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RNAs and Plant Disease Resistance
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RNAs and Plant Disease Resistance

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 43656

Special Issue Editor

Dr. Alberto Carbonell

E-Mail Website
Guest Editor
Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
Interests: RNA; small RNA; RNA silencing; ARGONAUTES; viroid; plant virus; antiviral resistance; plant biotechnology

Special Issue Information

Dear Colleagues,

One of the main challenges for humanity is to ensure the availability of sufficient safe and nutritious food worldwide. Plants, one of the major sources of human food, are continuously threatened by the endless emergence of new diseases caused by pathogens and variable environmental conditions, particularly during the current global warming period. Thus, there is an unceasing need to better understand the basic mechanisms controlling plant immunity and to develop more sustainable and effective strategies for the production of highly disease-resistant next-generation crops.

Ribonucleic acid (RNA), a polymeric molecule assembled as a chain of nucleotides, plays key biological roles in regulating gene expression in all known forms of life. In plants, RNAs—particularly small RNAs, such as microRNAs—are also at the core of the RNA silencing-based defense responses to biotic and abiotic stresses. In addition to plant endogenous RNAs, a large repertoire of RNAs, such as ribozymes, artificial microRNAs, artificial (synthetic) trans-acting small interfering RNAs or CRISPR guide RNAs can be artificially engineered and applied to plants to regulate gene expression and repress pathogenic RNA or DNA and generate disease resistance.

In this Special Issue, I would like to invite research articles and reviews that highlight the key contribution of any form of RNA in generating disease resistance in plants. I expect this collection of articles to open new horizons in the study of RNA as a key player to combat plant diseases and preserve crop production.

Dr. Alberto Carbonell
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • disease resistance
  • plant defense
  • plant immunity
  • RNA
  • microRNA
  • RNA silencing
  • RNAi
  • artificial microRNA
  • synthetic trans-acting small interfering RNA
  • ribozyme
  • guide RNA
  • CRISPR

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Published Papers (7 papers)

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Research

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20 pages, 3717 KiB  
Article
Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus
by Jana Jarošová, Khushwant Singh, Jana Chrpová and Jiban Kumar Kundu
Plants 2020, 9(1), 60; https://doi.org/10.3390/plants9010060 - 2 Jan 2020
Cited by 8 | Viewed by 3802
Abstract
Barley yellow dwarf virus (BYDV) causes an often-devastating disease of cereals that is most effectively controlled by using plant genotypes that are resistant or tolerant to the virus. New barley lines Vir8:3 and Vir13:8, with pyramided resistance genes against different pathogens and resistance [...] Read more.
Barley yellow dwarf virus (BYDV) causes an often-devastating disease of cereals that is most effectively controlled by using plant genotypes that are resistant or tolerant to the virus. New barley lines Vir8:3 and Vir13:8, with pyramided resistance genes against different pathogens and resistance gene Ryd2 against BYDV, are currently being tested. Because microRNAs (miRNAs) are associated with antiviral plant defense, here we compared the miRNA profiles in these lines and in cultivar Wysor (carrying one resistance gene, Ryd2), with and without BYDV infection and after feeding by virus-free aphids, to determine whether the miRNA profile in the resistant variety bear similarities with the newly developed lines. The BYDV titer for each group was also determined and compared to the titer in sensitive cultivar Graciosa. Among 746 miRNAs identified in barley, 66 were known miRNAs, and 680 were novel. The expression of 73 miRNAs differed significantly after BYDV infection, including the strong, specific upregulation of novel miRNA10778 that was conserved across all the barley genotypes. This miRNA belongs to the H box and ACA box (H/ACA) snoR14 family of RNAs (Rf01280) and is associated with pseudourydilation. The expression of 48 miRNAs also differed depending on the barley genotype. The profile of miRNAs expressed in Vir8:3 and Vir13:8 in response to BYDV was similar and differed from that of Wysor. Insights into the expression patterns of miRNAs in response to BYDV in barley provided here will benefit further studies toward understanding the resistance mechanisms and developing novel strategies against virus infections. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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17 pages, 2369 KiB  
Article
Innovative RNAi Strategies and Tactics to Tackle Plum Pox Virus (PPV) Genome in Prunus domestica-Plum
by Michel Ravelonandro, Ralph Scorza and Pascal Briard
Plants 2019, 8(12), 565; https://doi.org/10.3390/plants8120565 - 2 Dec 2019
Cited by 8 | Viewed by 3573
Abstract
We developed an innovative RNAi concept based on two gene constructs built from the capsid gene (CP) cistron of the Plum pox virus (PPV) genome. First, designated as amiCPRNA, a potential molecule interfering with PPV genome translation and the second one is the [...] Read more.
We developed an innovative RNAi concept based on two gene constructs built from the capsid gene (CP) cistron of the Plum pox virus (PPV) genome. First, designated as amiCPRNA, a potential molecule interfering with PPV genome translation and the second one is the ami-siCPRNA to target viral genome translation and PPV RNA replication. Following the previous engineering of these constructs in an experimental herbaceous host, they were introduced into Prunus domestica (plum tree) genome. Previously propagated onto a susceptible rootstock, these clones were graft-inoculated with PPV. After four dormancy cycles, and consistent with our experience of PPV infection, some clones showed a common phenomenon of silencing that can differ between the detailed plant phenotypes. Three different phenotypes were developed by the amisiCPRNA clones. First, the high resistance character shown by the amisiCPRNA plum-7 that was similar to the resistance expressed by HoneySweet plum. Secondly, a recovery reaction was developed by the two other amisiCPRNA plum-3 and plum-4 that differed from the rest, characterized as susceptible clones, among these were the amiCPRNA plums. Having assessed the behavior of these plums versus the herbaceous host accumulating the similar form of RNAi: ami-, si-, and ami-siRNA, challenging assays in perennials consistently reflect the natural context of viral genome targeting. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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10 pages, 1487 KiB  
Article
Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)
by Imen Belgacem, Sonia Pangallo, Ahmed Abdelfattah, Flora V. Romeo, Santa O. Cacciola, Maria G. Li Destri Nicosia, Gabriele Ballistreri and Leonardo Schena
Plants 2019, 8(4), 101; https://doi.org/10.3390/plants8040101 - 17 Apr 2019
Cited by 21 | Viewed by 4447
Abstract
A Pomegranate Peel Extract (PGE) has been proposed as a natural antifungal substance with a wide range of activity against plant diseases. Previous studies showed that the extract has a direct antimicrobial activity and can elicit resistance responses in plant host tissues. In [...] Read more.
A Pomegranate Peel Extract (PGE) has been proposed as a natural antifungal substance with a wide range of activity against plant diseases. Previous studies showed that the extract has a direct antimicrobial activity and can elicit resistance responses in plant host tissues. In the present study, the transcriptomic response of orange fruit toward PGE treatments was evaluated. RNA-seq analyses, conducted on wounded fruits 0, 6, and 24 h after PGE applications, showed a significantly different transcriptome in treated oranges as compared to control samples. The majority (273) of the deferentially expressed genes (DEGs) were highly up-regulated compared to only 8 genes that were down-regulated. Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed the involvement of 1233 gene ontology (GO) terms and 35 KEGG metabolic pathways. Among these, important defense pathways were induced and antibiotic biosynthesis was the most enriched one. These findings may explain the underlying preventive and curative activity of PGE against plant diseases. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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Review

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16 pages, 849 KiB  
Review
Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms
by Igor V. Maksimov, Antonina V. Sorokan, Guzel F. Burkhanova, Svetlana V. Veselova, Valentin Yu. Alekseev, Mikhail Yu. Shein, Azamat M. Avalbaev, Prashant D. Dhaware, Gajanan T. Mehetre, Bhim Pratap Singh and Ramil M. Khairullin
Plants 2019, 8(12), 575; https://doi.org/10.3390/plants8120575 - 5 Dec 2019
Cited by 21 | Viewed by 9487
Abstract
Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it [...] Read more.
Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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18 pages, 2094 KiB  
Review
Bacterium-Mediated RNA Interference: Potential Application in Plant Protection
by Simon Goodfellow, Daai Zhang, Ming-Bo Wang and Ren Zhang
Plants 2019, 8(12), 572; https://doi.org/10.3390/plants8120572 - 5 Dec 2019
Cited by 18 | Viewed by 8359
Abstract
RNAi has emerged as a promising tool for targeting agricultural pests and pathogens and could provide an environmentally friendly alternative to traditional means of control. However, the deployment of this technology is still limited by a lack of suitable exogenous- or externally applied [...] Read more.
RNAi has emerged as a promising tool for targeting agricultural pests and pathogens and could provide an environmentally friendly alternative to traditional means of control. However, the deployment of this technology is still limited by a lack of suitable exogenous- or externally applied delivery mechanisms. Numerous means of overcoming this limitation are being explored. One such method, bacterium-mediated RNA interference, or bmRNAi, has been explored in other systems and shows great potential for application to agriculture. Here, we review the current state of bmRNAi, examine the technical limitations and possible improvements, and discuss its potential applications in crop protection. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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11 pages, 516 KiB  
Review
The Role of MicroRNAs in Genome Response to Plant–Lepidoptera Interaction
by Katarína Ražná and Ľudovít Cagáň
Plants 2019, 8(12), 529; https://doi.org/10.3390/plants8120529 - 20 Nov 2019
Cited by 4 | Viewed by 3515
Abstract
RNA interference is a known phenomenon of plant immune responses, involving the regulation of gene expression. The key components triggering the silencing of targeted sequences are double-stranded RNA molecules. The regulation of host–pathogen interactions is controlled by miRNA molecules, which regulate the expression [...] Read more.
RNA interference is a known phenomenon of plant immune responses, involving the regulation of gene expression. The key components triggering the silencing of targeted sequences are double-stranded RNA molecules. The regulation of host–pathogen interactions is controlled by miRNA molecules, which regulate the expression of host resistance genes or the genes of the pathogen. The review focused on basic principles of RNA interference as a gene-silencing-based defense mechanism and the role of miRNA molecules in insect genomes. RNA interference as a tool for plant protection management is discussed. The review summarizes current miRNA-based biotechnology approaches for plant protection management. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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18 pages, 1582 KiB  
Review
RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants
by Khushwant Singh, Chris Dardick and Jiban Kumar Kundu
Plants 2019, 8(10), 359; https://doi.org/10.3390/plants8100359 - 22 Sep 2019
Cited by 15 | Viewed by 9232
Abstract
Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) [...] Read more.
Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs with hairpin structures by Dicer-like proteins (DCLs), they are loaded onto Argonaute (AGO) protein complexes to induce gene silencing of their complementary targets by promoting messenger RNA (mRNA) cleavage or degradation, translation inhibition, DNA methylation, and/or histone modifications. This mechanism of regulating RNA activity, collectively referred to as RNA interference (RNAi), which is an evolutionarily conserved process in eukaryotes. Plant RNAi pathways play a fundamental role in plant immunity against viruses and have been exploited via genetic engineering to control disease. Plant viruses of RNA origin that contain double-stranded RNA are targeted by the RNA-silencing machinery to produce virus-derived small RNAs (vsRNAs). Some vsRNAs serve as an effector to repress host immunity by capturing host RNAi pathways. High-throughput sequencing (HTS) strategies have been used to identify endogenous sRNA profiles, the “sRNAome”, and analyze expression in various perennial plants. Therefore, the review examines the current knowledge of sRNAs in perennial plants and fruits, describes the development and implementation of RNA interference (RNAi) in providing resistance against economically important viruses, and explores sRNA targets that are important in regulating a variety of biological processes. Full article
(This article belongs to the Special Issue RNAs and Plant Disease Resistance)
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