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14 pages, 630 KiB

Open AccessArticle

Development of a Method for Detecting and Estimating Moniliophthora roreri Spore Loads Based on Spore Traps and qPCR

by Diana L. Jiménez-Zapata, Manuela Quiroga-Pérez, Manuela Quiroz-Yepes, Alejandro Marulanda-Tobón, Javier C. Álvarez and Sandra Mosquera-López

J. Fungi 2023, 9(1), 47; https://doi.org/10.3390/jof9010047 - 28 Dec 2022

Viewed by 2002

Abstract

Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in [...] Read more.

Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in time and space due to the lack of a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that relies on spore traps and qPCR to detect and quantify M. roreri spore loads. This study demonstrated that the qPCR protocol can detect down to 0.025 ng of M. roreri DNA and quantify between 0.006 ng and 60 ng. Moreover, it demonstrated that qPCR protocol can detect and quantify DNA extracted from spore suspension and spore traps containing at least 2.9 × 10⁴ M. roreri spores. However, the variability of the estimates for spore samples was high. Finally, we described a spore-trap device designed to carry spore traps in the field. The qPCR protocol and spore-trap device here developed will help in the understanding of the M. roreri dissemination patterns since they can be used to assess the environmental loads of M. roreri spore in cacao fields. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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17 pages, 2581 KiB

Open AccessArticle

Geographical Correlation and Genetic Diversity of Newly Emerged Races within the Ug99 Lineage of Stem Rust Pathogen, Puccinia graminis f. sp. tritici, in Different Wheat-Producing Areas

by Atef Shahin, Yasser S. A. Mazrou, Reda Ibrahim Omara, Gamalat Hermas, Mohamed Gad, Ola Ibrahim Mabrouk, Kamel A. Abd-Elsalam and Yasser Nehela

J. Fungi 2022, 8(10), 1041; https://doi.org/10.3390/jof8101041 - 30 Sep 2022

Cited by 4 | Viewed by 2334

Abstract

Wheat stem rust caused by Puccinia graminis f. sp. tritici is one of the most destructive wheat diseases worldwide. Identifying stem rust races in general, Ug99 lineage particularly, and determining resistance genes are critical goals for disease assessment. Thirty wheat varieties and monogenic [...] Read more.

Wheat stem rust caused by Puccinia graminis f. sp. tritici is one of the most destructive wheat diseases worldwide. Identifying stem rust races in general, Ug99 lineage particularly, and determining resistance genes are critical goals for disease assessment. Thirty wheat varieties and monogenic lines with major stem rust resistance genes (Sr) were examined here over the course of three succeeding seasons from 2020 to 2022. Fourteen stem rust races have been identified in ten African countries, as well as Central and West Asia and North Africa (CWANA) and ten European countries. The Ug99 group (Clade I) included four races (TTKSK, TTKST, TTKTK, and TTKTT) and was reported in five African countries (Egypt, Kenya, Rwanda, Tanzania, and Uganda) and Iran, but none of the European countries. On the other hand, none of the races in Clade III-B (TTRTF) and Clade IV-B (TKTTF and TTTTF) were found in Egypt. Furthermore, Egyptian races were clustered separately from races identified from other countries, and six races were found only in Egypt, including PKSTC, RKTTH, TKTTC, TTTSK, TCKTC, and TKTTH. Races from Kenya, Tanzania, Uganda, Rwanda, and Iran were all closely associated with one another, according to correlation analysis. However, most races identified from other investigated regions, including Eritrea, Spain, Ethiopia, Morocco, Italy, Poland, Kenya, Tanzania, and Uganda, were adversely linked with Egyptian races. The diagnostic 350 bp long PCR fragment linked with virulence to Sr31, Clement (Sr31), and Brigardier (Sr31) was used to identify the TTKSK (Ug99) race. The identification of the regional associations and genetic diversity of newly emerged races within the Ug99 lineage of P. graminis tritici in Africa, Asia, and Europe is one of the key goals of this study. It will help plant breeders to develop new resistant lines against the virulent races, especially TTKSK (Ug99) and TTTSK. This helps in ensuring global food security in the context of climate change. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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15 pages, 3045 KiB

Open AccessArticle

Characterization of Alternaria and Colletotrichum Species Associated with Pomegranate (Punica granatum L.) in Maharashtra State of India

by Nanjundappa Manjunatha, Jyotsana Sharma, Somnath S. Pokhare, Ruchi Agarrwal, Prakash G. Patil, Jaydip D. Sirsat, Mansi G. Chakranarayan, Aarti Bicchal, Anmol S. Ukale and Rajiv A. Marathe

J. Fungi 2022, 8(10), 1040; https://doi.org/10.3390/jof8101040 - 30 Sep 2022

Cited by 4 | Viewed by 2890

Abstract

Fungal pathogens are a major constraint affecting the quality of pomegranate production around the world. Among them, Alternaria and Colletotrichum species cause leaf spot, fruit spot or heart rot (black rot), and fruit rot (anthracnose) or calyx end rot, respectively. Accurate identification of [...] Read more.

Fungal pathogens are a major constraint affecting the quality of pomegranate production around the world. Among them, Alternaria and Colletotrichum species cause leaf spot, fruit spot or heart rot (black rot), and fruit rot (anthracnose) or calyx end rot, respectively. Accurate identification of disease-causing fungal species is essential for developing suitable management practices. Therefore, characterization of Alternaria and Colletotrichum isolates representing different geographical regions, predominantly Maharashtra—the Indian hub of pomegranate production and export—was carried out. Fungal isolates could not be identified based on morphological characteristics alone, hence were subjected to multi-gene phylogeny for their accurate identification. Based on a maximum likelihood phylogenetic tree, Alternaria isolates were identified as within the A. alternata species complex and as A. burnsii, while Colletotrichum isolates showed genetic closeness to various species within the C. gloeosporioides species complex. Thus, the current study reports for the first time that, in India, the fruit rots of pomegranate are caused by multiple species and not a single species of Alternaria and Colletotrichum alone. Since different species have different epidemiology and sensitivity toward the commercially available and routinely applied fungicides, the precise knowledge of the diverse species infecting pomegranate, as provided by the current study, is the first step towards devising better management strategies. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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11 pages, 2057 KiB

Open AccessArticle

Morphological and Molecular Characterization of Calonectria foliicola Associated with Leaf Blight on Rubber Tree (Hevea brasiliensis) in Thailand

by Narit Thaochan, Chaninun Pornsuriya, Thanunchanok Chairin, Putarak Chomnunti and Anurag Sunpapao

J. Fungi 2022, 8(10), 986; https://doi.org/10.3390/jof8100986 - 20 Sep 2022

Cited by 9 | Viewed by 5200

Abstract

Leaf blight is commonly observed in rubber trees (Hevea brasiliensis) and can be caused by several fungal species. From October to December 2021, the emergence rubber tree disease was observed in Krabi province, southern Thailand. Small brown to dark brown spots [...] Read more.

Leaf blight is commonly observed in rubber trees (Hevea brasiliensis) and can be caused by several fungal species. From October to December 2021, the emergence rubber tree disease was observed in Krabi province, southern Thailand. Small brown to dark brown spots developed on the leaves of rubber trees and later expanded into most parts of the leaves. Fungal isolates were isolated from infected tissues and a total of 15 Calonectria-like isolates were recovered from 10 infected leaf samples. Pathogenicity testing using the agar plug method revealed that four isolates caused leaf blight on rubber tree, similar to the situation in natural infections. Based on morphological study and the molecular properties of internal transcribed spacer (ITS), calmodulin (cal), translation elongation factor 1-α (tef1-α), and β-tubulin 2 (tub2) sequences, the four fungal isolates were identified as Calonectria foliicola. To the best of our knowledge, this is the first report of rubber trees pas a new host for C. foliicola in Thailand and elsewhere. This study reports on an emerging disease affecting rubber trees in Thailand, and the results are of benefit for the development of an appropriate method to manage this emerging disease in Thailand. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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23 pages, 3189 KiB

Open AccessArticle

Interlaboratory Performance of a Real-Time PCR Method for Detection of Ceratocystis platani, the Agent of Canker Stain of Platanus spp.

by Angela Brunetti, Kurt Heungens, Jacqueline Hubert, Renaud Ioos, Gian Luca Bianchi, Francesca De Amicis, Anne Chandelier, Sietse Van Der Linde, Ana Perez-Sierra, Valeria Gualandri, Maria Rosaria Silletti, Vito Nicola Trisciuzzi, Silvia Rimondi, Tiziana Baschieri, Elio Romano, Valentina Lumia, Marta Luigi, Francesco Faggioli and Massimo Pilotti

J. Fungi 2022, 8(8), 778; https://doi.org/10.3390/jof8080778 - 26 Jul 2022

Cited by 1 | Viewed by 2699

Abstract

Ceratocystis platani (CP), an ascomycetous fungus, is the agent of canker stain, a lethal vascular disease of Platanus species. Ceratocystis platani has been listed as a quarantine pest (EPPO A2 list) due to extensive damage caused in Southern Europe and the Mediterranean region. [...] Read more.

Ceratocystis platani (CP), an ascomycetous fungus, is the agent of canker stain, a lethal vascular disease of Platanus species. Ceratocystis platani has been listed as a quarantine pest (EPPO A2 list) due to extensive damage caused in Southern Europe and the Mediterranean region. As traditional diagnostic assays are ineffective, a Real-Time PCR detection method based on EvaGreen, SYBR Green, and Taqman assays was previously developed, validated in-house, and included in the official EPPO standard PM7/14 (2). Here, we describe the results of a test performance study performed by nine European laboratories for the purpose of an interlaboratory validation. Verification of the DNA extracted from biological samples guaranteed the high quality of preparations, and the stability and the homogeneity of the aliquots intended for the laboratories. All of the laboratories reproduced nearly identical standard curves with efficiencies close to 100%. Testing of blind-coded DNA extracted from wood samples revealed that all performance parameters—diagnostic sensitivity, diagnostic specificity, accuracy and reproducibility—were best fit in most cases both at the laboratory and at the assay level. The previously established limit of detection, 3 fg per PCR reaction, was also validated with similar excellent results. The high interlaboratory performance of this Real-Time PCR method confirms its value as a primary tool to safeguard C. platani-free countries by way of an accurate monitoring, and to investigate the resistance level of potentially canker stain-resistant Platanus genotypes. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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19 pages, 4985 KiB

Open AccessArticle

Stilbocrea banihashemiana sp. nov. a New Fungal Pathogen Causing Stem Cankers and Twig Dieback of Fruit Trees

by Zeinab Bolboli, Behnaz Tavakolian, Reza Mostowfizadeh-Ghalamfarsa, Moslem Jafari and Santa Olga Cacciola

J. Fungi 2022, 8(7), 694; https://doi.org/10.3390/jof8070694 - 30 Jun 2022

Cited by 16 | Viewed by 3187

Abstract

Stem cankers and twig dieback were the most serious disease of fig (Ficus carica) and loquat (Eriobotrya japonica) noticed in a survey of fruit tree orchards in the Fars Province, Iran. Isolates of Bionectriaceae were consistently recovered from symptomatic [...] Read more.

Stem cankers and twig dieback were the most serious disease of fig (Ficus carica) and loquat (Eriobotrya japonica) noticed in a survey of fruit tree orchards in the Fars Province, Iran. Isolates of Bionectriaceae were consistently recovered from symptomatic fig and loquat trees. Phylogenetic analyses of multiple nuclear loci, internal transcribed spacer regions (ITS) of rDNA, RNA polymerase II subunit 2 (rpb2), and translation elongation factor 1-α (tef1), combined with morphological observations, revealed that isolates could be referred to a still unknown taxon, which was formally described as Stilbocrea banihashemiana sp. nov. Phylogenetically, isolates from fig and loquat trees clustered in a well-supported monophyletic group within the Stilbocrea clade of Bionectriaceae, closely related to S. walteri. Stilbocrea banihashemiana sp. nov. was characterized by the lack of stilbella-like asexual structure in both natural substrates and pure cultures and produced two morphologically distinct types of conidia, globose and cylindrical, formed on short and long simple phialides. In pathogenicity tests, S. banihashemiana sp. nov. induced stem cankers in both fig and loquat, wood discoloration in fig and twig dieback in loquat. Pathogenicity tests also showed that the potential host range of this novel pathogen includes other economically relevant horticultural trees. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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13 pages, 1742 KiB

Open AccessArticle

Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China

by Seyed Ali Mirghasempour, David J. Studholme, Weiliang Chen, Weidong Zhu and Bizeng Mao

J. Fungi 2022, 8(5), 515; https://doi.org/10.3390/jof8050515 - 17 May 2022

Cited by 15 | Viewed by 4137

Abstract

Saffron (Crocus sativus L.) is a commercial spice crop well-known throughout the world, valued for culinary, colorant, and pharmaceutical purposes. In China, Fusarium nirenbergiae was detected as causative agent of saffron corm rot, the most pervasive disease for the first time in [...] Read more.

Saffron (Crocus sativus L.) is a commercial spice crop well-known throughout the world, valued for culinary, colorant, and pharmaceutical purposes. In China, Fusarium nirenbergiae was detected as causative agent of saffron corm rot, the most pervasive disease for the first time in 2020. In the present study, 261 Fusarium-like isolates were recovered from 120 rotted corms in four saffron producing fields at Zhejiang, Shanghai, and Yunnan provinces, China, in 2021. A combination of morpho-cultural features and multilocus sequence analysis (MLSA) of the concatenated rpb2 (DNA-directed RNA polymerase II largest subunit) and tef1 (translation elongation factor 1-α) partial sequences showed that the isolates from saffron belong to Fusarium nirenbergiae as well as F. commune, and F. annulatum with isolation frequencies of 58.2%, 26.8%, and 14.9%, respectively. Notably, F. commune was more prevalent than F. annulatum in the collected samples. Pathogenicity tests confirmed that both species were pathogenic on saffron corm. This is the first report of F. annulatum and F. commune causing corm rot of saffron, globally. Outcomes of the current research demonstrate that Fusarium spp. associated with saffron corm rot are more diverse than previously reported. Furthermore, some plants were infected by two or more Fusarium species. Our findings broaden knowledge about Fusarium spp. that inflict corm rot and assist the development of control measures. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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18 pages, 5833 KiB

Open AccessArticle

Postharvest Rot of Pomegranate Fruit in Southern Italy: Characterization of the Main Pathogens

by Annamaria Mincuzzi, Simona Marianna Sanzani, Lluís Palou, Marco Ragni and Antonio Ippolito

J. Fungi 2022, 8(5), 475; https://doi.org/10.3390/jof8050475 - 30 Apr 2022

Cited by 20 | Viewed by 5615

Abstract

Pomegranate (Punica granatum L.) is an emerging crop in Italy and particularly in southern regions, such as Apulia, Basilicata, and Sicily, due to favorable climatic conditions. The crop is affected by several pathogenic fungi, primarily in the field, but also during postharvest [...] Read more.

Pomegranate (Punica granatum L.) is an emerging crop in Italy and particularly in southern regions, such as Apulia, Basilicata, and Sicily, due to favorable climatic conditions. The crop is affected by several pathogenic fungi, primarily in the field, but also during postharvest phases. The most important postharvest fungal diseases in pomegranate are gray and blue molds, black heart and black spot, anthracnose, dry rot, and various soft rots. The limited number of fungicides allowed for treatment in the field and the lack of postharvest fungicides make it difficult to control latent, quiescent, and incipient fungal infections. Symptomatic pomegranates from southern Italy were sampled and isolated fungi were morphologically and molecularly characterized. The data obtained revealed that various species of Penicillium sensu lato (including Talaromyces genus), Alternaria spp., Coniella granati, and Botrytis cinerea were the principal etiological agents of postharvest pomegranate fruit diseases; other relevant pathogens, although less represented, were ascribable to Aspergillus sect. nigri, Colletotrichum acutatum sensu stricto, and Cytospora punicae. About two thirds of the isolated pathogens were responsible for latent infections. The results obtained may be useful in planning phytosanitary control strategies from the field to storage, so as to reduce yield losses. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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18 pages, 4349 KiB

Open AccessArticle

Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes

by Sherif Mohamed El-Ganainy, Zafar Iqbal, Hossam Mohamed Awad, Muhammad Naeem Sattar, Abdel Mohsen Tohamy, Ahmed O. Abbas, Julie Squires and David E. L. Cooke

J. Fungi 2022, 8(5), 468; https://doi.org/10.3390/jof8050468 - 30 Apr 2022

Cited by 8 | Viewed by 2868

Abstract

Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from [...] Read more.

Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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12 pages, 3955 KiB

Open AccessArticle

Morphological and Molecular Identification of Plant Pathogenic Fungi Associated with Dirty Panicle Disease in Coconuts (Cocos nucifera) in Thailand

by Anurag Sunpapao, Nakarin Suwannarach, Jaturong Kumla, Reajina Dumhai, Kanamon Riangwong, Sunisa Sanguansub, Samart Wanchana and Siwaret Arikit

J. Fungi 2022, 8(4), 335; https://doi.org/10.3390/jof8040335 - 23 Mar 2022

Cited by 17 | Viewed by 4420

Abstract

Dirty panicle disease in coconuts (Cocos nucifera) was first observed in the KU-BEDO Coconut BioBank, Nakhon Pathom province, Thailand. The occurrence of the disease covers more than 30% of the total coconut plantation area. The symptoms include small brown to dark [...] Read more.

Dirty panicle disease in coconuts (Cocos nucifera) was first observed in the KU-BEDO Coconut BioBank, Nakhon Pathom province, Thailand. The occurrence of the disease covers more than 30% of the total coconut plantation area. The symptoms include small brown to dark brown spots and discoloration of male flowers. Herein, three fungal strains were isolated from infected samples. Based on the morphological characteristics the fungal isolates, they were classified into two genera, namely, Alternaria (Al01) and Fusarium (FUO01 and FUP01). DNA sequences of internal transcribed spacer (ITS), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), translation elongation factor 1-α (tef1-α), and RNA polymerase II second largest subunit (rpb2) revealed Al01 as Alternaria burnsii, whereas DNA sequences of ITS, rpb2, and tef1-α identified FUO01 and FUP01 as Fusarium clavum and F. tricinctum, respectively. A pathogenicity test by the agar plug method demonstrated that these pathogens cause dirty panicle disease similar to that observed in natural infections. To the best of our knowledge, this is the first report on the novel dirty panicle disease in coconuts in Thailand or elsewhere, demonstrating that it is associated with the plant pathogenic fungi A. burnsii, F. clavum, and F. tricinctum. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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21 pages, 2818 KiB

Open AccessArticle

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

by Federico La Spada, Peter J. A. Cock, Eva Randall, Antonella Pane, David E. L. Cooke and Santa Olga Cacciola

J. Fungi 2022, 8(4), 330; https://doi.org/10.3390/jof8040330 - 22 Mar 2022

Cited by 19 | Viewed by 3640

Abstract

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. [...] Read more.

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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18 pages, 11915 KiB

Open AccessArticle

Monitoring of Host Suitability and Defense-Related Genes in Wheat to Bipolaris sorokiniana

by Mehtap Alkan, Harun Bayraktar, Mustafa İmren, Fatih Özdemir, Rachid Lahlali, Fouad Mokrini, Timothy Paulitz, Abdelfattah A. Dababat and Göksel Özer

J. Fungi 2022, 8(2), 149; https://doi.org/10.3390/jof8020149 - 31 Jan 2022

Cited by 17 | Viewed by 4206

Abstract

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat worldwide. This study investigated the aggressiveness of B. sorokiniana isolates from different wheat-growing areas of Bolu province in Turkey on the cultivar Seri-82. Host susceptibility of 55 wheat cultivars was evaluated [...] Read more.

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat worldwide. This study investigated the aggressiveness of B. sorokiniana isolates from different wheat-growing areas of Bolu province in Turkey on the cultivar Seri-82. Host susceptibility of 55 wheat cultivars was evaluated against the most aggressive isolate. Our results indicated that the cultivars Anafarta and Koç-2015 were the most resistant. A specific and sensitive qPCR assay was developed for detecting the pathogen in plant tissues and evaluating wheat plants with different resistance levels. Three primer sets, BsGAPDHF/BsGAPDHR, BsITSF/BsITSR, and BsSSUF/BsSSUR, were designed based on glyceraldehyde-3-phosphate dehydrogenase, internal transcribed spacers, and 18S rRNA loci of B. sorokiniana with detection limits of 1, 0.1, and 0.1 pg of pathogen DNA, respectively. The qPCR assay was highly sensitive and did not amplify DNA from the other closely related fungal species and host plants. The protocol differentiated wheat plants with varying degrees of resistance. The assay developed a useful tool for the quantification of the pathogen in the early stages of infection and may provide a significant contribution to a more efficient selection of wheat genotypes in breeding studies. In the present study, expression levels of PR proteins, phenylalanine ammonia-lyase, catalase, ascorbate peroxidase, and superoxide dismutase enzymes were upregulated in Anafarta (resistant) and Nenehatun (susceptible) cultivars at different post-infection time points, but more induced in the susceptible cultivar. The results showed considerable variation in the expression levels and timing of defense genes in both cultivars. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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17 pages, 1290 KiB

Open AccessArticle

A Novel Real Time PCR Method for the Detection and Quantification of Didymella pinodella in Symptomatic and Asymptomatic Plant Hosts

by Adnan Šišić, Thomas Oberhänsli, Jelena Baćanović-Šišić, Pierre Hohmann and Maria Renate Finckh

J. Fungi 2022, 8(1), 41; https://doi.org/10.3390/jof8010041 - 31 Dec 2021

Cited by 9 | Viewed by 3021

Abstract

Didymella pinodella is the major pathogen of the pea root rot complex in Europe. This wide host range pathogen often asymptomatically colonizes its hosts, making the control strategies challenging. We developed a real-time PCR assay for the detection and quantification of D. pinodella [...] Read more.

Didymella pinodella is the major pathogen of the pea root rot complex in Europe. This wide host range pathogen often asymptomatically colonizes its hosts, making the control strategies challenging. We developed a real-time PCR assay for the detection and quantification of D. pinodella based on the TEF-1 alpha gene sequence alignments. The assay was tested for specificity on a 54-isolate panel representing 35 fungal species and further validated in symptomatic and asymptomatic pea and wheat roots from greenhouse tests. The assay was highly consistent across separate qPCR reactions and had a quantification/detection limit of 3.1 pg of target DNA per reaction in plant tissue. Cross-reactions were observed with DNA extracts of five Didymella species. The risk of cross contamination, however, is low as the non-targets have not been associated with pea previously and they were amplified with at least 1000-fold lower sensitivity. Greenhouse inoculation tests revealed a high correlation between the pathogen DNA quantities in pea roots and pea root rot severity and biomass reduction. The assay also detected D. pinodella in asymptomatic wheat roots, which, despite the absence of visible root rot symptoms, caused wheat biomass reduction. This study provides new insights into the complex life style of D. pinodella and can assist in better understanding the pathogen survival and spread in the environment. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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19 pages, 4791 KiB

Open AccessArticle

First Documentation of Life Cycle Completion of the Alien Rust Pathogen Melampsoridium hiratsukanum in the Eastern Alps Proves Its Successful Establishment in This Mountain Range

by Salvatore Moricca, Alessandra Benigno, Claudia Maria Oliveira Longa, Santa Olga Cacciola and Giorgio Maresi

J. Fungi 2021, 7(8), 617; https://doi.org/10.3390/jof7080617 - 29 Jul 2021

Cited by 4 | Viewed by 2190

Abstract

Melampsoridium hiratsukanum is an alien rust fungus which has spread pervasively throughout several European countries following introduction into North Europe at the end of the 20th century. The authenticity of several records of the Melampsoridium species infecting alder (Alnus spp.) in the [...] Read more.

Melampsoridium hiratsukanum is an alien rust fungus which has spread pervasively throughout several European countries following introduction into North Europe at the end of the 20th century. The authenticity of several records of the Melampsoridium species infecting alder (Alnus spp.) in the northern hemisphere is questionable, due to the misidentification and confusion that surround many of the older reports. Given this complicated taxonomic history, and since a M. hiratsukanum-like rust is strongly impacting Alnus incana stands in the Alps, probably affecting the bank protection role of this species along rivers, the unambiguous identification of this pathogen was a pressing epidemiological and ecological issue. In this study, field surveys, light (LM) and scanning electron microscopy (SEM), and molecular characterization were put together in an attempt to solve the conundrum. Field monitoring data, LM and SEM analyses of key taxonomic traits (length of ostiolar cells of uredinium, uredinio-spore shape and size, spore echinulation, number and position of germ pores) and ITS-rDNA sequence-based identification, convergently and unambiguously connected the rust that is causing the current epidemic to the non-native M. hiratsukanum. We documented the completion of the M. hiratsukanum life cycle on its two taxonomically unrelated broadleaf/conifer hosts. This is the first report of M. hiratsukanum from naturally infected Larix decidua in Europe. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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16 pages, 6395 KiB

Open AccessArticle

Bot Gummosis of Lemon (Citrus × limon) Caused by Neofusicoccum parvum

by Francesco Aloi, Mario Riolo, Rossana Parlascino, Antonella Pane and Santa Olga Cacciola

J. Fungi 2021, 7(4), 294; https://doi.org/10.3390/jof7040294 - 14 Apr 2021

Cited by 10 | Viewed by 6180

Abstract

Neofusicoccum parvum, in the family Botryosphaeriaceae, was identified as the causal agent of bot gummosis of lemon (Citrus × limon) trees, in the two major lemon-producing regions in Italy. Gummy cankers on trunk and scaffold branches of mature trees were [...] Read more.

Neofusicoccum parvum, in the family Botryosphaeriaceae, was identified as the causal agent of bot gummosis of lemon (Citrus × limon) trees, in the two major lemon-producing regions in Italy. Gummy cankers on trunk and scaffold branches of mature trees were the most typical disease symptoms. Neofusicoccum parvum was the sole fungus constantly and consistently isolated from the canker bark of symptomatic lemon trees. It was identified on the basis of morphological characters and the phylogenetic analysis of three loci, i.e., the internal transcribed spacer of nuclear ribosomal DNA (ITS) as well as the translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes. The pathogenicity of N. parvum was demonstrated by wound inoculating two lemon cultivars, ‘Femminello 2kr’ and ‘Monachello’, as well as citrange (C. sinensis × Poncirus trifoliata) ‘Carrizo’ rootstock. In artificial inoculations, the fungus was very aggressive on lemons and weakly virulent on citrange, consistently with symptoms observed in the field as a consequence of natural infections. This is the first report of N. parvum, both in a wide and in a strict taxonomic sense, as a pathogen of lemon in Italy. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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Review

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21 pages, 1920 KiB

Open AccessReview

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

by Maria Aragona, Anita Haegi, Maria Teresa Valente, Luca Riccioni, Laura Orzali, Salvatore Vitale, Laura Luongo and Alessandro Infantino

J. Fungi 2022, 8(7), 737; https://doi.org/10.3390/jof8070737 - 16 Jul 2022

Cited by 23 | Viewed by 5190

Abstract

The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, [...] Read more.

The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as “What’s in my soil?”, to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported. Full article

(This article belongs to the Special Issue Diagnosis of Plant Pathogenic Fungi and Oomycetes and Plant Breeding for Disease Resistance)

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