France Climate Change and Global Trade Will

Total Page:16

File Type:pdf, Size:1020Kb

France Climate Change and Global Trade Will ABSTRACTS SUBMISSION 66_Amir Hossein FARTASH ‐ inp ‐ France amirhossein.fartash@toulouse‐inp.fr Climate change and global trade will challenge genetic resistance to Verticillium wilt in the legume plant Medicago truncatula Fartash A. A, Mazurier M. A, Ghalandar M.B Ebrahimi A. C, Ben C. A, Gentzbittel L.A, Rickauer M.A ALaboratoire Ecologie Fonctionnelle et Environnement, Universit´e de Toulouse, CNRS, Toulouse, France, B Agricultural Research Centre of Markazi Province, PO Box 889, Arak, Iran, C Faculty of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Ashrafi Esfehani Highway, BP 1477893855 Tehran, Iran. Verticillium wilt is caused by species of the soilborne fungus Verticillium and affects more than 200 plant species. Verticillium wilt of alfalfa (Medicago sativa) is a major problem for this crop. Its close relative Medicago truncatula, a wild species growing all around the Mediterranean, is a model plant in legume biology and is used widely to study genetic control of disease resistance. We previously described the genetic architecture for quantitative resistance to the French V. alfalfae strain V31.2 (1, 2) and described correlation between resistance and population structure (3). Our present study aims to assess effects of climate change and globalization on genetic resistance to V. alfalfae. Hence we isolated V. alfalfae strains from alfalfa in Iran and conducted inoculation experiments at 25°C compared to the standard temperature of 21°C. Fungal isolates were identified by PCR with V. alfalfae ‐specific primers and characterized by their reproductive and vegetative characteristics at 3 temperature. One Iranian isolate was selected for further studies. The plant’s response to this strain was assessed by scoring disease symptoms during 4 weeks after root inoculation in 242 M. truncatula accessions. Area Under disease progress curve (AUDPC) and Maximum symptom scoring (MSS) were computed as phenotypic traits. Genome‐wide association analysis was performed with 5,671,743 SNPs and revealed 30 loci associated to resistance traits MSS and AUDPC. Except one, all loci are different from those identified previously with V31.2 at 20°C. This clearly shows the strong effect of environment and fungal strain and not only challenges crop breeders to prepare for future conditions influenced by climate change and the introduction of pathogens by global trade, but also calls for surveillance in natural ecosystems. 1. Ben et al., 2012, J. Exp. Bot, 64(1):317‐32. 2. Mazurier 2018, PhD thesis Université de Toulouse, INP‐ENSAT 3. Gentzbittel et al., 2019, Genome Biol., 20, 106. 1. What is your pathogen? Multiple options possible (e.g. if working on coinfections) Fungi : Verticillium alfalfae 2. On a scale of 1‐5 is your work mostly eco/epidemiological or evolutionary? 1 (100% eco/epidemiological) 3. On a scale of 1‐5 is your work mostly theoretical or experimental/empirical? 5 (100% empirical) Extraction du 10/5/2021 .
Recommended publications
  • How Transposons Drive Evolution of Virulence in a Fungal Pathogen
    bioRxiv preprint doi: https://doi.org/10.1101/038315; this version posted January 30, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 How transposons drive evolution of virulence in a fungal pathogen 2 Luigi Faino1#, Michael F Seidl1#, Xiaoqian Shi-Kunne1, Marc Pauper1, Grardy CM van den 3 Berg1, Alexander HJ Wittenberg2, and Bart PHJ Thomma1* 4 5 1Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB 6 Wageningen, The Netherlands 7 2Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands 8 9 #These authors contributed equally to this work 10 *Corresponding author: Prof. dr. Bart PHJ Thomma 11 Chair, Laboratory of Phytopathology 12 Wageningen University 13 Droevendaalsesteeg 1 14 6708 PB Wageningen 15 The Netherlands 16 Email: [email protected] 17 18 19 Running title: Genome evolution by transposable elements 20 Keywords: Genome evolution; Transposable element; Plant pathogen; Verticillium dahliae; 21 segmental genome duplication 1 bioRxiv preprint doi: https://doi.org/10.1101/038315; this version posted January 30, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 22 Abstract 23 Genomic plasticity enables adaptation to changing environments, which is especially relevant 24 for pathogens that engage in arms races with their hosts. In many pathogens, genes 25 mediating aggressiveness cluster in highly variable, transposon-rich, physically distinct 26 genomic compartments. However, understanding of the evolution of these compartments, 27 and the role of transposons therein, remains limited.
    [Show full text]
  • Comprehensive Analysis of Verticillium Nonalfalfae in Silico Secretome
    bioRxiv preprint doi: https://doi.org/10.1101/237255; this version posted December 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion 1 Kristina Marton1, Marko Flajšman1, Sebastjan Radišek2, Katarina Košmelj1, Jernej Jakše1, 2 Branka Javornik1, Sabina Berne1* 3 1Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia 4 2Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia 5 * Correspondence: 6 Sabina Berne 7 [email protected] 8 Abstract 9 Background: The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several 10 important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in 11 the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins 12 (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. 13 nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. 14 Results: The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins 15 involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several 16 homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, 17 hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI 18 database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were bioRxiv preprint doi: https://doi.org/10.1101/237255; this version posted December 21, 2017.
    [Show full text]
  • Transposons Passively and Actively Contribute to Evolution of the Two-Speed Genome
    Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Transposons passively and actively contribute to evolution of the two-speed genome 2 of a fungal pathogen 3 4 Luigi Faino1#, Michael F Seidl1#, Xiaoqian Shi-Kunne1, Marc Pauper1, Grardy CM van den 5 Berg1, Alexander HJ Wittenberg2, and Bart PHJ Thomma1* 6 7 1Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB 8 Wageningen, The Netherlands 9 2Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands 10 11 #These authors contributed equally to this work 12 *Corresponding author: Prof. dr. Bart PHJ Thomma 13 Chair, Laboratory of Phytopathology 14 Wageningen University 15 Droevendaalsesteeg 1 16 6708 PB Wageningen 17 The Netherlands 18 Email: [email protected] 19 20 21 Running title: Genome evolution by transposable elements 22 Keywords: Genome evolution; transposable element; plant pathogen; Verticillium dahliae; 23 segmental genome duplication 1 Downloaded from genome.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press 24 Abstract 25 Genomic plasticity enables adaptation to changing environments, which is especially relevant 26 for pathogens that engage in “arms races” with their hosts. In many pathogens, genes 27 mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic 28 compartments. However, understanding of the evolution of these compartments, and the role 29 of transposons therein, remains limited. Here, we show that transposons are the major 30 driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. 31 We show that highly variable lineage-specific (LS) regions evolved by genomic 32 rearrangements that are mediated by erroneous double-strand repair, often utilizing 33 transposons.
    [Show full text]
  • Root-Associated Fungal Microbiota of Nonmycorrhizal Arabis Alpina and Its Contribution to Plant Phosphorus Nutrition
    Root-associated fungal microbiota of nonmycorrhizal PNAS PLUS Arabis alpina and its contribution to plant phosphorus nutrition Juliana Almarioa,b,1, Ganga Jeenaa,b, Jörg Wunderc, Gregor Langena,b, Alga Zuccaroa,b, George Couplandb,c, and Marcel Buchera,b,2 SEE COMMENTARY aBotanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany; bCluster of Excellence on Plant Sciences, University of Cologne, 50674 Cologne, Germany; and cDepartment of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany Edited by Luis Herrera-Estrella, Center for Research and Advanced Studies, Irapuato, Guanajuato, Mexico, and approved September 1, 2017 (received for review June 9, 2017) Most land plants live in association with arbuscular mycorrhizal to account for these cross-kingdom interactions to be complete. (AM) fungi and rely on this symbiosis to scavenge phosphorus (P) Here, we integrate these concepts and study the role of root- from soil. The ability to establish this partnership has been lost in associated fungi other than AM in plant P nutrition. some plant lineages like the Brassicaceae, which raises the question In some plant lineages, AM co-occurs with other mycorrhizal of what alternative nutrition strategies such plants have to grow in symbioses like ectomycorrhiza (woody plants), orchid mycorrhiza P-impoverished soils. To understand the contribution of plant–micro- (orchids), and ericoid mycorrhiza (Ericaceae) (10). These associ- biota interactions, we studied the root-associated fungal microbiome ations can also promote plant nutrition; however, they have not of Arabis alpina (Brassicaceae) with the hypothesis that some of its been described in Brassicaceae. Endophytic microbes can promote components can promote plant P acquisition.
    [Show full text]
  • Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species
    Phylogenetics and Taxonomy of the Fungal Vascular Wilt Pathogen Verticillium, with the Descriptions of Five New Species Patrik Inderbitzin1, Richard M. Bostock1, R. Michael Davis1, Toshiyuki Usami2, Harold W. Platt3, Krishna V. Subbarao1* 1 Department of Plant Pathology, University of California Davis, Davis, California, United States of America, 2 Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan, 3 Agriculture and Agri-Food Canada, Charlottetown Research Centre, Charlottetown, Prince Edward Island, Canada Abstract Knowledge of pathogen biology and genetic diversity is a cornerstone of effective disease management, and accurate identification of the pathogen is a foundation of pathogen biology. Species names provide an ideal framework for storage and retrieval of relevant information, a system that is contingent on a clear understanding of species boundaries and consistent species identification. Verticillium, a genus of ascomycete fungi, contains important plant pathogens whose species boundaries have been ill defined. Using phylogenetic analyses, morphological investigations and comparisons to herbarium material and the literature, we established a taxonomic framework for Verticillium comprising ten species, five of which are new to science. We used a collection of 74 isolates representing much of the diversity of Verticillium, and phylogenetic analyses based on the ribosomal internal transcribed spacer region (ITS), partial sequences of the protein coding genes actin (ACT), elongation factor 1-alpha (EF), glyceraldehyde-3-phosphate dehydrogenase (GPD) and tryptophan synthase (TS). Combined analyses of the ACT, EF, GPD and TS datasets recognized two major groups within Verticillium, Clade Flavexudans and Clade Flavnonexudans, reflecting the respective production and absence of yellow hyphal pigments. Clade Flavexudans comprised V. albo-atrum and V.
    [Show full text]
  • Elucidating Disease Dynamics in the Biocontrol of Ailanthus Altissima While Confirming the Host Specificity of the Vascular Wilt
    Graduate Theses, Dissertations, and Problem Reports 2019 Elucidating disease dynamics in the biocontrol of Ailanthus altissima while confirming the host specificity of theascular v wilt pathogen Verticillium nonalfalfae Kristen L. Wickert [email protected] Follow this and additional works at: https://researchrepository.wvu.edu/etd Part of the Other Forestry and Forest Sciences Commons Recommended Citation Wickert, Kristen L., "Elucidating disease dynamics in the biocontrol of Ailanthus altissima while confirming the host specificity of the vascular wilt pathogen Verticillium nonalfalfae" (2019). Graduate Theses, Dissertations, and Problem Reports. 3854. https://researchrepository.wvu.edu/etd/3854 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Elucidating disease dynamics in the biocontrol of Ailanthus altissima while confirming the host specificity of the vascular wilt pathogen Verticillium nonalfalfae Kristen L. Wickert Dissertation submitted to the Davis College of Agriculture, Natural Resources and Design at West Virginia University in partial fulfillment of the requirements for the degree of PhD in Plant Pathology Matthew T.
    [Show full text]
  • Evaluation of PCR-Based Methods for Rapid, Accurate Detection and Monitoring of Verticillium Dahliae in Woody Hosts by Real- Time Polymerase Chain Reaction
    University of Kentucky UKnowledge Theses and Dissertations--Plant Pathology Plant Pathology 2014 Evaluation of PCR-Based Methods for Rapid, Accurate Detection and Monitoring of Verticillium Dahliae in Woody Hosts by Real- Time Polymerase Chain Reaction Baker Diwan Getheeth Aljawasim University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Aljawasim, Baker Diwan Getheeth, "Evaluation of PCR-Based Methods for Rapid, Accurate Detection and Monitoring of Verticillium Dahliae in Woody Hosts by Real-Time Polymerase Chain Reaction" (2014). Theses and Dissertations--Plant Pathology. 13. https://uknowledge.uky.edu/plantpath_etds/13 This Master's Thesis is brought to you for free and open access by the Plant Pathology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Plant Pathology by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.
    [Show full text]
  • Sodiomyces Alkalinus, a New Holomorphic Alkaliphilic Ascomycete Within the Plectosphaerellaceae
    Persoonia 31, 2013: 147–158 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158513X673080 Sodiomyces alkalinus, a new holomorphic alkaliphilic ascomycete within the Plectosphaerellaceae A.A. Grum-Grzhimaylo1,3, A.J.M. Debets1, A.D. van Diepeningen2, M.L. Georgieva3, E.N. Bilanenko3 Key words Abstract In this study we reassess the taxonomic reference of the previously described holomorphic alkaliphilic fungus Heleococcum alkalinum isolated from soda soils in Russia, Mongolia and Tanzania. We show that it is not alkaliphilic fungi an actual member of the genus Heleococcum (order Hypocreales) as stated before and should, therefore, be ex- growth cluded from it and renamed. Multi-locus gene phylogeny analyses (based on nuclear ITS, 5.8S rDNA, 28S rDNA, Heleococcum alkalinum 18S rDNA, RPB2 and TEF1-alpha) have displayed this fungus as a new taxon at the genus level within the family molecular phylogeny Plectosphaerellaceae, Hypocreomycetidae, Ascomycota. The reference species of actual Heleococcum members scanning electron microscopy showed clear divergence from the strongly supported Heleococcum alkalinum position within the Plectosphaerel- taxonomy laceae, sister to the family Glomerellaceae. Eighteen strains isolated from soda lakes around the world show remarkable genetic similarity promoting speculations on their possible evolution in harsh alkaline environments. We established the pH growth optimum of this alkaliphilic fungus at c. pH 10 and tested growth on 30 carbon sources at pH 7 and 10. The new genus and species, Sodiomyces alkalinus gen. nov. comb. nov., is the second holomorphic fungus known within the family, the first one being Plectosphaerella – some members of this genus are known to be alkalitolerant.
    [Show full text]
  • Supplementary Materials Journal of Fungi New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lene L
    Supplementary Materials Journal of Fungi New Method for identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences Lene Lange1, Kristian Barrett2, and Anne S. Meyer2 1 BioEconomy, Research & Advisory, Copenhagen, 2500 Valby, Denmark; [email protected] (L.L) 2 Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; [email protected] (KB), [email protected] (ASM) Table S1. List of the rank of all 1.932 fungal species/strains with regard to biomass degrading capacity based on bioinformatics analysis of their genome sequence. The species are ranked with regard to the Total number of “Function;Family” observations, yet specifying the total number of “Function;Family” observations in each substrate category. The data shown is the full list of data supporting Table 1 in the main manuscript. ACC Submitter Total Xylan Xylan Lignin Pectin Cellulose No Species Class Phylum 1 Pecoramyces ruminatium Neocallimastigo Chytridio 248 85 208 0 541 GCA_000412615.1 Oklahoma State University 2 Neocallimastix californiae Neocallimastigo Chytridio 232 122 172 0 526 GCA_002104975.1 DOE Joint Genome Institute 3 Mycena citricolor Agarico Basidio 91 204 50 149 494 GCA_003987915.1 Universidade de Sao Paulo 4 Verticillium longisporum Sordario Asco 139 176 74 95 484 GCA_001268165.1 SLU 5 Coniochaeta sp. 2T2.1 Sordario Asco 117 102 108 98 425 GCA_009194965.1 DOE Joint Genome Institute 6 Paramyrothecium roridum Sordario Asco 106 163 63 79 411 GCA_003012165.1 USDA, ARS, NCAUR 7 Cadophora sp. DSE1049 Leotio Asco 105 138 75 91 409 GCA_003073865.1 DOE Joint Genome Institute 8 Diaporthe ampelina Sordario Asco 116 129 58 97 400 GCA_001630405.1 Bangalore University 9 Diaporthe longicolla Sordario Asco 111 128 56 90 385 GCA_000800745.1 Purdue University 10 Diaporthe sp.
    [Show full text]
  • Étude De L'interaction Entre Medicago Truncatula Et Verticillium Alfalfae
    En vue de l'obtention du DOCTORAT DE L'UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (INP Toulouse) Discipline ou spécialité : Interactions plantes-microorganismes Présentée et soutenue par : M. MAOULIDA TOUENI le lundi 17 novembre 2014 Titre : ETUDE DE L'INTERACTION ENTRE VERTICILLIUM ALFALFAE ET MEDICAGO TRUNCATULA Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : Ecologie Fonctionnelle (ECOLAB) Directeur(s) de Thèse : MME MARTINA RICKAUER MME CECILE BEN Rapporteurs : Mme DIANA FERNANDEZ, IRD MONTPELLIER M. PHILIPPE REIGNAULT, UNIVERSITE DU LITTORAL COTE D'OPALE Membre(s) du jury : 1 M. PHILIPPE REIGNAULT, UNIVERSITE DU LITTORAL COTE D'OPALE, Président 2 Mme CECILE BEN, INP TOULOUSE, Membre 2 Mme DIANA FERNANDEZ, IRD MONTPELLIER, Membre 2 Mme MARTINA RICKAUER, INP TOULOUSE, Membre AA.. INTROINTRODUCTIONDUCTION ............................................................................................................................................................................................................................................................................ 777 I. Les maladies des Plantes........................................................................................................ 9 1. Introduction : les maladies des plantes ............................................................................ 9 2. Les pathogènes vasculaires .............................................................................................
    [Show full text]
  • BIOINFORMATICS of GENOME REGULATION and STRUCTURE\SYSTEMS BIOLOGY (BGRS\SB-2018) the Eleventh International Conference
    Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences Novosibirsk State University BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY (BGRS\SB-2018) The Eleventh International Conference Abstracts 20–25 August, 2018 Novosibirsk, Russia Novosibirsk ICG SB RAS 2018 УДК 575 B60 Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2018) : The Eleventh International Conference (20–25 Aug. 2018, Novosibirsk, Russia); Abstracts / Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences; Novosibirsk State University. – Novosibirsk: ICG SB RAS, 2018. – 267 pp. – ISBN 978-5-91291-036-4. ISBN 978-5-91291-036-4 © ICG SB RAS, 2018 International program committee • Nikolai Kolchanov, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia (Conference Chair) • Ralf Hofestädt, University of Bielefeld, Germany • Mikhail Fedoruk, Novosibirsk State University, Novosibirsk, Russia • Lubomir Aftanas, State Scientific-Research Institute of Physiology & Basic Medicine, Novosibirsk, Russia • Ivo Grosse, Halle-Wittenberg University, Halle, Germany • Olga Lavrik, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia • Dmitry Afonnikov, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia • Andrey Lisitsa, IBMC, Moscow, Russia • Mikhail Voevoda, Institute of Internal Medicine and Preventive Medicine – ICG SB RAS, Russia • Vladimir Ivanisenko, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia • Sergey
    [Show full text]
  • Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops—A Review
    molecules Review Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops—A Review Dominika Malarczyk , Jacek Panek * and Magdalena Fr ˛ac Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland; [email protected] (D.M.); [email protected] (M.F.) * Correspondence: [email protected]; Tel.: +48-81-744-5061 (int. 207) Academic Editors: Jacek Namie´snikand Justyna Płotka-Wasylka Received: 13 February 2019; Accepted: 23 March 2019; Published: 27 March 2019 Abstract: Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS. Keywords: Colletotrichum acutatum; Verticillium spp.; Phytophthora spp.; Botrytis cinerea; PCR; qPCR; molecular identification; phytopathogenic fungi; strawberry; organic agriculture 1. Introduction Organic fruit production has been increasing constantly in recent decades and has also increased its market share in the production of food worldwide. Strawberry, blueberry and raspberry fruits are important products of Central Europe and increasing consumer demand to introduce organic methods of fruit cultivation is a major reason to seek alternative ways to reduce losses.
    [Show full text]