smadi’ showed high tolerance, while other genotypes were susceptible. In a trial in a naturally infested field, the cultivar ‘Smadi’ outperformed the commercial cultivar ‘Blair’. ‘Smadi’ provides a cropping solution to many Israeli farmers, yet this winter cultivar bolts early in the summer. There is a further need to characterize the tolerance mechanism and inheritance for informed breeding of late-bolting Fusarium-resistant coriander