Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens

AbstractDowny mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant–pathogen interactions in the early stage of infection and quickly assess resistance/susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA-Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops.

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Characterization of a Resistance Locus (Pfs-1) to the Spinach Downy Mildew Pathogen (Peronospora farinosa f. sp. spinaciae) and Development of a Molecular Marker Linked to Pfs-1

Phytopathology ◽

10.1094/phyto-98-8-0894 ◽

2008 ◽

Vol 98 (8) ◽

pp. 894-900 ◽

Cited By ~ 14

Author(s):

B. M. Irish ◽

J. C. Correll ◽

C. Feng ◽

T. Bentley ◽

B. G. de los Reyes

Keyword(s):

Disease Resistance ◽

Downy Mildew ◽

Scar Marker ◽

Mapping Population ◽

Dominant Gene ◽

Resistance Locus ◽

Sequence Characterized Amplified Region ◽

Wide Range ◽

Spinach Downy Mildew ◽

Homozygous Resistant

Downy mildew is a destructive disease of spinach worldwide. There have been 10 races described since 1824, six of which have been identified in the past 10 years. Race identification is based on qualitative disease reactions on a set of diverse host differentials which include open-pollinated cultivars, contemporary hybrid cultivars, and older hybrid cultivars that are no longer produced. The development of a set of near-isogenic open-pollinated spinach lines (NILs), having different resistance loci in a susceptible and otherwise common genetic background, would facilitate identification of races of the downy mildew pathogen, provide a tool to better understand the genetics of resistance, and expedite the development of molecular markers linked to these disease resistance loci. To achieve this objective, the spinach cv. Viroflay, susceptible to race 6 of Peronospora farinosa f. sp. spinaciae, was used as the recurrent susceptible parent in crosses with the hybrid spinach cv. Lion, resistant to race 6. Resistant F1 progeny were subsequently backcrossed to Viroflay four times with selection for race 6 resistance each time. Analysis of the segregation data showed that resistance was controlled by a single dominant gene, and the resistance locus was designated Pfs-1. By bulk segregant analysis, an amplified fragment length polymorphism (AFLP) marker (E-ACT/M-CTG) linked to Pfs-1 was identified and used to develop a co-dominant Sequence characterized amplified region (SCAR) marker. This SCAR marker, designated Dm-1, was closely linked (≈1.7 cM) to the Pfs-1 locus and could discriminate among spinach genotypes that were homozygous resistant (Pfs-1Pfs-1), heterozygous resistant (Pfs-1pfs-1), or homozygous susceptible (pfs-1pfs-1) to race 6 within the original mapping population. Evaluation of a wide range of commercial spinach lines outside of the mapping population indicated that Dm-1 could effectively identify Pfs-1 resistant genotypes; the Dm-1 marker correctly predicted the disease resistance phenotype in 120 out of 123 lines tested. In addition, the NIL containing the Pfs-1 locus (Pfs-1Pfs-1) was resistant to multiple races of the downy mildew pathogen indicating Pfs-1 locus may contain a cluster of resistance genes.

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Detecting Aphanomyces Invadans in Pure Cultures and EUS-infected Fish Lesions by Applying PCR

Malaysian Journal of Medical and Biological Research ◽

10.18034/mjmbr.v3i2.410 ◽

2016 ◽

Vol 3 (2) ◽

pp. 75-84

Author(s):

Fatemeh Afzali ◽

Hassan Hj Mohd Daud ◽

Shiv Shankar ◽

M Shuaib Khan ◽

Samanesadat Afzali

Keyword(s):

Early Stage ◽

Disease Onset ◽

Fish Tissue ◽

Polymerase Chain Reaction Method ◽

Infected Fish ◽

Economic Losses ◽

Gold Fish ◽

Wide Range ◽

Pure Cultures ◽

Dead Fish

Aphanomyces invadans is an oomycete fungus which causes Epizootic Ulcerative Syndrome (EUS) disease in wide range of fresh and brackish water fish worldwide imposing serious economic losses. A diagnostic procedure, based on a polymerase chain reaction method (PCR) was developed to detect infection of fish with the A.invadans. A set of primers (1APM 1F and 1APM 6R) was used to specifically amplify A. invadans DNA. The PCR amplifies a 400 bp amplicon. A protocol for the extraction of A. invadans DNA from infected fish tissue and pure fungal cultures was developed. The method was tested on seven EUS-susceptible fish species (snakehead, snakeskin gourami, moonlight gourami, koi carp, catfish, gold fish, climbing perch) and one EUS-resistant fish (tilapia), artificially infected with A. invadans and pure cultures of Aphanomyces spp., Saprolegnia spp., Achlya spp., and Allomyces sp. Detection of A. invadans was possible at the early stage of sampling, which was 24 hours post injection in both EUS-susceptible and resistant fish. Resistant fish was found to be PCR-negative after 6 days of inoculation but in susceptible fish PCR-positive results obtained even after day 28 or in dead fish. Therefore PCR may be a useful method for detection EUS infection in fish from early stage of disease onset.

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Phenotypic Variation for Downy Mildew Resistance among Inbred Broccoli

HortScience ◽

10.21273/hortsci.35.5.925 ◽

2000 ◽

Vol 35 (5) ◽

pp. 925-929 ◽

Cited By ~ 10

Author(s):

Min Wang ◽

Mark W. Farnham ◽

Claude E. Thomas

Keyword(s):

Downy Mildew ◽

Plant Resistance ◽

Developmental Stages ◽

Downy Mildew Resistance ◽

Mildew Resistance ◽

Leaf Stage ◽

True Leaf ◽

Cotyledon Stage ◽

Geographic Regions ◽

Dh Lines

Downy mildew, caused by Peronospora parasitica (Pers. Fr.) Fr., is one of the most economically important diseases of broccoli (Brassica oleracea L. Italica group). Previous studies have shown that resistance to downy mildew in broccoli is dependent on plant age with seedling resistance being independent of mature-plant resistance. The objectives of this study were to: 1) determine if valid evaluations for downy mildew resistance can be conducted at both the cotyledon and the three to four true-leaf stages on the same plants of a given broccoli entry; 2) determine if doubled-haploid (DH) lines derived from the resistant hybrid `Everest' also exhibit resistance to downy mildew and if so, characterize the resistance phenotype(s) in these lines; and 3) determine if identified resistant DH lines exhibit resistance to isolates of P. parasitica acquired from different geographic regions of the United States. Twenty-three DH broccoli inbreds and two commercial hybrids were evaluated for reaction at different developmental stages to infection by P. parasitica in a controlled environment. Results showed that broccoli plants can be evaluated for downy mildew resistance in a two-stage process. Inoculation at the cotyledon stage did not offer any cross-protection or otherwise influence the expression of reaction phenotype (RP) when the same plants were subsequently inoculated at the three to four true-leaf stage. Three different RPs to infection by P. parasitica were identified in DH inbreds. These were: 1) susceptibility at both the cotyledon stage and the true-leaf stage; 2) resistance at both the cotyledon and true-leaf stage; and 3) susceptibility at the cotyledon stage but resistance at the true-leaf stage. There was no effect of two pathogenic isolates from different geographic regions on RP of DH broccoli inbreds. Selection of plant resistance to downy mildew at the cotyledon stage will effectively identify plants with high levels of resistance at subsequent developmental stages.

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Toxin Production in Soybean (Glycine max L.) Plants with Charcoal Rot Disease and by Macrophomina phaseolina, the Fungus that Causes the Disease

Toxins ◽

10.3390/toxins11110645 ◽

2019 ◽

Vol 11 (11) ◽

pp. 645 ◽

Cited By ~ 8

Author(s):

Hamed K. Abbas ◽

Nacer Bellaloui ◽

Cesare Accinelli ◽

James R. Smith ◽

W. Thomas Shier

Keyword(s):

Culture Media ◽

Leaf Disc ◽

Toxin Production ◽

Macrophomina Phaseolina ◽

Economic Losses ◽

Limit Of Quantification ◽

Charcoal Rot ◽

Wide Range ◽

Soybean Plants ◽

Rot Disease

Charcoal rot disease, caused by the fungus Macrophomina phaseolina, results in major economic losses in soybean production in southern USA. M. phaseolina has been proposed to use the toxin (-)-botryodiplodin in its root infection mechanism to create a necrotic zone in root tissue through which fungal hyphae can readily enter the plant. The majority (51.4%) of M. phaseolina isolates from plants with charcoal rot disease produced a wide range of (-)-botryodiplodin concentrations in a culture medium (0.14–6.11 µg/mL), 37.8% produced traces below the limit of quantification (0.01 µg/mL), and 10.8% produced no detectable (-)-botryodiplodin. Some culture media with traces or no (-)-botryodiplodin were nevertheless strongly phytotoxic in soybean leaf disc cultures, consistent with the production of another unidentified toxin(s). Widely ranging (-)-botryodiplodin levels (traces to 3.14 µg/g) were also observed in the roots, but not in the aerial parts, of soybean plants naturally infected with charcoal rot disease. This is the first report of (-)-botryodiplodin in plant tissues naturally infected with charcoal rot disease. No phaseolinone was detected in M. phaseolina culture media or naturally infected soybean tissues. These results are consistent with (-)-botryodiplodin playing a role in the pathology of some, but not all, M. phaseolina isolates from soybeans with charcoal rot disease in southern USA.

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Photonic Crystal Nanobeam Cavities for Nanoscale Optical Sensing: A Review

Micromachines ◽

10.3390/mi11010072 ◽

2020 ◽

Vol 11 (1) ◽

pp. 72 ◽

Cited By ~ 2

Author(s):

Da-Quan Yang ◽

Bing Duan ◽

Xiao Liu ◽

Ai-Qiang Wang ◽

Xiao-Gang Li ◽

...

Keyword(s):

Photonic Crystal ◽

Optical Waveguides ◽

Optical Sensing ◽

Early Stage ◽

Disease Diagnosis ◽

Label Free ◽

Quality Factors ◽

Integrated Sensor ◽

Early Stage Disease ◽

Wide Range

The ability to detect nanoscale objects is particular crucial for a wide range of applications, such as environmental protection, early-stage disease diagnosis and drug discovery. Photonic crystal nanobeam cavity (PCNC) sensors have attracted great attention due to high-quality factors and small-mode volumes (Q/V) and good on-chip integrability with optical waveguides/circuits. In this review, we focus on nanoscale optical sensing based on PCNC sensors, including ultrahigh figure of merit (FOM) sensing, single nanoparticle trapping, label-free molecule detection and an integrated sensor array for multiplexed sensing. We believe that the PCNC sensors featuring ultracompact footprint, high monolithic integration capability, fast response and ultrahigh sensitivity sensing ability, etc., will provide a promising platform for further developing lab-on-a-chip devices for biosensing and other functionalities.

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Non-Albumin Proteinuria (NAP) as a Complementary Marker for Diabetic Kidney Disease (DKD)

Life ◽

10.3390/life11030224 ◽

2021 ◽

Vol 11 (3) ◽

pp. 224

Author(s):

Jaehyun Bae ◽

Young Jun Won ◽

Byung-Wan Lee

Keyword(s):

Kidney Disease ◽

Filtration Rate ◽

Diabetic Kidney Disease ◽

Estimated Glomerular Filtration Rate ◽

Early Stage ◽

Screening Tools ◽

Tubular Injury ◽

Current Standard ◽

Diabetic Kidney ◽

Wide Range

Diabetic kidney disease (DKD) is one of the most common forms of chronic kidney disease. Its pathogenic mechanism is complex, and it can affect entire structures of the kidney. However, conventional approaches to early stage DKD have focused on changes to the glomerulus. Current standard screening tools for DKD, albuminuria, and estimated glomerular filtration rate are insufficient to reflect early tubular injury. Therefore, many tubular biomarkers have been suggested. Non-albumin proteinuria (NAP) contains a wide range of tubular biomarkers and is convenient to measure. We reviewed the clinical meanings of NAP and its significance as a marker for early stage DKD.

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Response of Palmer amaranth (Amaranthus palmeri S. Watson) and sugarbeet to desmedipham and phenmedipham

Weed Technology ◽

10.1017/wet.2021.1 ◽

2021 ◽

pp. 1-9

Author(s):

Clint W. Beiermann ◽

Cody F. Creech ◽

Stevan Z. Knezevic ◽

Amit J. Jhala ◽

Robert Harveson ◽

...

Keyword(s):

Mortality Rates ◽

Selectivity Index ◽

Palmer Amaranth ◽

Greenhouse Experiment ◽

Amaranthus Palmeri ◽

True Leaf ◽

Cotyledon Stage ◽

Equivalent Rate ◽

Herbicide Treatments ◽

High Level

Abstract A prepackaged mixture of desmedipham + phenmedipham was previously labeled for control of Amaranthus spp. in sugarbeet. Currently, there are no effective POST herbicide options to control glyphosate-resistant Palmer amaranth in sugarbeet. Sugarbeet growers are interested in using desmedipham + phenmedipham to control escaped Palmer amaranth. In 2019, a greenhouse experiment was initiated near Scottsbluff, NE, to determine the selectivity of desmedipham and phenmedipham between Palmer amaranth and sugarbeet. Three populations of Palmer amaranth and four sugarbeet hybrids were evaluated. Herbicide treatments consisted of desmedipham and phenmedipham applied singly or as mixtures at an equivalent rate. Herbicides were applied when Palmer amaranth and sugarbeet were at the cotyledon stage, or two true-leaf sugarbeet stage and when Palmer amaranth was 7 cm tall. The selectivity indices for desmedipham, phenmedipham, and desmedipham + phenmedipham were 1.61, 2.47, and 3.05, respectively, at the cotyledon stage. At the two true-leaf application stage, the highest rates of desmedipham and phenmedipham were associated with low mortality rates in sugarbeet, resulting in a failed response of death. The highest rates of desmedipham + phenmedipham caused a death response of sugarbeet; the selectivity index was 2.15. Desmedipham treatments resulted in lower LD50 estimates for Palmer amaranth compared to phenmedipham, indicating that desmedipham can provide greater levels of control for Palmer amaranth. However, desmedipham also caused greater injury in sugarbeet, producing lower LD50 estimates compared to phenmedipham. Desmedipham + phenmedipham provided 90% or greater control of cotyledon-size Palmer amaranth at a labeled rate but also caused high levels of sugarbeet injury. Neither desmedipham, phenmedipham, nor desmedipham + phenmedipham was able to control 7-cm tall Palmer amaranth at previously labeled rates. Results indicate that desmedipham + phenmedipham can only control Palmer amaranth if applied at the cotyledon stage and a high level of sugarbeet injury is acceptable.

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Contagion Management at the Méditerranée Infection University Hospital Institute

Journal of Clinical Medicine ◽

10.3390/jcm10122627 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2627

Author(s):

Pierre-Edouard Fournier ◽

Sophie Edouard ◽

Nathalie Wurtz ◽

Justine Raclot ◽

Marion Bechet ◽

...

Keyword(s):

Infectious Disease ◽

Early Diagnosis ◽

Personal Protective Equipment ◽

Early Stage ◽

Point Of Care ◽

University Hospital ◽

Protective Equipment ◽

Monitoring Point ◽

Epidemiological Monitoring ◽

Wide Range

The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.

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Citizen views on genome editing: effects of species and purpose

Agriculture and Human Values ◽

10.1007/s10460-021-10235-9 ◽

2021 ◽

Author(s):

Gesa Busch ◽

Erin Ryan ◽

Marina A. G. von Keyserlingk ◽

Daniel M. Weary

Keyword(s):

Disease Resistance ◽

Product Quality ◽

Genome Editing ◽

Total Sample ◽

Moral Foundations ◽

Perceived Risks ◽

Public Response ◽

The Public ◽

Wide Range ◽

The Us

AbstractPublic opinion can affect the adoption of genome editing technologies. In food production, genome editing can be applied to a wide range of applications, in different species and with different purposes. This study analyzed how the public responds to five different applications of genome editing, varying the species involved and the proposed purpose of the modification. Three of the applications described the introduction of disease resistance within different species (human, plant, animal), and two targeted product quality and quantity in cattle. Online surveys in Canada, the US, Austria, Germany and Italy were carried out with a total sample size of 3698 participants. Using a between-subject design, participants were confronted with one of the five applications and asked to decide whether they considered it right or wrong. Perceived risks, benefits, and the perception of the technology as tampering with nature were surveyed and were complemented with socio-demographics and a measure of the participants’ moral foundations. In all countries, participants evaluated the application of disease resistance in humans as most right to do, followed by disease resistance in plants, and then in animals, and considered changes in product quality and quantity in cattle as least right to do. However, US and Italian participants were generally more positive toward all scenarios, and German and Austrian participants more negative. Cluster analyses identified four groups of participants: ‘strong supporters’ who saw only benefits and little risks, ‘slight supporters’ who perceived risks and valued benefits, ‘neutrals’ who showed no pronounced opinion, and ‘opponents’ who perceived higher risks and lower benefits. This research contributes to understanding public response to applications of genome editing, revealing differences that can help guide decisions related to adoption of these technologies.

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Design of Personalized Devices—The Tradeoff between Individual Value and Personalization Workload

Applied Sciences ◽

10.3390/app11010241 ◽

2020 ◽

Vol 11 (1) ◽

pp. 241

Author(s):

Juliane Kuhl ◽

Andreas Ding ◽

Ngoc Tuan Ngo ◽

Andres Braschkat ◽

Jens Fiehler ◽

...

Keyword(s):

Customer Value ◽

Early Stage ◽

Treatment Success ◽

Product Family ◽

Flow Diverter ◽

New Method ◽

Product Families ◽

Wide Range ◽

The Individual ◽

Individual Value

Personalized medical devices adapted to the anatomy of the individual promise greater treatment success for patients, thus increasing the individual value of the product. In order to cater to individual adaptations, however, medical device companies need to be able to handle a wide range of internal processes and components. These are here referred to collectively as the personalization workload. Consequently, support is required in order to evaluate how best to target product personalization. Since the approaches presented in the literature are not able to sufficiently meet this demand, this paper introduces a new method that can be used to define an appropriate variety level for a product family taking into account standardized, variant, and personalized attributes. The new method enables the identification and evaluation of personalizable attributes within an existing product family. The method is based on established steps and tools from the field of variant-oriented product design, and is applied using a flow diverter—an implant for the treatment of aneurysm diseases—as an example product. The personalization relevance and adaptation workload for the product characteristics that constitute the differentiating product properties were analyzed and compared in order to determine a tradeoff between customer value and personalization workload. This will consequently help companies to employ targeted, deliberate personalization when designing their product families by enabling them to factor variety-induced complexity and customer value into their thinking at an early stage, thus allowing them to critically evaluate a personalization project.

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