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Molecular Variability of Crop Pathogens
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Molecular Variability of Crop Pathogens

A special issue of Crops (ISSN 2673-7655).

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 15762

Special Issue Editors

Dr. Marta Nunes Da Silva

E-Mail Website
Guest Editor
CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
Interests: plant-pathogen interactions; environmental contamination; plant fitness and productivity; genotype x environment interactions; plant protection
Special Issues, Collections and Topics in MDPI journals
Dr. Carla Sofia Sancho Dos Santos

E-Mail Website
Guest Editor
CBQF–Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
Interests: plant nutrition; sustainable agricultural management; plant biotechnology; legumes; abiotic stress; seed genetic variability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crops account for over 80% of the human diet, but plant diseases and pests are responsible for up to 40% of loss in food production worldwide. Food shortage caused by crop pathogens can lead to increased food insecurity, particularly in populations deeply dependent on plant-based diets. This subject is of particular concern under predicted scenarios of climate change, which could alter the genetics, prevalence and virulence of crop pathogenic organisms.

This Special Issue aims to uncover the influence of genetic and environmental factors on the molecular variability of crop pathogens (including fungi, bacteria, phytoplasmas, viruses, and nematodes) that underpin disease incidence and spread. We welcome original research articles, review articles, perspectives, opinions and methodological articles focusing on the molecular mechanisms involved in the crosstalk between pathogens and crops that could support effective disease management strategies. Topics of interest include, but are not limited to:

  1. Origin and evolutionary processes that led to the appearance of pathogenic populations of crop plants;
  2. Influence of environmental factors and climate change on pathogen virulence and prevalence;
  3. Gene-for-gene relationship, particularly concerning avirulence, effector repertoire and toxin production;
  4. Genome-based tools for accurate intra- and inter-specific discrimination of pathogenic populations;
  5. Molecular-based strategies to anticipate the emergence of virulent populations and prevent disease outbreaks.

Dr. Marta Nunes Da Silva
Dr. Carla Sofia Sancho Dos Santos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Crops is an international peer-reviewed open access quarterly 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 1000 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

  • phytopathology
  • phytopathogens
  • agronomy
  • plant protection
  • genome
  • molecular biology, detection
  • evolution
  • gene expression
  • virulence

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 189 KiB  
Editorial
Molecular Variability of Crop Pathogens
by Carla S. Santos and Marta Nunes da Silva
Crops 2023, 3(2), 136-138; https://doi.org/10.3390/crops3020013 - 19 Apr 2023
Viewed by 975
Abstract
Crops account for over 80% of the human diet; however, plant diseases and pests are responsible for up to 40% of the loss in food production worldwide, costing approximately EUR 200 billion [...] Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)

Research

Jump to: Editorial, Review

13 pages, 4828 KiB  
Article
Comparative Transcriptomic Analysis Reveals Variable Responses to the Brown Planthopper Nilaparvata lugens in Different Rice Cultivars
by Longqing Shi, Haifang He, Junian Zhang, Zhaowei Jiang, Liangmiao Qiu and Zhixiong Zhan
Crops 2023, 3(1), 40-52; https://doi.org/10.3390/crops3010005 - 30 Jan 2023
Cited by 1 | Viewed by 1337
Abstract
Rice is an indispensable crop in East and Southeast Asia, and the study of its biological characteristics has important value. We observed that different cultivars of rice have different levels of resistance to the brown planthopper (BPH), Nilaparvata lugens. In this study, [...] Read more.
Rice is an indispensable crop in East and Southeast Asia, and the study of its biological characteristics has important value. We observed that different cultivars of rice have different levels of resistance to the brown planthopper (BPH), Nilaparvata lugens. In this study, transcriptome sequencing was used to analyze the differentially expressed genes (DEGs) of three rice varieties caused by BPH damage combined with physical stimulation and controls. We performed weighted correlation network analysis (WGCNA) and found a module positively related to physical stimulation. KEGG analysis showed that this module is strongly related to the ribosome pathway. Through comparative analysis with controls, we found the differential genes of each cultivar after BPH damage; through trend analysis, we found the differential genes shared by the three varieties after BPH damage. The KEGG/GO enrichment analysis of these genes found that they are mainly functionally concentrated in signal transduction, redox reactions, etc. The results of this research will be helpful to study the molecular mechanism of the BPH-rice interaction, identify resistance genes, and facilitate further studies on molecular resistance breeding and pest control. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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15 pages, 1444 KiB  
Article
Quantitative-Genetic Evaluation of Resistances to Five Fungal Diseases in A Large Triticale Diversity Panel (×Triticosecale)
by Thomas Miedaner, Kerstin Flath, Norbert Starck, Sigrid Weißmann and Hans Peter Maurer
Crops 2022, 2(3), 218-232; https://doi.org/10.3390/crops2030016 - 30 Jun 2022
Cited by 4 | Viewed by 1976
Abstract
The man-made cereal triticale was fully resistant to the biotrophic diseases powdery mildew, leaf rust, yellow rust, and stem rust from its introduction in Europe in the mid-1970s until about 1990. In the following years, new races that were able to infect at [...] Read more.
The man-made cereal triticale was fully resistant to the biotrophic diseases powdery mildew, leaf rust, yellow rust, and stem rust from its introduction in Europe in the mid-1970s until about 1990. In the following years, new races that were able to infect at least some triticale genotypes developed in all four pathogen populations, and resistance breeding came into focus. Here, we analyzed 656 winter triticale cultivars from 12 countries for resistance to these biotrophic diseases and Fusarium head blight (FHB) at up to 8 location-year combinations (environments). FHB ratings were corrected for plant height and heading stage by comparing three statistical methods. Significant (p < 0.001) genetic variances were found for all resistances with moderate to high entry-mean heritabilities. All traits showed a normal distribution, with the exception of stem rust, where the ratings were skewed towards resistance. There were no substantial correlations among the five disease resistances (r = −0.04 to 0.26). However, several genotypes were detected with multi-disease resistance with a disease rating below average for all five diseases simultaneously. In future, such genotypes must be selected primarily to cope with future challenges of less pesticide use and global climate change. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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16 pages, 1298 KiB  
Article
Growth-Promoting and Protective Effect of Trichoderma atrobrunneum and T. simmonsii on Tomato against Soil-Borne Fungal Pathogens
by Dimitrios Natsiopoulos, Apostolos Tziolias, Ioannis Lagogiannis, Spyridon Mantzoukas and Panagiotis A. Eliopoulos
Crops 2022, 2(3), 202-217; https://doi.org/10.3390/crops2030015 - 29 Jun 2022
Cited by 12 | Viewed by 3173
Abstract
Trichoderma fungi are promising candidates for biocontrol agents and plant growth promoters. Trichoderma atrobrunneum and T. simmonsii were evaluated for the control of soil-borne phytopathogenic fungi, in the present study. Dual culture tests with Rhizoctonia solani and Fusarium oxysporum f. sp. lycopersici were [...] Read more.
Trichoderma fungi are promising candidates for biocontrol agents and plant growth promoters. Trichoderma atrobrunneum and T. simmonsii were evaluated for the control of soil-borne phytopathogenic fungi, in the present study. Dual culture tests with Rhizoctonia solani and Fusarium oxysporum f. sp. lycopersici were used to conduct in vitro evaluation. In the presence of Trichoderma, phytopathogen’s growth rate was inhibited up to 59.70% for R. solani and 42.57% for F. oxysporum. Greenhouse trials with potted tomato plants demonstrated that Trichoderma caused a significant increase of stem height and fresh stem weight in pathogen-inoculated plants, compared with the negative control (plants artificially inoculated with the phytopathogen only). Except for T. simmonsii, plant growth was not significantly enhanced by a Trichoderma presence in the positive control (healthy plants). The overall performance of the two Trichoderma species studied was equivalent to that of the T. harzianum T22 commercial strain. All the tested species were found to be effective in suppressing colony growth and disease development of the soil borne pathogens in dual cultures and potted plants, indicating that they could be used as biocontrol agents. Our findings are discussed in the context of enhancing endophytic microorganisms’ application in crop production systems. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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12 pages, 2129 KiB  
Article
Response of Senegalese Sorghum Seedlings to Pathotype 5 of Sporisorium reilianum
by Ezekiel Ahn, Louis K. Prom, Coumba Fall and Clint Magill
Crops 2022, 2(2), 142-153; https://doi.org/10.3390/crops2020011 - 02 May 2022
Cited by 6 | Viewed by 1826
Abstract
Sporisorium reilianum causes head smut in sorghum. A total of 36 Senegalese sorghum accessions comprised of sorghum lines that have not been explored with response to pathotype 5 of S. reilianum were evaluated with 3 different treatments. First, seedling shoots were inoculated while [...] Read more.
Sporisorium reilianum causes head smut in sorghum. A total of 36 Senegalese sorghum accessions comprised of sorghum lines that have not been explored with response to pathotype 5 of S. reilianum were evaluated with 3 different treatments. First, seedling shoots were inoculated while still in soil with teliospores in agar, and then submerged under water at 4 days post inoculation. Signs of infection (noticeable spots) on the first leaf were observed up to 6 days post submergence. Second, seedlings at the same stage were inoculated by placing the teliospore impregnated agar around the stem in pots, moved to a greenhouse and grown to full panicle development stage. Third, seedings were inoculated via syringe inoculation in the greenhouse. Although soil inoculated seedlings grown in the greenhouse did not result in systemic infection as determined by lack of symptoms at panicle exsertion, 88.9% of tested cultivars showed systemic infections when syringe inoculated in the greenhouse. Inoculation of seedlings maintained under water led to broad range of noticeable spots that are assumed to be potential infection sites based on a previous study. In addition, seedling inoculation led to slightly upregulated expression of chitinase and PR10, genes that are associated with defense in aerial parts of plants. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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22 pages, 3171 KiB  
Article
Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and Their Potential Use in Biocontrol of Coffee Wilt Disease
by Afrasa Mulatu, Negussie Megersa, Tariku Abena, Selvaraju Kanagarajan, Qinsong Liu, Tesfaye Alemu Tenkegna and Ramesh R. Vetukuri
Crops 2022, 2(2), 120-141; https://doi.org/10.3390/crops2020010 - 26 Apr 2022
Cited by 9 | Viewed by 3181
Abstract
The present study investigated the distribution status and biodiversity of Trichoderma species surveyed from coffee rhizosphere soil samples from Ethiopia and their potential for biocontrol of coffee wilt disease (CWD) caused by Fusarium xylarioides. Trichoderma isolates were identified based on molecular approaches [...] Read more.
The present study investigated the distribution status and biodiversity of Trichoderma species surveyed from coffee rhizosphere soil samples from Ethiopia and their potential for biocontrol of coffee wilt disease (CWD) caused by Fusarium xylarioides. Trichoderma isolates were identified based on molecular approaches and morphological characteristics followed by biodiversity analysis using different biodiversity indices. The antagonistic potential of Trichoderma isolates was evaluated against F. xylarioides using the dual confrontation technique and agar diffusion bioassays. A relatively high diversity of species was observed, including 16 taxa and 11 undescribed isolates. Trichoderma asperellum, T. asperelloides and T. longibrachiatum were classified as abundant species, with dominance (Y) values of 0.062, 0.056 and 0.034, respectively. Trichoderma asperellum was the most abundant species (comprising 39.6% of all isolates) in all investigated coffee ecosystems. Shannon’s biodiversity index (H), the evenness (E), Simpson’s biodiversity index (D) and the abundance index (J) were calculated for each coffee ecosystem, revealing that species diversity and evenness were highest in the Jimma zone (H = 1.97, E = 0.76, D = 0.91, J = 2.73). The average diversity values for Trichoderma species originating from the coffee ecosystem were H = 1.77, D = 0.7, E = 0.75 and J = 2.4. In vitro confrontation experiments revealed that T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The potential use of these Trichoderma species for disease management of F. xylarioides and to reduce its impact on coffee cultivation is discussed in relation to Ethiopia’s ongoing coffee wilt disease crisis. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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Review

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27 pages, 2462 KiB  
Review
Mitigation of Emergent Bacterial Pathogens Using Pseudomonas syringae pv. actinidiae as a Case Study—From Orchard to Gene and Everything in Between
by Marta Nunes da Silva, Miguel G. Santos, Marta W. Vasconcelos and Susana M. P. Carvalho
Crops 2022, 2(4), 351-377; https://doi.org/10.3390/crops2040025 - 30 Sep 2022
Cited by 4 | Viewed by 2193
Abstract
Globalization propelled human migration and commercial exchanges at the global level, but woefully led to the introduction of non-indigenous organisms into several agroecological systems. These include pathogenic bacteria with devastating consequences for numerous crops of agronomical importance for food production worldwide. In the [...] Read more.
Globalization propelled human migration and commercial exchanges at the global level, but woefully led to the introduction of non-indigenous organisms into several agroecological systems. These include pathogenic bacteria with devastating consequences for numerous crops of agronomical importance for food production worldwide. In the last decade, research efforts have focused on these noxious organisms, aiming to understand their evolutionary processes, degree of pathogenicity, and mitigation strategies, which have allowed stakeholders and policymakers to develop evidence-based regulatory norms to improve management practices and minimize production losses. One of these cases is the bacterium Pseudomonas syringae pv. actinidiae (Psa), the causal agent of the kiwifruit bacterial canker, which has been causing drastic production losses and added costs related to orchard management in the kiwifruit industry. Although Psa is presently considered a pandemic pathogen and far from being eradicated, the implementation of strict regulatory norms and the efforts employed by the scientific community allowed the mitigation, to some extent, of its negative impacts through an integrated pest management approach. This included implementing directive guidelines, modifying cultural practices, and searching for sources of plant resistance. However, bacterial pathogens often have high spatial and temporal variability, with new strains constantly arising through mutation, recombination, and gene flow, posing constant pressure to agroecosystems. This review aims to critically appraise the efforts developed to mitigate bacterial pathogens of agronomical impact, from orchard management to genome analysis, using Psa as a case study, which could allow a prompter response against emerging pathogens in agroecosystems worldwide. Full article
(This article belongs to the Special Issue Molecular Variability of Crop Pathogens)
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