Correction Notice: Labeling and Isolation of Fluorouracil Tagged RNA by Cytosine Deaminase Expression

Basnet, Harihar; Massague, Joan

doi:10.21769/bioprotoc.3857

Cited by 10 publications

(15 citation statements)

References 1 publication

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“…To identify GSR-resistant lines, we assessed the disease phenotypes of a maize population consisting of 66 inbred lines using the seedling assay as previously described ( Sun et al, 2018 ). As shown in Supplementary Figure 1 , the majority of lines showed the moderate disease severity to GSR, whereas several lines displayed obvious resistance (such as CML496, Zhong106, CIMBL133, etc.)…”

Section: Resultsmentioning

confidence: 99%

“…Fusarium graminearum strain 0609, kindly provided by Prof. Mingliang Xu at China Agricultural University, was cultured and maintained on PDA media as regular. The fungal inoculum and artificial inoculation on seedlings were conducted according to our previous study ( Sun et al, 2018 ). Briefly, the fungus was cultured freshly in liquid common bean soup for 2 to 3 days, and fungal culture was centrifuged, resuspended, and washed twice with sterile water, and then the spore suspension was examined under microscope and adjusted to a concentration of 1.0 × 10 6 /mL in 0.001% Tween-20.…”

Section: Methodsmentioning

confidence: 99%

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Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot

et al. 2021

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Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases causing significant yield loss of maize, and GSR resistance is a quantitative trait controlled by multiple genes. Although a few quantitative trait loci/resistance genes have been identified, the molecular mechanisms underlying GSR resistance remain largely unexplored. To identify potential resistance genes and to better understand the molecular mechanism of GSR resistance, a joint analysis using a comparative transcriptomic and metabolomic approaches was conducted using two inbred lines with contrasting GSR resistance, K09 (resistant) and A08 (susceptible), upon infection with F. graminearum. While a substantial number of differentially expressed genes associated with various defense-related signaling pathways were identified between two lines, multiple hub genes likely associated with GSR resistance were pinpointed using Weighted Gene Correlation Network Analysis and K-means clustering. Moreover, a core set of metabolites, including anthocyanins, associated with the hub genes was determined. Among the complex co-expression networks, ZmHIR3 showed strong correlation with multiple key genes, and genetic and histological studies showed that zmhir3 mutant is more susceptible to GSR, accompanied by enhanced cell death in the stem in response to infection with F. graminearum. Taken together, our study identified differentially expressed key genes and metabolites, as well as co-expression networks associated with distinct infection stages of F. graminearum. Moreover, ZmHIR3 likely plays a positive role in disease resistance to GSR, probably through the transcriptional regulation of key genes, functional metabolites, and the control of cell death.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot

et al. 2021

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“…Nitrate content was determined in Arabidopsis seedlings and barley shoot tissue according to nitration of salicylic acid under acidic conditions as described by Hachiya and Okamoto (2017) and quantified as mg⋅g –1 DW. Free amino acids and ammonium extraction was performed by mixing 40 mg of barley shoot tissue with 800 μl of ethanol 70% (v/v), kept overnight at 4°C under dark and centrifuged at 20,000 × g for 10 min at 4°C.…”

Section: Methodsmentioning

confidence: 99%

“…The reaction was stopped by adding 120 μl of 0.6 M zinc acetate and the samples were centrifuged at 25,000 × g for 5 min. The amount of produced nitrite was determined spectrophotometrically at 540 nm according Hachiya and Okamoto (2017) and NR activity was expressed as nmol NO 2 – ⋅h –1 ⋅mg –1 protein. The activation state of NR was defined as the activity measured in the presence of 5 mM MgCl 2 divided by the activity measured in the presence of 5 mM EDTA (expressed as a percentage).…”

Section: Methodsmentioning

confidence: 99%

Reducing Nitrogen Input in Barley Crops While Maintaining Yields Using an Engineered Biostimulant Derived From Ascophyllum nodosum to Enhance Nitrogen Use Efficiency

et al. 2021

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Intensive agricultural production utilizes large amounts of nitrogen (N) mineral fertilizers that are applied to the soil to secure high crop yields. Unfortunately, up to 65% of this N fertilizer is not taken up by crops and is lost to the environment. To compensate these issues, growers usually apply more fertilizer than crops actually need, contributing significantly to N pollution and to GHG emissions. In order to combat the need for such large N inputs, a better understanding of nitrogen use efficiency (NUE) and agronomic solutions that increase NUE within crops is required. The application of biostimulants derived from extracts of the brown seaweed Ascophyllum nodosum has long been accepted by growers as a sustainable crop production input. However, little is known on how Ascophyllum nodosum extracts (ANEs) can influence mechanisms of N uptake and assimilation in crops to allow reduced N application. In this work, a significant increase in nitrate accumulation in Arabidopsis thaliana 6 days after applying the novel proprietary biostimulant PSI-362 was observed. Follow-up studies in barley crops revealed that PSI-362 increases NUE by 29.85–60.26% under 75% N input in multi-year field trials. When PSI-362 was incorporated as a coating to the granular N fertilizer calcium ammonium nitrate and applied to barley crop, a coordinated stimulation of N uptake and assimilation markers was observed. A key indicator of biostimulant performance was increased nitrate content in barley shoot tissue 22 days after N fertilizer application (+17.9–72.2%), that was associated with gene upregulation of root nitrate transporters (NRT1.1, NRT2.1, and NRT1.5). Simultaneously, PSI-362 coated fertilizer enhanced nitrate reductase and glutamine synthase activities, while higher content of free amino acids, soluble protein and photosynthetic pigments was measured. These biological changes at stem elongation stage were later translated into enhanced NUE traits in harvested grain. Overall, our results support the agronomic use of this engineered ANE that allowed a reduction in N fertilizer usage while maintaining or increasing crop yield. The data suggests that it can be part of the solution for the successful implementation of mitigation policies for water quality and GHG emissions from N fertilizer usage.

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“…The solution was replaced with chloral hydrate after cooling, and the samples were shaken until fully destained. 3,3′-Diaminobenzidine (DAB)-HCl (Sigma-Aldrich) was used to detect H 2 O 2 visually in leaves as previously described ( Daudi and O’Brien, 2012 ; Yang et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification Reveals That Nicotiana benthamiana Hypersensitive Response (HR)-Like Lesion Inducing Protein 4 (NbHRLI4) Mediates Cell Death and Salicylic Acid-Dependent Defense Responses to Turnip Mosaic Virus

Lai

Rao

et al. 2021

Front. Plant Sci.

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Hypersensitive response (HR)-like cell death is an important mechanism that mediates the plant response to pathogens. In our previous study, we reported that NbHIR3s regulate HR-like cell death and basal immunity. However, the host genes involved in HR have rarely been studied. Here, we used transcriptome sequencing to identify Niben101Scf02063g02012.1, an HR-like lesion inducing protein (HRLI) in Nicotiana benthamiana that was significantly reduced by turnip mosaic virus (TuMV). HRLIs are uncharacterized proteins which may regulate the HR process. We identified all six HRLIs in N. benthamiana and functionally analyzed Niben101Scf02063g02012.1, named NbHRLI4, in response to TuMV. Silencing of NbHRLI4 increased TuMV accumulation, while overexpression of NbHRLI4 conferred resistance to TuMV. Transient overexpression of NbHRLI4 caused cell death with an increase in the expression of salicylic acid (SA) pathway genes but led to less cell death level and weaker immunity in plants expressing NahG. Thus, we have characterized NbHRLI4 as an inducer of cell death and an antiviral regulator of TuMV infection in a SA-mediated manner.

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Correction Notice: Labeling and Isolation of Fluorouracil Tagged RNA by Cytosine Deaminase Expression

Cited by 10 publications

References 1 publication

Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot

Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot

Reducing Nitrogen Input in Barley Crops While Maintaining Yields Using an Engineered Biostimulant Derived From Ascophyllum nodosum to Enhance Nitrogen Use Efficiency

Genome-Wide Identification Reveals That Nicotiana benthamiana Hypersensitive Response (HR)-Like Lesion Inducing Protein 4 (NbHRLI4) Mediates Cell Death and Salicylic Acid-Dependent Defense Responses to Turnip Mosaic Virus

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