Genetics and Molecular Biology of Pathogens in Agricultural Crops

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: closed (25 January 2024) | Viewed by 9633

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Guest Editor
Italian National Research Council, Institute for Sustainable Plant Protection, 10138 Torino, Italy
Interests: molecular biology of plant pathogens; quarantine plant pathogens; innovative precision diagnostics
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Special Issue Information

Dear Colleagues,

Notwithstanding the progress of science and technology, yield losses in agricultural production from crop pathogens and pests currently reach about 30% of global production. The yield drops are highly correlated with the genetic structure and molecular basis of the crop pathogens that influence importantly their competitiveness, aggressiveness, and distribution. Furthermore, market globalization coupled with climate change might increase the risks of introducing new emerging pathogens or the recrudescence of existing pathogens, which greatly impacts agricultural production.

Given the above, deepening the knowledge of genetics and molecular biology of crop pathogens might provide new insights into more efficient and eco-friendly management of plant diseases through traditional breeding and plant resistance combined with innovative laboratory methods, and the use of biocontrol agents and natural compounds. This Special Issue will highlight the cutting edge and innovative proposals addressing the above-written key topics.

We welcome reviews, research papers, and opinions concerning advances in genetics and molecular biology of pathogens in agricultural crops in this Special Issue.

Dr. Slavica Matic
Guest Editor

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Keywords

  • plant pathogens
  • genetics
  • molecular biology
  • epidemiology
  • detection
  • disease pest management

Published Papers (6 papers)

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Research

13 pages, 2730 KiB  
Article
Gradual Emergence of East African cassava mosaic Cameroon virus in Cassava Farms in Côte d’Ivoire
by Bekanvié S. M. Kouakou, Aya Ange Naté Yoboué, Justin S. Pita, J. Musembi Mutuku, Daniel H. Otron, Nazaire K. Kouassi, Kan Modeste Kouassi, Linda Patricia L. Vanié-Léabo, Cyrielle Ndougonna, Michel Zouzou and Fatogoma Sorho
Agronomy 2024, 14(3), 418; https://doi.org/10.3390/agronomy14030418 - 21 Feb 2024
Viewed by 716
Abstract
Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are endemic threats to cassava production, causing significant yield losses. They are caused respectively by begomoviruses and ipomoviruses that are transmitted by whiteflies and infected cuttings. This study aimed to monitor and characterize [...] Read more.
Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are endemic threats to cassava production, causing significant yield losses. They are caused respectively by begomoviruses and ipomoviruses that are transmitted by whiteflies and infected cuttings. This study aimed to monitor and characterize viruses responsible for these diseases in order to fill existing gaps in understanding their epidemiology in Côte d’Ivoire. Field surveys were conducted in 2016, 2017, and 2020, and no CBSD symptoms were observed. However, an increase in CMD incidence was noted from 45.95% in 2016 to 51.37% in 2020, while CMD severity remained moderate over the years with a mean value of 2.29. The number of whiteflies was relatively low and decreased over the years. Molecular diagnostics carried out on cassava leaf samples allowed the detection of East African cassava mosaic Cameroon virus (EACMCMV) that occurs in single as well as in mixed infection with African cassava mosaic virus (ACMV). Single EACMCMV infection, which was detected only in three agroecological zones of eastern Côte d’Ivoire in 2016, spread throughout the country in 2017 and became more widespread in 2020 with a preponderance in central and southern zones, whereas ACMV and EACMCMV coinfection has spread to the entire zones. Phylogenetic analysis of the viral isolates showed that they are closely related to those from Burkina Faso, Ghana, and Nigeria. This changing population of cassava virus species constitutes a serious threat to cassava cultivation. Understanding the evolutionary dynamics of these viruses could help in adopting better disease management strategies to control the disease. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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23 pages, 5316 KiB  
Article
Potential Source of Resistance in Introgressed, Mutant and Synthetic Brassica juncea L. Lines against Diverse Isolates of White Rust Pathogen, Albugo candida
by Samridhi Mehta, Faten Dhawi, Pooja Garg, Mahesh Rao, R. C. Bhattacharya, Jameel Akthar, Rashmi Yadav, Mamta Singh, Kartar Singh, P. Nallathambi, C. Uma Maheswari, P. D. Meena, Hari Singh Meena, P. K. Rai, Usha Pant, Mohd. Harun, Ravish Choudhary, Slavica Matic and Ashish Kumar Gupta
Agronomy 2023, 13(5), 1215; https://doi.org/10.3390/agronomy13051215 - 25 Apr 2023
Cited by 1 | Viewed by 1896
Abstract
The existing resistance genes against white rust disease are often ineffective due to racial variation of the causal fungal pathogen, Albugo candida. Therefore, new sources of resistance effective against multiple races are needed for durable resistance. Large-scale phenotyping of advanced introgressed (ILs), [...] Read more.
The existing resistance genes against white rust disease are often ineffective due to racial variation of the causal fungal pathogen, Albugo candida. Therefore, new sources of resistance effective against multiple races are needed for durable resistance. Large-scale phenotyping of advanced introgressed (ILs), mutant, and resynthesized (RBJ) lines of Brassica juncea L., under artificial inoculation at cotyledonary and true leaf stages, against thirteen diverse isolates of Albugo candida and simultaneously at the adult plant stage under multi-location field evaluation from 2019–2022, revealed significant differences in white rust reactions. Amongst 194 introgressed lines, three lines, namely ERJ 39, ERJ 12, and ERJ 15, and three lines among 90 resynthesized and 9 mutant lines, including RBJ 18, DRMR 18-36-12, and DRMR 18-37-13, were identified as potential sources of resistance against multiple isolates at all three developmental stages of the plant. Furthermore, correlation and principal component analysis revealed a positive correlation between white rust resistance at true leaf and adult plant stages for ILs as well as mutant and RBJ lines. These novel sources of host resistance will play vital roles are required for the mustard improvement program and to establish a strong genetic and molecular foundation for identifying white rust resistance linked marker(s), QTLs, or gene(s) for sustainable disease management in India. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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11 pages, 1201 KiB  
Article
Efficiency of Rph genes against Puccinia hordei in Southern Russia in 2019–2021
by Anastasia Danilova and Galina Volkova
Agronomy 2023, 13(4), 1046; https://doi.org/10.3390/agronomy13041046 - 02 Apr 2023
Viewed by 1170
Abstract
Barley leaf rust (Puccinia hordei Otth.) is considered a harmful disease that occurs in barley-growing regions worldwide. In Russia, the disease is among the most prevalent in the Krasnodar region, which is the leader in the production of barley grain and has [...] Read more.
Barley leaf rust (Puccinia hordei Otth.) is considered a harmful disease that occurs in barley-growing regions worldwide. In Russia, the disease is among the most prevalent in the Krasnodar region, which is the leader in the production of barley grain and has a favorable climate for disease development. In this paper, we studied the efficiency of 17 varieties and lines of barley from the International and Australian sets containing currently known Rph resistance genes or their combinations to P. hordei in the field, and 15 varieties and lines in the seedling phase in greenhouse conditions during 2019–2021. We concluded that the lines carrying the Rph7 and Rph13 genes remained immune throughout the three years of studies in the seedling and adult plant stages. The Rph1 and Rph23 genes showed moderate efficiency during the three years. The Rph2, Rph3, Rph4, Rph5, Rph6+2, Rph8, Rph12, Rph19, and Rph21+2 genes showed low efficiency over the three years. This was also confirmed by the results of their assessment in the seedling phase: the number of monopustular isolates virulent to lines with the majority of the studied genes for three years was above 90%. Fluctuations in the virulence of the P. hordei population were observed under sufficiently unfavorable weather for disease development in 2019, 2020, and 2021. This proves the ability of the fungus to adapt to changing conditions. Therefore, annual monitoring of the response of lines and varieties carrying resistance genes and studying the virulence of the pathogen are crucial for the selection of rust-resistant varieties, and, hence, the prevention of barley leaf rust epidemics in all grain-producing regions worldwide. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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18 pages, 449 KiB  
Article
Annotation of the 12th Chromosome of the Forest Pathogen Fusarium circinatum
by Tadeusz Malewski, Slavica Matić, Adam Okorski, Piotr Borowik and Tomasz Oszako
Agronomy 2023, 13(3), 773; https://doi.org/10.3390/agronomy13030773 - 07 Mar 2023
Cited by 1 | Viewed by 1319
Abstract
The genus Fusarium comprises more than 300 species, and many of them are pathogens that cause severe diseases in agricultural, horticultural and forestry plants in both antropogenic and natural ecosystems. Because of their importance as plant pathogens, the genomes of several Fusarium spp. [...] Read more.
The genus Fusarium comprises more than 300 species, and many of them are pathogens that cause severe diseases in agricultural, horticultural and forestry plants in both antropogenic and natural ecosystems. Because of their importance as plant pathogens, the genomes of several Fusarium spp. have been sequenced. Within this genus, Fusarium circinatum is one of the most harmful pathogens of pine trees attacking up to 60 Pinus species. Till now, the genomes of 13 strains of F. circinatum have been sequenced. The strain GL1327 we studied lacks a twelfth chromosome, which allows the study of virulence genes on this chromosome. Although the genome of several strains of F. circinatum has been sequenced, it is still almost completely unannotated, which severely limits the possibilities to further investigate the molecular mechanisms of virulence of Fusarium. Therefore, this study aimed to annotate the 12th chromosome of F. circinatum and integrate currently available resources. In silico annotation of the 12th chromosome of F. circinatum revealed the presence of 118 open reading frames (ORFs) encoding 141 proteins which were predicted using an ab initio gene prediction tool. The InterProScan and SMART analyses identified known domains in 30 proteins and eggNOG additionally in 12 of them. Among them, four groups can be distinguished: genes possibly related to heterokaryon incompatibility (4 genes), regulation of transcription (5 genes), plant cell wall degrading enzymes (7 genes) and trichothecene synthesis (3 genes). This study also integrated data of F.circinatum reference strain CMWF1803 assembled to chromosome level but not annotated with currently best annotated but assembled only to scaffold level strain NRRL 25331. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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12 pages, 2241 KiB  
Article
Intraspecific Variability and Distribution Difference within the Ribosomal Introns of the Discrete Plasmodiophora brassicae Group in Japan: A Case Study for Complex Dynamics of Intron Evolution
by Anh Tung Phan Lam, Kazunori Sasaki, Yukiko Yanagi, Shuhei Tanaka and Shin-ichi Ito
Agronomy 2022, 12(9), 2154; https://doi.org/10.3390/agronomy12092154 - 10 Sep 2022
Viewed by 1301
Abstract
Analysis of the ribosomal introns of Plasmodiophora brassicae populations infecting the cruciferous weed Cardamine occulta revealed the complex dynamics of size, intraspecific variability, and distribution. The results showed that P. brassicae populations from the weed have lost multiple introns in the small and [...] Read more.
Analysis of the ribosomal introns of Plasmodiophora brassicae populations infecting the cruciferous weed Cardamine occulta revealed the complex dynamics of size, intraspecific variability, and distribution. The results showed that P. brassicae populations from the weed have lost multiple introns in the small and large subunits of the ribosomal RNA genes. Moreover, the retained introns, despite a largely mutual share of conserved parts with the cosmopolitan strains, contained numerous novel structures. These structural differences comprise a high level of polymorphisms, such as transversion point mutations occurring at sites involving the intronic splicing sites or insertions/deletions at the binding sites. Two geographical P. brassicae populations from C. occulta carried a lengthy intron-encoded ORF and putative mobile elements established in the large subunit. A few P. brassicae populations from the Brassica crops also harbored polymorphic introns that shared common mutated motifs with the weed-affecting group. The diversity of ribosomal introns observed from those investigated populations demonstrated the genetic distinction of the P. brassicae populations from C. occulta. The genetic variations might play a key role in the adaptability of the weed-infecting populations and are more likely related to the process of pathogenesis for the cosmopolitan P. brassicae infecting the Brassica crops. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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18 pages, 2077 KiB  
Article
In-Field LAMP Detection of Flavescence Dorée Phytoplasma in Crude Extracts of the Scaphoideus titanus Vector
by Slavica Matić, Valentina Candian, Chiara D’Errico, Roberto Pierro, Stefano Panno, Salvatore Davino, Emanuela Noris and Rosemarie Tedeschi
Agronomy 2022, 12(7), 1645; https://doi.org/10.3390/agronomy12071645 - 08 Jul 2022
Cited by 5 | Viewed by 2074
Abstract
One of the most destructive diseases affecting grapevine in Europe is caused by Flavescence Dorée phytoplasma (FDp), which belongs to the 16Sr-V group and is a European Union quarantine pathogen. Although many molecular techniques such as loop-mediated isothermal amplification (LAMP) are widely used [...] Read more.
One of the most destructive diseases affecting grapevine in Europe is caused by Flavescence Dorée phytoplasma (FDp), which belongs to the 16Sr-V group and is a European Union quarantine pathogen. Although many molecular techniques such as loop-mediated isothermal amplification (LAMP) are widely used for the rapid detection of FDp in infected grapevine plants, there is no developed isothermal amplification assay for FDp detection in the insect vectors that are fundamental for the spread of the disease. For this reason, a simple in-field real-time LAMP protocol was optimized and developed for the specific detection of FDp in the insect vector Scaphoideus titanus. The LAMP assay was optimized to work with crude insect extracts obtained by manually shaking a single insect in a buffer for 5 min. Such a simple, sensitive, specific, economic, and user-friendly LAMP assay allowed the detection of FDp in S. titanus in less than half an hour, directly in the field. The developed insect tissue preparation procedure, combined with the LAMP protocol, promptly revealed the presence of FDp in infected S. titanus directly in the vineyards, allowing for monitoring of the spread of the pathogen in the field and to apply timely strategies required for the mandatory control of this pathogen. Full article
(This article belongs to the Special Issue Genetics and Molecular Biology of Pathogens in Agricultural Crops)
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