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Agronomy
Special Issues
Fungal and Oomycete Pathogens in Tropical Crop Plants
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Fungal and Oomycete Pathogens in Tropical Crop Plants

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 18838

Special Issue Editors

Dr. Dora Batista

E-Mail Website
Guest Editor
Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/ Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, 1349-017 Lisboa, Portugal
Interests: evolutionary biology; population and adaptive genomics
Dr. Marco Cristancho

E-Mail Website
Guest Editor
Center for Bioinformatics and Computational Biology, Universidad de los Andes, Cra. 1 #18a-12, Bogotá, Colombia
Interests: sequencing; genetic analysis; gene expression

Special Issue Information

Dear Colleagues,

Infectious diseases have a massive economic impact on crop production worldwide with particularly dramatic repercussions on tropical countries, as agriculture is the key backbone for broad-based economic growth, poverty alleviation and food security in many tropical regions. Given the rapid intensification of global trade, biodiversity loss and climate change, and considering the generalized lack of resources, the effect of crop diseases is expected to be exacerbated in these countries. Fungi and oomycetes are among the most devas­tating plant pathogens, exhibiting remarkable genomic and reproductive plas­ticity, and consequently a huge capacity to rapidly evolve and adapt to new host resistance and environmental change. In the last several years, access to genomic data with greater resolution has been instrumental to elucidate processes that contribute to generating genetic diversity, host specialization and rapid evolution in these plant pathogens. Host jumps and shifts seem more common than anticipated, and hybridization, horizontal gene transfer and transposable elements likely drive the emergence of genetic novelty.

Despite the indisputable importance of the tropics at a global scale, research on tropical crop diseases has failed to receive considerable attention and we still lack fundamental knowledge on the occurrence, distribution and epidemiology of fungal and oomycete pathogens in these environments. Moreover, in order to develop sustainable management strategies for plant production and protection, as well as to improve pathogen surveillance and prediction of future invasive species or development of new variants, we must understand the origin of pathogen lineages, the geographic patterns of genetic diversity, and the genomic and transcriptomic mechanisms that may drive pathogen adaptive evolution.

The aim of this Special Issue is to cover the current research advances in tropical crop-fungal/oomycete pathosystems and provide a multidisciplinary platform for the networking of knowledge on pathogen population dynamics, evolution, epidemiology, diagnosis and management. We welcome manuscripts on the best-known tropical crops such as coffee, cocoa, pineapple, banana, sugarcane, coconuts and palm oil, but also those neglected, under-utilized or under-researched tropical crops such as plantain, cashew nut, pigeon pea, millet and cassava. We invite research articles as well as reviews, mini-reviews, short communications, opinion and perspective papers dealing with, but not limited to, genomics, transcriptomics, proteomics, metabolomics or epigenetics to uncover population diversity and adaptive patterns, pathogenicity, virulence and evolutionary mechanisms. Manuscripts addressing pathogen identification and distribution, epidemiology and surveillance, impact of climate change and sustainable management strategies are also welcome.

Dr. Dora Batista
Dr. Marco Cristancho
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. Agronomy is an international peer-reviewed open access monthly 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 2600 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

  • plant pathogens
  • tropical crops
  • impact of climate change
  • disease management
  • genetic diversity
  • pathogen evolution

Published Papers (6 papers)

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Research

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12 pages, 1673 KiB  
Article
Comparative Analysis of Powdery Mildew Disease Resistance and Susceptibility in Brassica Coenospecies
by Zahoor Ahmad Mir, Sajad Ali, Anshika Tyagi, Prashant Yadav, N Chandrashekar, Mohamed A. El-Sheikh, Saleh Alansi and Anita Grover
Agronomy 2023, 13(4), 1033; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy13041033 - 31 Mar 2023
Cited by 1 | Viewed by 2281
Abstract
Erysiphe cruciferarum, a causative agent of powdery mildew disease, has emerged as a serious threat in Brassica juncea and its closely related species. To date, no resistant cultivars have been identified in Brassica species against powdery mildew. Here, we used histopathological, biochemical, [...] Read more.
Erysiphe cruciferarum, a causative agent of powdery mildew disease, has emerged as a serious threat in Brassica juncea and its closely related species. To date, no resistant cultivars have been identified in Brassica species against powdery mildew. Here, we used histopathological, biochemical, and molecular approaches to elucidate the powdery mildew disease progression and host responses in three Brassica cenospecies, namely B. juncea, Camelina sativa, and Sinapis alba. Based on the results of disease progression, S. alba was found to be extremely resistant to powdery mildew infection, whereas B. juncea and C. sativa were highly vulnerable. In addition, the disease spread rate to uninfected parts was comparatively higher in B. juncea and C. sativa. Histopathological results revealed more pathogen-induced cell death in B. juncea and C. sativa compared to S. alba. We also examined the role of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in B. juncea, C. sativa, and S. alba after powdery mildew infection. Based on our findings, the enzyme activity of SOD, POD, and CAT was relatively higher in S. alba then that of B. juncea and C. sativa after powdery mildew infection. Furthermore, we evaluated the expression levels of salicylic acid (SA) signature genes, including pathogenesis-related protein viz., PR1, PR2, and PR5 in B. juncea, C. sativa, and S. alba after E. cruciferarum infection. Based on our findings, the expression levels of SA marker genes PR1, PR2, and PR5 increased in all three species after infection. However, the fold change was relatively higher in S. alba than in B. juncea and C. sativa. In future, further studies are required to identify the potential candidates in S. alba that are involved in powdery mildew disease resistance. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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17 pages, 2047 KiB  
Article
Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia vastatrix)
by Simon Orozco-Arias, Mariana S. Candamil, Paula A. Jaimes, Marco Cristancho, Reinel Tabares-Soto and Romain Guyot
Agronomy 2022, 12(7), 1665; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12071665 - 13 Jul 2022
Cited by 1 | Viewed by 1987
Abstract
Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caused by a fungal pathogen, Hemileia vastatrix (Hva), belonging to the phylum Basidiomycota. Coffee leaf rust causes significant yield losses and increases costs related to [...] Read more.
Coffee leaf rust is the most damaging disease for coffee cultivation around the world. It is caused by a fungal pathogen, Hemileia vastatrix (Hva), belonging to the phylum Basidiomycota. Coffee leaf rust causes significant yield losses and increases costs related to its control, with evaluated losses of USD 1–2 billion annually. It attacks both the cultivated coffee species Coffea canephora (Robusta coffee) and Coffea arabica (Arabica coffee). New races, or pathotypes, are constantly emerging with increased virulence, suggesting a rapid evolution of the pathogen. Previous genetic and genomic studies have indicated a limited nucleotide diversity of Hva despite a high genetic diversity and large genome size estimated to be ~800 Mb, with a high content of repeated sequences (>74%). Despite several genomic resources and the release of a recent partial genome sequence, the diversity of these repeated sequences and how they may impact the evolution of the leaf rust genome have not been investigated in detail. In an attempt to characterize the transposable elements within the Hva genomes, we report here new lineages of long terminal repeat (LTR) retrotransposons, called CO-HUI, Soroa, and Baco, which are classified into Gypsy, and and Labe and Mapi, which are classified as Copia. The CO-HUI and Soroa elements represent the main part of all Hva transposable elements, as well as approximately 37% of the available genome assemblies. Mapi and CO-HUI are the main expressed families in RNA-seq data. Although Soroa is the lineage showing more insertions into exons and genes, Mapi seems to be more frequently involved in co-expression with genes. All these new families are also present in the Pucciniales, suggesting that they dynamically participate in their genome evolution. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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20 pages, 47301 KiB  
Article
Transcriptome Analysis Uncovers the Gene Expression Profile of Hemileia vastatrix (Race XXXIII) during the Interactions with Resistant and Susceptible Coffee
by Isabel Samila Lima Castro, Rejane do Livramento Freitas-Lopes, Sávio de Siqueira Ferreira, Talles Eduardo Ferreira Maciel, Juan Carlos Florez, Eunize Maciel Zambolim, Laércio Zambolim and Eveline Teixeira Caixeta
Agronomy 2022, 12(2), 444; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12020444 - 10 Feb 2022
Cited by 4 | Viewed by 2555
Abstract
Coffee leaf rust is caused by Hemileia vastatrix Berk. and Broome and is the most important coffee disease in all regions where coffee is cultivated. Here, we sought to sequence the transcriptome of H. vastatrix race XXXIII to obtain a database for use [...] Read more.
Coffee leaf rust is caused by Hemileia vastatrix Berk. and Broome and is the most important coffee disease in all regions where coffee is cultivated. Here, we sought to sequence the transcriptome of H. vastatrix race XXXIII to obtain a database for use as a reference in studies of the interaction between the fungus and coffee. In addition, we aimed to identify differentially expressed genes that have the potential to act as effector proteins during the interaction. Sequencing of cDNA libraries from uredospores and from compatible and incompatible interactions at different key time points generated about 162 million trimmed reads. We identified 3523 differentially expressed genes. The results suggested that the fungal transcriptome is dynamically altered over the course of infection and that the interaction with a susceptible plant upregulates a larger set of fungal genes than the interaction with a resistant plant. Co-expression network analysis allowed us to identify candidate genes with the same expression pattern as that of other effectors of H. vastatrix. Quantitative PCR analysis identified seven transcripts that may be effectors involved in the coffee–H. vastatrix interaction. This information provides a basis for obtaining new insights into the molecular mechanisms of infection in this pathosystem. Understanding gene expression during the infection process may contribute to elucidating the molecular mechanisms leading to the breakdown of resistance by new physiological races of the fungus. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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16 pages, 1716 KiB  
Article
Proposal for Integrated Management of Verticillium Wilt Disease in Avocado Cultivar Hass Crops
by Joaquín Guillermo Ramírez-Gil and Juan Gonzalo Morales-Osorio
Agronomy 2021, 11(10), 1932; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy11101932 - 26 Sep 2021
Cited by 6 | Viewed by 2886
Abstract
The area planted with avocado crops in Colombia has been growing rapidly in recent years, especially for export varieties such as Hass. The increase in planted area coincided with increased phytosanitary problems, where pathogens such as fungi of the genus Verticillium spp. are [...] Read more.
The area planted with avocado crops in Colombia has been growing rapidly in recent years, especially for export varieties such as Hass. The increase in planted area coincided with increased phytosanitary problems, where pathogens such as fungi of the genus Verticillium spp. are becoming of economic importance. The objective of this study was to evaluate different control strategies for avocado wilt disease caused by Verticillium spp., under in vitro, net house, and field conditions. Strategies tested included fungicides (benomyl, azoxystrobin, captan, and carbendazim), beneficial and antagonistic microorganisms (Trichoderma sp., and Rhizoglomus fasciculatum), and physical and cultural practices such as solarization, drainage and removal of diseased tissues. Treatments T7fi (pruning-solarization-Trichoderma-mycorrhiza-sucrose-organic matter-drainage) and T8fi (fungicide-pruning-solarization-Trichoderma-mycorrhiza-sucrose-organic matter-drainage), showed the greatest reduction in the area under disease progress curve and Verticillium dahliae inoculum in soil and plant tissues under field conditions. Fruit with extra quality increased 120.8% with T7fi and 108% with T8fi, compared to the control with diseased trees. The highest costs were identified for T7fi and T8fi; however, these treatments also showed the best cost/benefit relationship. Integrated approaches as in T7fi and T8fi showed the best results for Verticillium wilt control. As no fungicides of chemical synthesis are included in T7fi (pruning-solarisation-Trichoderma-mycorrhiza-sucrose-organic matter-drainage), it should be preferred to T8fi, which does include them, to avoid their negative impacts on avocado production. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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Review

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20 pages, 3365 KiB  
Review
Colletotrichum Species Complexes Associated with Crops in Northern South America: A Review
by Marcela Guevara-Suarez, Martha Cárdenas, Pedro Jiménez, Lucía Afanador-Kafuri and Silvia Restrepo
Agronomy 2022, 12(3), 548; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12030548 - 23 Feb 2022
Cited by 8 | Viewed by 3923
Abstract
Colletotrichum genus comprises a high number of plant pathogens causing anthracnose disease in different tropical and non-tropical crops. We aimed to review northern South American studies in the online SCOPUS database to: create a taxonomically updated list of the species complexes found in [...] Read more.
Colletotrichum genus comprises a high number of plant pathogens causing anthracnose disease in different tropical and non-tropical crops. We aimed to review northern South American studies in the online SCOPUS database to: create a taxonomically updated list of the species complexes found in the region, describe their most important phytopathological characteristics, revise the methods used in the region to control disease, and discuss the role of fungus as a plant endophyte. A total of 19 Colletotrichum species within five complexes—acutatum, boninense, gigasporum, gloeosporioides, and orbiculare—have been reported in northern South America. Few studies have been conducted, particularly in Peru and Ecuador, despite the diversity of Colletotrichum hosts cultivated in the region. Important information can be extracted from our review: species do not appear to show host specificity, although some isolates show host preferences, certain plant species can host several Colletotrichum species, some studies show the importance of using plant extracts to control the disease, but biological control using microorganisms is certainly an open area of research in the region. In northern South America, only a few hosts have been reported to harbor Colletotrichum as endophyte, and the potential of these endophytes as biological control agents has not yet been explored. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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Other

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15 pages, 1698 KiB  
Systematic Review
Disease-Causing Agents in Cashew: A Review in a Tropical Cash Crop
by Filipa Monteiro, Maria M. Romeiras, João Barnabé, Silvia Catarino, Dora Batista and Mónica Sebastiana
Agronomy 2022, 12(10), 2553; https://0-doi-org.brum.beds.ac.uk/10.3390/agronomy12102553 - 18 Oct 2022
Cited by 1 | Viewed by 2798
Abstract
Due to the high market value of cashew nut, cashew became a significantly important cash crop in many countries. Originating from Brazil, the plant was introduced into Africa, India, and Southeast Asia and is nowadays found across most of the tropical regions. However, [...] Read more.
Due to the high market value of cashew nut, cashew became a significantly important cash crop in many countries. Originating from Brazil, the plant was introduced into Africa, India, and Southeast Asia and is nowadays found across most of the tropical regions. However, the diseases that threaten and compromise crop production have not yet been comprehensively documented. The aim of this study was to examine the published scientific data on cashew diseases, to identify current knowledge gaps, and to present a review of the most important diseases and pathogens affecting cashew productivity. The most described diseases are caused by fungi genera—mainly Colletotrichum, Lasiodiplodia, and Erysiphe (worldwide); Cryptosporiopsis (East Africa); and recently Fusarium in Tanzania. Other fungal genera (e.g., Septoria, Pilgeriella, and Pestalotia) may correspond to emerging local cashew diseases that have not yet expanded to other geographic regions or for which records are lacking. Gummosis (Lasiodiplodia spp.), which is considered the most prevalent and damaging disease of cashew, has a pantropical distribution. There is large discrepancy concerning the causal agents of cashew diseases that might be explained by the lack of proper species identification through morpho-cultural and molecular approaches. This, in turn, can easily lead to misdiagnoses that have serious negative consequences for the implementation of specific control actions. It is important to establish a standardized identification workflow that will allow a reliable identification of the disease-causing agent and to determine the occurrence and/or expansion of a given pathogen across cashew-producing regions. Full article
(This article belongs to the Special Issue Fungal and Oomycete Pathogens in Tropical Crop Plants)
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