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Nguyen TBH, Foulongne-Oriol M, Jany JL, le Floch G, Picot A. New insights into mycotoxin risk management through fungal population genetics and genomics. Crit Rev Microbiol 2024:1-22. [PMID: 39188135 DOI: 10.1080/1040841x.2024.2392179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/08/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024]
Abstract
Mycotoxin contamination of food and feed is a major global concern. Chronic or acute dietary exposure to contaminated food and feed can negatively affect both human and animal health. Contamination occurs through plant infection by toxigenic fungi, primarily Aspergillus and Fusarium spp., either before or after harvest. Despite the application of various management strategies, controlling these pathogens remains a major challenge primarily because of their ability to adapt to environmental changes and selection pressures. Understanding the genetic structure of plant pathogen populations is pivotal for gaining new insights into their biology and epidemiology, as well as for understanding the mechanisms behind their adaptability. Such deeper understanding is crucial for developing effective and preemptive management strategies tailored to the evolving nature of pathogenic populations. This review focuses on the population-level variations within the two most economically significant toxigenic fungal genera according to space, host, and pathogenicity. Outcomes in terms of migration patterns, gene flow within populations, mating abilities, and the potential for host jumps are examined. We also discuss effective yet often underutilized applications of population genetics and genomics to address practical challenges in the epidemiology and disease control of toxigenic fungi.
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Affiliation(s)
- Toan Bao Hung Nguyen
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | | | - Jean-Luc Jany
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Gaétan le Floch
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
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2
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Nsibo DL, Barnes I, Berger DK. Recent advances in the population biology and management of maize foliar fungal pathogens Exserohilum turcicum, Cercospora zeina and Bipolaris maydis in Africa. FRONTIERS IN PLANT SCIENCE 2024; 15:1404483. [PMID: 39148617 PMCID: PMC11324496 DOI: 10.3389/fpls.2024.1404483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Maize is the most widely cultivated and major security crop in sub-Saharan Africa. Three foliar diseases threaten maize production on the continent, namely northern leaf blight, gray leaf spot, and southern corn leaf blight. These are caused by the fungi Exserohilum turcicum, Cercospora zeina, and Bipolaris maydis, respectively. Yield losses of more than 10% can occur if these pathogens are diagnosed inaccurately or managed ineffectively. Here, we review recent advances in understanding the population biology and management of the three pathogens, which are present in Africa and thrive under similar environmental conditions during a single growing season. To effectively manage these pathogens, there is an increasing adoption of breeding for resistance at the small-scale level combined with cultural practices. Fungicide usage in African cropping systems is limited due to high costs and avoidance of chemical control. Currently, there is limited knowledge available on the population biology and genetics of these pathogens in Africa. The evolutionary potential of these pathogens to overcome host resistance has not been fully established. There is a need to conduct large-scale sampling of isolates to study their diversity and trace their migration patterns across the continent.
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Affiliation(s)
- David L Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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3
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Subedi A, Barrera LBTDL, Ivey ML, Egel DS, Kebede M, Kara S, Aysan Y, Minsavage GV, Roberts PD, Jones JB, Goss EM. Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper. PHYTOPATHOLOGY 2024; 114:241-250. [PMID: 37432099 DOI: 10.1094/phyto-04-23-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.
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Affiliation(s)
- Aastha Subedi
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Melanie Lewis Ivey
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Daniel S Egel
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN, U.S.A
| | - Misrak Kebede
- Biotechnology Department, Collage of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Serhat Kara
- Alata Horticulture Research Institute, Mersin, Turkey
| | - Yesim Aysan
- Department of Plant Protection, Cukurova University, Adana, Turkey
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pamela D Roberts
- Southwest Florida Research & Education Center, University of Florida, Immokalee, FL, U.S.A
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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4
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Sapkota S, Burlakoti RR, Lubberts M, Lamour K. Genome resources and whole genome resequencing of Phytophthora rubi isolates from red raspberry. FRONTIERS IN PLANT SCIENCE 2023; 14:1161864. [PMID: 37457337 PMCID: PMC10339809 DOI: 10.3389/fpls.2023.1161864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 07/18/2023]
Abstract
Phytophthora rubi is a primary causal agent of Phytophthora root rot and wilting of raspberry (Rubus idaeus L.) worldwide. The disease is a major concern for raspberry growers in Canada and USA. To date, no information is available on genomic diversity of P. rubi population from raspberry in Canada. Using a PCR-free library prep with dual-indexing for an Illumina HiSEQX running a 2x150 bp configuration, we generated whole genome sequence data of P. rubi isolates (n = 25) recovered during 2018 to 2020 from nine fields, four locations and four cultivars of raspberry growing areas of British Columbia, Canada. The assembled genome of 24 isolates of P. rubi averaged 8,541 scaffolds, 309× coverage, and 65,960,000 bp. We exploited single nucleotide polymorphisms (SNPs) obtained from whole genome sequence data to analyze the genome structure and genetic diversity of the P. rubi isolates. Low heterozygosity among the 72% of pathogen isolates and standardized index of association revealed that those isolates were clonal. Principal component analysis, discriminant analysis of principal component, and phylogenetic tree revealed that P. rubi isolates clustered with the raspberry specific cultivars. This study provides novel resources and insight into genome structure, genetic diversity, and reproductive biology of P rubi isolated from red raspberry. The availability of the P. rubi genomes also provides valuable resources for future comparative genomic and evolutionary studies for oomycetes pathogens.
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Affiliation(s)
- Sanjib Sapkota
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Rishi R. Burlakoti
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Mark Lubberts
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
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5
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Gilabert A, Rieux A, Robert S, Vitalis R, Zapater M, Abadie C, Carlier J, Ravigné V. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa. Ecol Evol 2023; 13:e10013. [PMID: 37091563 PMCID: PMC10116021 DOI: 10.1002/ece3.10013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.
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Affiliation(s)
- A. Gilabert
- Université de la Réunion, UMR PVBMTSaint‐PierreFrance
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
- Present address:
CIRAD, UMR AGAP InstitutMontpellierFrance
- Present address:
UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - A. Rieux
- CIRAD, UMR PVBMTSaint‐PierreFrance
| | - S. Robert
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - R. Vitalis
- CBGPUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - M.‐F. Zapater
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - C. Abadie
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - J. Carlier
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - V. Ravigné
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
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Saubin M, Louet C, Bousset L, Fabre F, Frey P, Fudal I, Grognard F, Hamelin F, Mailleret L, Stoeckel S, Touzeau S, Petre B, Halkett F. Improving sustainable crop protection using population genetics concepts. Mol Ecol 2022; 32:2461-2471. [PMID: 35906846 DOI: 10.1111/mec.16634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 10/16/2022]
Abstract
Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) 'plant breeding' (generating new genetic material), (ii) 'molecular interactions' (exploring the molecular dialogue governing plant-pathogen interactions) and (iii) 'epidemiology and evolution' (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary-epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.
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Affiliation(s)
| | - Clémentine Louet
- Université de Lorraine, INRAE, IAM, Nancy, France.,Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Lydia Bousset
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, F-33882 Villenave d'Ornon, France
| | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Isabelle Fudal
- Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
| | - Frédéric Hamelin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Suzanne Touzeau
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
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Dacones LS, Kemerait RC, Brewer MT. Comparative genomics of host-specialized populations of Corynespora cassiicola causing target spot epidemics in the southeastern United States. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:910232. [PMID: 37746203 PMCID: PMC10512278 DOI: 10.3389/ffunb.2022.910232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/27/2022] [Indexed: 09/26/2023]
Abstract
Numerous plant-pathogenic fungi secrete necrotrophic effectors (syn. host-selective toxins) that are important determinants of pathogenicity and virulence in species that have a necrotrophic lifestyle. Corynespora cassiicola is a necrotrophic fungus causing emerging target spot epidemics in the southeastern United States (US). Previous studies revealed that populations of C. cassiicola from cotton, soybean, and tomato are clonal, host specialized and genetically distinct. Additionally, cassiicolin - the necrotrophic effector identified in some C. cassiicola isolates - is an important toxin for virulence on rubber. It is encoded by seven Cas gene variants. Our goal was to conduct comparative genomic analyses to identify variation among putative necrotrophic effector genes and to determine if lack of one of the mating-types explained clonal populations in C. cassiicola causing outbreaks in the southeastern US and the apparent absence of sexual reproduction worldwide. A total of 12 C. cassiicola genomes, with four each from isolates from tomato, soybean, and cotton, were sequenced using an Illumina Next Seq platform. Each genome was assembled de novo, compared with the reference genome from rubber, and searched for known Cas, and other gene clusters with homologs of secondary metabolites. Cas2 and/or Cas6 were present in isolates from soybean in the southeastern US, whereas Cas1 and Cas2 were present in isolates from cotton in the southeastern US. In addition, several toxin genes, including the T-toxin biosynthetic genes were present in all C. cassiicola from cotton, soybean, and tomato. The mating-type locus was identified in all of the sequenced genomes, with the MAT1-1 idiomorph present in all cotton isolates and the rubber isolate, whereas the MAT1-2 idiomorph was present in all soybean isolates. We developed a PCR-based marker for mating-type in C. cassiicola. Both mating types were present in isolates from tomato. Thus, C. cassiicola has both mating-types necessary for sexual reproduction, but the absence of both mating-types within soybean and cotton populations could explain clonality in these populations. Variation in necrotrophic effectors may underlie host specialization and disease emergence of target spot on cotton, soybean, and tomato in the southeastern US.
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Affiliation(s)
- Leilani S. Dacones
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Robert C. Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
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8
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Runno-Paurson E, Agho CA, Zoteyeva N, Koppel M, Hansen M, Hallikma T, Cooke DEL, Nassar H, Niinemets Ü. Highly Diverse Phytophthora infestans Populations Infecting Potato Crops in Pskov Region, North-West Russia. J Fungi (Basel) 2022; 8:472. [PMID: 35628727 PMCID: PMC9147476 DOI: 10.3390/jof8050472] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/24/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
There is limited understanding of the genetic variability in Phytophthora infestans in the major potato cultivation region of north-western Russia, where potato is grown primarily by small households with limited chemical treatment of late blight. In this study, the mating type, sensitivity to metalaxyl, and genotype and population genetic diversity (based on 12 simple sequence repeat (SSR) markers) of 238 isolates of P. infestans from the Pskov region during the years 2010-2013 were characterized. The aim was to examine the population structure, phenotypic and genotypic diversity, and the prevalent reproductive mode of P. infestans, as well as the influence of the location, time, and agricultural management practices on the pathogen population. The frequency of the A2 mating was stable over the four seasons and ranged from 33 to 48% of the sampled population. Both mating types occurred simultaneously in 90% of studied fields, suggesting the presence of sexual reproduction and oospore production in P. infestans in the Pskov region. Metalaxyl-sensitive isolates prevailed in all four years (72%), however, significantly fewer sensitive isolates were found in samples from large-scale conventional fields. A total of 50 alleles were detected in the 141 P. infestans isolates analyzed for genetic diversity. Amongst the 83 SSR multilocus genotypes (MLGs) detected, 65% were unique and the number of MLGs varied between locations from 3 to 20. These results, together with the high genotypic diversity observed in all the locations and the lack of significance of linkage disequilibrium, suggest that sexual recombination is likely responsible for the unique MLGs and the high genetic diversity found in the Pskov region population, resembling those of north-eastern European populations.
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Affiliation(s)
- Eve Runno-Paurson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | - Collins A. Agho
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | - Nadezda Zoteyeva
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 St. Petersburg, Russia;
| | - Mati Koppel
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | - Merili Hansen
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | - Tiit Hallikma
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | | | - Helina Nassar
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006 Tartu, Estonia; (C.A.A.); (M.K.); (M.H.); (T.H.); (H.N.); (Ü.N.)
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Abstract
Population genetics allow to address fundamental questions about the biology of plant pathogens. By testing specific hypotheses, population genetics provide insights into the population genetic variability of pathogens across different geographical areas, time, and associated plant hosts, as well as on the structure and differentiation of populations, and on the possibility that a population is introduced and from where it has originated. In this chapter, basic concepts of population genetics are introduced, as well as the five evolutionary factors affecting populations, that is, mutations, recombination, variation in population size, gene flow, and natural selection. A step-by-step workflow, from sampling to data analysis, on how to perform a genetic analysis of natural populations of plant pathogens is discussed. Increased knowledge of the population biology of pathogens is pivotal to improve management strategies of diseases in agricultural and forest ecosystems.
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Affiliation(s)
- Fabiano Sillo
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Torino, Italy.
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Phylogenetic Analysis and Genetic Diversity of Colletotrichum falcatum Isolates Causing Sugarcane Red Rot Disease in Bangladesh. BIOLOGY 2021; 10:biology10090862. [PMID: 34571739 PMCID: PMC8467384 DOI: 10.3390/biology10090862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Sugarcane is an important agro-industrial crop because it is one of the major sources of white sugar. Red rot which is caused by Colletotrichum falcatum is the most devastating disease of sugarcane because its infestation results in significant sugarcane yield loss. The intra- and inter-specific genetic diversity, population structure and phylogenetic relationship amongst C. falcatum isolates from Bangladesh remain unclear. This information is essential for the effective management of red rot and to also develop resistant sugarcane varieties through plant breeding programmes. This paper demonstrates the phylogenetic relationship and genetic diversity of C. falcatum isolates from Bangladesh. Also, it provides baseline information that can be used to establish red rot disease management strategies for future application. Abstract Colletotrichum falcatum Went causes red rot disease in sugarcane farming in the tropical and sub-tropical regions. This disease causes significant economic loss to the sugarcane production industry. Successful disease management strategies depend on understanding the evolutionary relationship between pathogens, genetic diversity, and population structure, particularly at the intra-specific level. Forty-one isolates of C. falcatum were collected from different sugarcane farms across Bangladesh for molecular identification, phylogeny and genetic diversity study. The four genes namely, ITS-rDNA, β-tubulin, Actin and GAPDH sequences were conducted. All the 41 C. falcatum isolates showed a 99–100% similarity index to the conserved gene sequences in the GenBank database. The phylogram of the four genes revealed that C. falcatum isolates of Bangladesh clustered in the same clade and no distinct geographical structuring were evident within the clade. The four gene sequences revealed that C. falcatum isolates from Bangladesh differed from other countries´ isolates because of nucleotides substitution at different loci. The genetic structure of C. falcatum isolates were determined using ISSR marker generated 404 polymorphic loci from 10 selected markers. The percentage of polymorphic loci was 99.01. The genetic variability at species level was slightly higher than at population level. Total mean gene diversity at the species level was 0.1732 whereas at population level it was 0.1521. The cluster analysis divided 41 isolates into four main genetic groups and the principal component analysis was consistent with cluster analysis. To the best of our knowledge, this is the first finding on characterizing C. falcatum isolates infesting sugarcane in Bangladesh. The results of this present study provide important baseline information vis a vis C. falcatum phylogeny analysis and genetic diversity study.
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Adhikari TB, Muzhinji N, Halterman D, Louws FJ. Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin. Sci Rep 2021; 11:17024. [PMID: 34426589 PMCID: PMC8382843 DOI: 10.1038/s41598-021-95486-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
Early blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association \documentclass[12pt]{minimal}
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\begin{document}$$\left( {\overline{r}_{d} } \right)$$\end{document}r¯d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.
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Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Norman Muzhinji
- Department of Applied and Natural Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Dennis Halterman
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Vegetable Crops Research Unit, Madison, WI, 53706, USA
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA.
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12
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Papaïx J, Burdon JJ, Walker E, Barrett LG, Thrall PH. Metapopulation Structure Predicts Population Dynamics in the Cakile maritima- Alternaria brassicicola Host-Pathogen Interaction. Am Nat 2021; 197:E55-E71. [PMID: 33523787 DOI: 10.1086/712248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractIn symbiotic interactions, spatiotemporal variation in the distribution or population dynamics of one species represents spatial and temporal heterogeneity of the landscape for the other. Such interdependent demographic dynamics result in situations where the relative importance of biotic and abiotic factors in determining ecological processes is complicated to decipher. Using a detailed survey of three metapopulations of the succulent plant Cakile maritima and the necrotrophic fungus Alternaria brassicicola located along the southeastern Australian coast, we developed a series of statistical analyses-namely, synchrony analysis, patch occupancy dynamics, and a spatially explicit metapopulation model-to understand how habitat quality, weather conditions, dispersal, and spatial structure determine metapopulation dynamics. Climatic conditions are important drivers, likely explaining the high synchrony among populations. Host availability, landscape features facilitating dispersal, and habitat conditions also impact the occurrence and spread of disease. Overall, we show that the collection of extensive data on host and pathogen population dynamics, in combination with spatially explicit epidemiological modeling, makes it possible to accurately predict disease dynamics-even when there is extreme variability in host population dynamics. Finally, we discuss the importance of genetic information for predicting demographic dynamics in this pathosystem.
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13
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Nsibo DL, Barnes I, Omondi DO, Dida MM, Berger DK. Population genetic structure and migration patterns of the maize pathogenic fungus, Cercospora zeina in East and Southern Africa. Fungal Genet Biol 2021; 149:103527. [PMID: 33524555 DOI: 10.1016/j.fgb.2021.103527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/13/2020] [Accepted: 12/20/2020] [Indexed: 11/16/2022]
Abstract
Cercospora zeina is a causal pathogen of gray leaf spot (GLS) disease of maize in Africa. This fungal pathogen exhibits a high genetic diversity in South Africa. However, little is known about the pathogen's population structure in the rest of Africa. In this study, we aimed to assess the diversity and gene flow of the pathogen between major maize producing countries in East and Southern Africa (Kenya, Uganda, Zambia, Zimbabwe, and South Africa). A total of 964 single-spore isolates were made from GLS lesions and confirmed as C.zeina using PCR diagnostics. The other causal agent of GLS, Cercospora zeae-maydis, was absent. Genotyping all the C.zeina isolates with 11 microsatellite markers and a mating-type gene diagnostic revealed (i) high genetic diversity with some population structure between the five African countries, (ii) cryptic sexual recombination, (iii) that South Africa and Kenya were the greatest donors of migrants, and (iv) that Zambia had a distinct population. We noted evidence of human-mediated long-distance dispersal, since four haplotypes from one South African site were also present at five sites in Kenya and Uganda. There was no evidence for a single-entry point of the pathogen into Africa. South Africa was the most probable origin of the populations in Kenya, Uganda, and Zimbabwe. Continuous annual maize production in the tropics (Kenya and Uganda) did not result in greater genetic diversity than a single maize season (Southern Africa). Our results will underpin future management of GLS in Africa through effective monitoring of virulent C.zeina strains.
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Affiliation(s)
- David L Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, FABI, University of Pretoria, South Africa
| | | | | | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa.
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14
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Taîbi A, Rivallan R, Broussolle V, Pallet D, Lortal S, Meile JC, Constancias F. Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island. Front Microbiol 2021; 11:619226. [PMID: 33584584 PMCID: PMC7874004 DOI: 10.3389/fmicb.2020.619226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.
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Affiliation(s)
- Ahmed Taîbi
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Véronique Broussolle
- INRAE, Avignon Université, Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France
| | - Dominique Pallet
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
| | - Sylvie Lortal
- INRAE, Département Microbiologie et Chaine alimentaire, Jouy-en-Josas, France
| | - Jean-Christophe Meile
- CIRAD, UMR Qualisud, Saint-Pierre, France
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
| | - Florentin Constancias
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Université de La Réunion, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, France
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15
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Gur L, Reuveni M, Cohen Y, Cadle-Davidson L, Kisselstein B, Ovadia S, Frenkel O. Population structure of Erysiphe necator on domesticated and wild vines in the Middle East raises questions on the origin of the grapevine powdery mildew pathogen. Environ Microbiol 2021; 23:6019-6037. [PMID: 33459475 DOI: 10.1111/1462-2920.15401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Plant pathogens usually originate and diversify in geographical regions where hosts and pathogens co-evolve. Erysiphe necator, the causal agent of grape powdery mildew, is a destructive pathogen of grapevines worldwide. Although Eastern US is considered the centre of origin and diversity of E. necator, previous reports on resistant native wild and domesticated Asian grapevines suggest Asia as another possible origin of the pathogen. By using multi-locus sequencing, microsatellites and a novel application of amplicon sequencing (AmpSeq), we show that the population of E. necator in Israel is composed of three genetic groups: Groups A and B that are common worldwide, and a new group IL, which is genetically differentiated from any known group in Europe and Eastern US. Group IL showed distinguished ecological characteristics: it was dominant on wild and traditional vines (95%); its abundance increased along the season; and was more aggressive than A and B isolates on both wild and domesticated vines. The low genetic diversity within group IL suggests that it has invaded Israel from another origin. Therefore, we suggest that the Israeli E. necator population was founded by at least two invasions, of which one could be from a non-East American source, possibly from Asian origin.
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Affiliation(s)
- Lior Gur
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Rishon Lezion, Israel
| | - Moshe Reuveni
- Shamir Research Institute, University of Haifa, Katzrin, Israel
| | - Yigal Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Lance Cadle-Davidson
- USDA Agricultural Research Service, Geneva, NY, USA.,School of Integrative Plant Sciences, Cornell AgriTech, Geneva, NY, USA
| | - Breanne Kisselstein
- USDA Agricultural Research Service, Geneva, NY, USA.,School of Integrative Plant Sciences, Cornell AgriTech, Geneva, NY, USA
| | | | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Rishon Lezion, Israel
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16
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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17
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Jeger MJ. The Epidemiology of Plant Virus Disease: Towards a New Synthesis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1768. [PMID: 33327457 PMCID: PMC7764944 DOI: 10.3390/plants9121768] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
Epidemiology is the science of how disease develops in populations, with applications in human, animal and plant diseases. For plant diseases, epidemiology has developed as a quantitative science with the aims of describing, understanding and predicting epidemics, and intervening to mitigate their consequences in plant populations. Although the central focus of epidemiology is at the population level, it is often necessary to recognise the system hierarchies present by scaling down to the individual plant/cellular level and scaling up to the community/landscape level. This is particularly important for diseases caused by plant viruses, which in most cases are transmitted by arthropod vectors. This leads to range of virus-plant, virus-vector and vector-plant interactions giving a distinctive character to plant virus epidemiology (whilst recognising that some fungal, oomycete and bacterial pathogens are also vector-borne). These interactions have epidemiological, ecological and evolutionary consequences with implications for agronomic practices, pest and disease management, host resistance deployment, and the health of wild plant communities. Over the last two decades, there have been attempts to bring together these differing standpoints into a new synthesis, although this is more apparent for evolutionary and ecological approaches, perhaps reflecting the greater emphasis on shorter often annual time scales in epidemiological studies. It is argued here that incorporating an epidemiological perspective, specifically quantitative, into this developing synthesis will lead to new directions in plant virus research and disease management. This synthesis can serve to further consolidate and transform epidemiology as a key element in plant virus research.
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Affiliation(s)
- Michael J Jeger
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, UK
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18
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Santillán-Mendoza R, Montoya-Martínez AC, Pineda-Vaca D, Fernández-Pavía SP, Montero-Castro JC, Benítez-Malvido J, Ortega-Arreola R, Rodríguez-Alvarado G. Genetic diversity of Fusarium pseudocircinatum in the central western region of Mexico: the case of big-leaf mahogany malformation disease. Mol Biol Rep 2020; 47:6599-6609. [PMID: 32772344 DOI: 10.1007/s11033-020-05711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/02/2020] [Indexed: 11/29/2022]
Abstract
Fusarium pseudocircinatum is the main causal agent of big-leaf mahogany malformation disease (BLMMD) of mahogany (Swietenia macrophylla) in Mexico. Although, BLMMD is the most important disease for this high-value timber species, there is a lack of information on the genetic variation present in geographically diverse isolates of F. pseudocircinatum. The objective of this study was to determine the genetic diversity of populations of F. pseudocircinatum causing BLMMD in the central western region of Mexico. A total of 611 big-leaf mahogany trees were inspected at eight sites in four states (Colima, Guerrero, Jalisco and Michoacán); of these, 42.7% showed malformation symptoms similar to those of BLMMD. Of 374 Fusarium isolates that were recovered, 277 were identified as F. pseudocircinatum, 56 were F. mexicanum, and 41 were Fusarium spp. An ISSR analysis of the F. pseudocircinatum isolates generated 51 bands of which 38 were polymorphic (76.8%) with a mean of 17 bands per primer. A total of 87 multilocus genotypes (MLGs) were identified. Nei's genetic diversity analysis showed that the isolates had a high genetic diversity average (0.147), with values ranging from 0.070 to 0.365 depending of the geographical location. An analysis of molecular variance revealed that the variation within the populations was low (27.36%), while the variation within MLGs was significant (72.64%), indicating genetic flow. Overall, the genetic variability of F. pseudocircinatum populations was high and the MLGs from Colima (Colima) and Gabriel Zamora (Michoacán) were placed centrally, which possibly is evidence of ancestry and indicates its dispersion routes in the central western region of Mexico.
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Affiliation(s)
- Ricardo Santillán-Mendoza
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico.,Campo Experimental Ixtacuaco, CIRGOC, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tlapacoyan, Ver., Mexico
| | | | - Daniela Pineda-Vaca
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico
| | | | - Julieta Benítez-Malvido
- Ecología del Hábitat Alterado, IIES, Universidad Nacional Autónoma de México, Morelia, Mich., Mexico
| | - Rubén Ortega-Arreola
- Campo Experimental Tecomán, CIRPAC, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tecomán, Col., Mexico
| | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich., Mexico.
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DeLong JA, Stewart JE, Valencia-Botín A, Pedley KF, Buck JW, Brewer MT. Invasions of gladiolus rust in North America are caused by a widely-distributed clone of Uromycestransversalis. PeerJ 2019; 7:e7986. [PMID: 31799067 PMCID: PMC6885349 DOI: 10.7717/peerj.7986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Uromyces transversalis, the causal agent of Gladiolus rust, is an invasive plant pathogen in the United States and is regulated as a quarantine pathogen in Europe. The aim of this research was to: (i) determine the origin of introductions of U. transversalis to the United States, (ii) track the movement of genotypes, and (iii) understand the worldwide genetic diversity of the species. To develop molecular markers for genotyping, whole genome sequencing was performed on three isolates collected in the United States. Genomes were assembled de novo and searched for microsatellite regions. Primers were developed and tested on ten isolates from the United States resulting in the identification of 24 polymorphic markers. Among 92 isolates collected from Costa Rica, Mexico, New Zealand, Australia, and the United States there were polymorphisms within isolates with no genotypic diversity detected among isolates; however, missing data among the New Zealand and Australia isolates due to either poor amplification of degraded DNA or null alleles as a result of genetic differences made it difficult to generate conclusions about these populations. The microsatellite loci and flanking regions showed high diversity and two divergent genomes within dikaryotic individuals, yet no diversity among individuals, suggesting that the invasive U. transversalis populations from North America are strictly clonal.
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Affiliation(s)
- Jeffery A. DeLong
- Department of Plant Pathology, University of Georgia, Athens, GA, United States of America
| | - Jane E. Stewart
- Department of Plant Pathology, University of Georgia, Athens, GA, United States of America
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Alberto Valencia-Botín
- Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán, Jalisco, Mexico
| | - Kerry F. Pedley
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Fort Detrick, MD, United States of America
| | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA, United States of America
| | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, GA, United States of America
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20
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Mercier A, Carpentier F, Duplaix C, Auger A, Pradier JM, Viaud M, Gladieux P, Walker AS. The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations. Environ Microbiol 2019; 21:4808-4821. [PMID: 31608584 DOI: 10.1111/1462-2920.14829] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mould management, while suggesting spatial optimization of crop organization within agricultural landscapes.
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Affiliation(s)
- Alex Mercier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Florence Carpentier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,UR MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémentine Duplaix
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Jean-Marc Pradier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier Supagro, Université de Montpellier, Montpellier, France
| | - Anne-Sophie Walker
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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21
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Sedaghatkish A, Gossen BD, Yu F, Torkamaneh D, McDonald MR. Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada. BMC Genomics 2019; 20:744. [PMID: 31619176 PMCID: PMC6794840 DOI: 10.1186/s12864-019-6118-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/20/2019] [Indexed: 11/28/2022] Open
Abstract
Background Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistance breakdown was detected in 2013 and new pathotypes are increasing rapidly. Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta. Results The genomic sequences of 43 strains (34 field collections, 9 single-spore isolates) of P. brassicae from Canada, the United States, and China clustered into five clades based on SNP similarity. The strains from Canada separated into four clades, with two containing mostly strains from the Prairies (provinces of Alberta, Saskatchewan, and Manitoba) and two that were mostly from the rest of Canada or the USA. Several strains from China formed a separate clade. More than one pathotype and host were present in all four Canadian clades. The initial pathotypes from canola on the Prairies clustered separately from the pathotypes on canola that could overcome resistance to the initial pathotypes. Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown. Conclusion Clustering based on genome-wide DNA sequencing demonstrated that the initial pathotypes on canola on the Prairies clustered separately from the new virulent pathotypes on the Prairies. Analysis indicated that these ‘new’ pathotypes were likely present in the pathogen population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance.
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Affiliation(s)
- Afsaneh Sedaghatkish
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Bruce D Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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22
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Genetic diversity of Fusarium mexicanum, causal agent of mango and big-leaf mahogany malformation in Mexico. Mol Biol Rep 2019; 46:3887-3897. [PMID: 31037546 DOI: 10.1007/s11033-019-04832-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/19/2019] [Indexed: 10/26/2022]
Abstract
In Mexico, Fusarium mexicanum has been reported causing mango malformation disease and big-leaf mahogany malformation disease. Our objective was to determine the genetic diversity of F. mexicanum isolates obtained from malformed big-leaf mahogany and mango trees, using an internal simple sequence repeat (ISSR) analysis. A total of 61 isolates of F. mexicanum, 32 from mango and 29 from big-leaf mahogany, were initially genotyped using fourteen ISSR primers. Data from five primers that produced the highest number of polymorphic bands were selected for further analysis. The primers generated 49 polymorphic bands (85.96%) from a total of 57 fragments ranging in size from 250 to 2800 bp, with an average of 11.4 bands per primer. An analysis of molecular variance (AMOVA) indicated that the variation within populations, isolates grouped by host and geographic origin, was significant (43%), followed by the variation between the big-leaf mahogany versus mango isolates (34%), while among populations the variation was the lowest (22%). The genetic fingerprints suggested that genetic variability of F. mexicanum populations are structured by the host of origin rather than the geographic region.
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Owati A, Agindotan B, Burrows M. First microsatellite markers developed and applied for the genetic diversity study and population structure of Didymella pisi associated with ascochyta blight of dry pea in Montana. Fungal Biol 2019; 123:384-392. [PMID: 31053327 DOI: 10.1016/j.funbio.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/30/2019] [Accepted: 02/14/2019] [Indexed: 11/17/2022]
Abstract
Didymella pisi is the predominant causal pathogen of ascochyta blight of dry pea causing yield losses in Montana, where 415 000 acres were planted to dry pea in 2018. Thirty-three microsatellite markers were developed for dry pea pathogenic fungus, Didymella pisi, these markers were used to analyze genetic diversity and population structure of 205 isolates from four different geographical regions of Montana. These loci produced a total of 216 alleles with an average of 1.63 alleles per microsatellite marker. The polymorphic information content values ranged from 0.020 to 0.990 with an average of 0.323. The average observed heterozygosity across all loci varied from 0.000 to 0.018. The gene diversity among the loci ranged from 0.003 to 0.461. Unweighted Neighbor-joining and population structure analysis grouped these 205 isolates into two major sub-groups. The clusters did not match the geographic origin of the isolates. Analysis of molecular variance showed 85 % of the total variation within populations and only 15 % among populations. There was moderate genetic variation in the total populations (PhiPT = 0.153). Information obtained from this study could be useful as a base to design strategies for improved management such as breeding for resistance to ascochyta blight of dry pea in Montana.
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Affiliation(s)
- Ayodeji Owati
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Bright Agindotan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Mary Burrows
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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Sikdar P, Mazzola M, Xiao CL. Genetic and Pathogenic Characterization of Phacidiopycnis washingtonensis from Apple and Pacific Madrone from the Western United States. PHYTOPATHOLOGY 2019; 109:469-479. [PMID: 30156500 DOI: 10.1094/phyto-10-17-0358-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phacidiopycnis washingtonensis is the cause of speck rot of apple and leaf blight of Pacific madrone in Washington State. In total, 314 isolates were collected from apple production areas in eastern Washington and Pacific madrone in western Washington. Using eight microsatellite markers designed in this study, 58 unique multilocus haplotypes were identified. Only one of the haplotypes was shared between the apple and Pacific madrone populations. Analysis of molecular variance showed no genetic differentiation between the apple and Pacific madrone populations. Genetic variation was present within each subpopulation of apple from different geographic locations. The apple population possessed higher genotypic diversity than the Pacific madrone population, suggesting that isolates from apple may represent an older population and could have been introduced into the native habitat of Pacific madrone. P. washingtonensis likely reproduces asexually because populations examined in this study were not in linkage equilibrium. In pathogenicity tests, representative isolates from apple and Pacific madrone all incited leaf blight on Pacific madrone and speck rot on apple fruit regardless of their host of origin. Overall, our findings indicate that the P. washingtonensis population in Washington State is largely asexual, with high genotypic flow and that apple, crabapple, and Pacific madrone could serve as sources of P. washingtonensis inoculum for these hosts.
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Affiliation(s)
- P Sikdar
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
| | - M Mazzola
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
| | - C L Xiao
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
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Sumabat LG, Kemerait RC, Kim DK, Mehta YR, Brewer MT. Clonality and geographic structure of host-specialized populations of Corynespora cassiicola causing emerging target spot epidemics in the southeastern United States. PLoS One 2018; 13:e0205849. [PMID: 30321244 PMCID: PMC6188889 DOI: 10.1371/journal.pone.0205849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/02/2018] [Indexed: 11/21/2022] Open
Abstract
Corynespora cassiicola is a destructive plant-pathogenic fungus causing widespread target spot epidemics, including outbreaks on cotton, soybean, and tomato in the southeastern United States. Previous studies revealed that populations from the three hosts are genetically distinct and host specialized. Although variation in aggressiveness to cotton and tomato were observed, no genetic diversity was detected within populations sampled from each of these hosts. We aimed to gain a better understanding of the emerging target spot epidemics by developing microsatellite markers for C. cassiicola to assess genetic variation, population structure, and to infer modes of reproduction and mechanisms of dispersal. Two hundred sixty-five isolates from cotton, soybean, tomato, and other host plants were genotyped with 13 microsatellite markers. Genotypic diversity revealed genetic variation within each of the populations collected from different hosts, with the population from cotton dominated by clonal genotypes and showing the least genetic diversity. In addition, C. cassiicola populations on different host species were genetically distinct and structured based on host species. No association between genetic and geographic distances was identified in the tomato populations, and the association in cotton populations was low. However, significant regional geographic structure was detected in the soybean populations of C. cassiicola. These results further support previous findings of introduced host specialized isolates or the evolution of more aggressive strains on each host. The lack of geographic structure suggests that the clones on cotton and tomato spread rapidly, or similar founder populations were established by human-mediated dispersal, and that dispersal is not limited. However, regional geographic structure of populations on soybean suggests limited dispersal among more established populations of C. cassiicola, or genetic differences in founder populations that colonized different geographic areas.
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Affiliation(s)
- Leilani G. Sumabat
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Robert C. Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, United States of America
| | - Dong Kyun Kim
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | | | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
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Sumabat LG, Kemerait RC, Brewer MT. Phylogenetic Diversity and Host Specialization of Corynespora cassiicola Responsible for Emerging Target Spot Disease of Cotton and Other Crops in the Southeastern United States. PHYTOPATHOLOGY 2018; 108:892-901. [PMID: 29436985 DOI: 10.1094/phyto-12-17-0407-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Corynespora cassiicola is a ubiquitous fungus causing emerging plant diseases worldwide, including target spot of cotton, soybean, and tomato, which have rapidly increased in incidence and severity throughout the southeastern United States. The objectives of this study were to understand the causes for the emerging target spot epidemics in the United States by comparing phylogenetic relationships of isolates from cotton, tomato, soybean, and other crop plants and ornamental hosts, and through the determination of the host range of isolates from emerging populations. Fifty-three isolates were sampled from plants in the southeastern United States and 1,380 nucleotides from four nuclear loci were sequenced. Additionally, sequences of the same loci from 23 isolates representing each of the distinct lineages of C. cassiicola described from previous studies were included. Isolates clustered based on host of origin, regardless of the geographic location of sampling. There was no genetic diversity detected among isolates from cotton, which were genetically distinct from isolates from other host species. Furthermore, pathogenicity and virulence assays of 40 isolates from various hosts onto cotton, soybean, tomato, and cucumber showed that isolates from cotton were more aggressive to cotton than those from other hosts. Soybean and tomato were most susceptible to isolates that originated from the same host, providing evidence of host specialization. These results suggest that emerging target spot epidemics in the United States are caused by either the introduction of host-specific isolates or the evolution of more aggressive strains on each host.
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Affiliation(s)
- Leilani G Sumabat
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Robert C Kemerait
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Marin Talbot Brewer
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
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Ravelomanantsoa S, Vernière C, Rieux A, Costet L, Chiroleu F, Arribat S, Cellier G, Pruvost O, Poussier S, Robène I, Guérin F, Prior P. Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex. FRONTIERS IN PLANT SCIENCE 2018; 8:2258. [PMID: 29379515 PMCID: PMC5775269 DOI: 10.3389/fpls.2017.02258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 12/27/2017] [Indexed: 05/21/2023]
Abstract
The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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Affiliation(s)
- Santatra Ravelomanantsoa
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, University of Réunion, Saint-Denis, France
- Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | - Christian Vernière
- Unité Mixte de Recherche, Biologie et Génétique des Interactions Plante-Parasite, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Adrien Rieux
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Laurent Costet
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Frédéric Chiroleu
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Sandrine Arribat
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Gilles Cellier
- Tropical Pests and Diseases Unit, Plant Health Laboratory, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Saint-Pierre, France
| | - Olivier Pruvost
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Stéphane Poussier
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, University of Réunion, Saint-Denis, France
| | - Isabelle Robène
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, France
| | - Fabien Guérin
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, University of Réunion, Saint-Denis, France
| | - Philippe Prior
- Unité Mixte de Recherche, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Institut National de la Recherche Agronomique, Saint-Pierre, France
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Rotondo F, Hong SG, Peever T, Pryor BM. Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona. Fungal Biol 2017; 122:74-85. [PMID: 29248116 DOI: 10.1016/j.funbio.2017.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 10/12/2017] [Accepted: 10/23/2017] [Indexed: 12/13/2022]
Abstract
This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.
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Affiliation(s)
- Francesca Rotondo
- Department of Plant Pathology, The Ohio State University - OARDC, Wooster, OH 44691, USA; School of Plant Sciences, College of Agriculture, University of Arizona, Tucson, AZ 85721, USA
| | - Soon Gyu Hong
- Korea Polar Research Institute, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; School of Plant Sciences, College of Agriculture, University of Arizona, Tucson, AZ 85721, USA
| | - Tobin Peever
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Barry M Pryor
- School of Plant Sciences, College of Agriculture, University of Arizona, Tucson, AZ 85721, USA.
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Vaghefi N, Kikkert JR, Bolton MD, Hanson LE, Secor GA, Nelson SC, Pethybridge SJ. Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing. PLoS One 2017; 12:e0186488. [PMID: 29065114 PMCID: PMC5655429 DOI: 10.1371/journal.pone.0186488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/01/2017] [Indexed: 11/18/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs) obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10-4, and 1.298 × 10-3) were used for delineation of clonal lineages in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages; however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes (MLGs) were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal lineages in population genomics analyses that depend on individual assignment and identification of clonal lineages. Detection of recurrent clonal lineages shared between the USA and Europe, even in the relaxed-filtered SNP data set and with a conservative distance threshold for contraction of MLGs, provided strong evidence for global genotype flow in C. beticola populations. The implications of intercontinental migration in C. beticola populations for CLS management are discussed.
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Affiliation(s)
- Niloofar Vaghefi
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, New York, United States of America
| | - Julie R. Kikkert
- Cornell Cooperative Extension, Canandaigua, New York, United States of America
| | - Melvin D. Bolton
- United States Department of Agriculture–Agricultural Research Service (USDA-ARS), Red River Valley Agricultural Research Center, Fargo, North Dakota, United States of America
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Linda E. Hanson
- USDA-ARS, Sugar Beet and Bean Research Unit, Michigan State University, Michigan, United States of America
| | - Gary A. Secor
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Scot C. Nelson
- College of Tropical Agriculture and Human Resources, Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Sarah J. Pethybridge
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, New York, United States of America
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Vaghefi N, Nelson SC, Kikkert JR, Pethybridge SJ. Genetic structure of Cercospora beticola populations on Beta vulgaris in New York and Hawaii. Sci Rep 2017; 7:1726. [PMID: 28496148 PMCID: PMC5431814 DOI: 10.1038/s41598-017-01929-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/03/2017] [Indexed: 11/09/2022] Open
Abstract
Cercospora leaf spot (CLS), caused by Cercospora beticola, is a major disease of Beta vulgaris worldwide. No sexual stage is known for C. beticola but in its asexual form it overwinters on infected plant debris as pseudostromata, and travels short distances by rain splash-dispersed conidiospores. Cercospora beticola infects a broad range of host species and may be seedborne. The relative contribution of these inoculum sources to CLS epidemics on table beet is not well understood. Pathogen isolates collected from table beet, Swiss chard and common lambsquarters in mixed-cropping farms and monoculture fields in New York and Hawaii, USA, were genotyped (n = 600) using 12 microsatellite markers. All isolates from CLS symptoms on lambsquarters were identified as C. chenopodii. Sympatric populations of C. beticola derived from Swiss chard and table beet were not genetically differentiated. Results suggested that local (within field) inoculum sources may be responsible for the initiation of CLS epidemics in mixed-cropping farms, whereas external sources of inoculum may be contributing to CLS epidemics in the monoculture fields in New York. New multiplex PCR assays were developed for mating-type determination for C. beticola. Implications of these findings for disease management are discussed.
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Affiliation(s)
- Niloofar Vaghefi
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Scot C Nelson
- College of Tropical Agriculture and Human Resources, Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | | | - Sarah J Pethybridge
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
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Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici. J Microbiol Methods 2017; 139:113-122. [PMID: 28457942 DOI: 10.1016/j.mimet.2017.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 11/20/2022]
Abstract
Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.
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32
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Kim W, Park JJ, Dugan FM, Peever TL, Gang DR, Vandemark G, Chen W. Production of the antibiotic secondary metabolite solanapyrone A by the fungal plant pathogen Ascochyta rabiei during fruiting body formation in saprobic growth. Environ Microbiol 2017; 19:1822-1835. [PMID: 28109049 DOI: 10.1111/1462-2920.13673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/10/2017] [Accepted: 01/14/2017] [Indexed: 11/30/2022]
Abstract
Fungi are noted producers of a diverse array of secondary metabolites, many of which are of pharmacological importance. However, the biological roles of the vast majority of these molecules during the fungal life cycle in nature remain elusive. Solanapyrones are polyketide-derived secondary metabolites produced by diverse fungal species including the plant pathogen Ascochyta rabiei. This molecule was originally thought to function as a phytotoxin facilitating pathogenesis of A. rabiei. Chemical profiling and gene expression studies showed that solanapyrone A was specifically produced during saprobic, but not parasitic growth of A. rabiei. Expression of the gene encoding the final enzymatic step in solanapyrone biosynthesis was specifically associated with development of the asexual fruiting bodies of the fungus on certain substrates. In confrontation assays with saprobic fungi that were commonly found in chickpea debris in fields, A. rabiei effectively suppressed the growth of all competing fungi, such as Alternaria, Epicoccum and Ulocladium species. Solanapyrone A was directly detected in the inhibitory zone using a MALDI-imaging mass spectrometry, and the purified compound showed significant antifungal activities against the potential saprobic competitors. These results suggest that solanapyrone A plays an important role for competition and presumably the survival of the fungus.
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Affiliation(s)
- Wonyong Kim
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Jeong-Jin Park
- Tissue Imaging & Proteomics Laboratory, Washington State University, Pullman, Washington, USA
| | - Frank M Dugan
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Western Regional Plant Introduction Station, Washington State University, Pullman, Washington, USA
| | - Tobin L Peever
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - David R Gang
- Tissue Imaging & Proteomics Laboratory, Washington State University, Pullman, Washington, USA.,Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - George Vandemark
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, Washington, USA
| | - Weidong Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA.,USDA-ARS Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, Washington, USA
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Odilbekov F, Edin E, Garkava-Gustavsson L, Hovmalm HP, Liljeroth E. Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden. Hereditas 2016; 153:10. [PMID: 28096772 PMCID: PMC5226105 DOI: 10.1186/s41065-016-0014-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/13/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides. RESULTS Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin. CONCLUSIONS Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.
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Affiliation(s)
- Firuz Odilbekov
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, SE-230 53 Alnarp, Sweden
| | - Eva Edin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-750 07 Uppsala, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box, 101, SE-230 53 Alnarp, Sweden
| | - Helena Persson Hovmalm
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box, 101, SE-230 53 Alnarp, Sweden
| | - Erland Liljeroth
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, SE-230 53 Alnarp, Sweden
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da Graça JV, Douhan GW, Halbert SE, Keremane ML, Lee RF, Vidalakis G, Zhao H. Huanglongbing: An overview of a complex pathosystem ravaging the world's citrus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:373-87. [PMID: 26466921 DOI: 10.1111/jipb.12437] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/12/2015] [Indexed: 05/24/2023]
Abstract
Citrus huanglongbing (HLB) has become a major disease and limiting factor of production in citrus areas that have become infected. The destruction to the affected citrus industries has resulted in a tremendous increase to support research that in return has resulted in significant information on both applied and basic knowledge concerning this important disease to the global citrus industry. Recent research indicates the relationship between citrus and the causal agent of HLB is shaped by multiple elements, in which host defense responses may also play an important role. This review is intended to provide an overview of the importance of HLB to a wider audience of plant biologists. Recent advances on host-pathogen interactions, population genetics and vectoring of the causal agent are discussed.
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Affiliation(s)
- John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, Texas 78599, USA
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA
| | - Susan E Halbert
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, P.O. Box 147100, Gainesville, Florida 32614, USA
| | - Manjunath L Keremane
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507, USA
| | - Richard F Lee
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA
| | - Hongwei Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Moges AD, Admassu B, Belew D, Yesuf M, Njuguna J, Kyalo M, Ghimire SR. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia. PLoS One 2016; 11:e0151257. [PMID: 26978654 PMCID: PMC4792483 DOI: 10.1371/journal.pone.0151257] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 01/10/2023] Open
Abstract
Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.
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Affiliation(s)
- Asmare D. Moges
- Department of Horticulture, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, Jimma, Ethiopia
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Belayneh Admassu
- Department of Agricultural Biotechnology, Ethiopian Institute of Agricultural Research, Holetta, Ethiopia
| | - Derbew Belew
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, Jimma, Ethiopia
| | - Mohammed Yesuf
- Department of Horticulture, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Joyce Njuguna
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Martina Kyalo
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Sita R. Ghimire
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
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Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O. Bridgehead invasion of a monomorphic plant pathogenic bacterium:Xanthomonas citripv. citri, an emerging citrus pathogen in Mali and Burkina Faso. Environ Microbiol 2015; 17:4429-42. [DOI: 10.1111/1462-2920.12876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Leduc
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | | | - K. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - M. Magne
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - P. Grygiel
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. C. Juhasz
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - F. Guerin
- UMR PVBMT; Université de la Réunion; 97410 Saint Pierre La Réunion France
| | - I. Wonni
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - L. Ouedraogo
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - C. Vernière
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - V. Ravigné
- UMR BGPI; CIRAD; 34398 Montpellier France
| | - O. Pruvost
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
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Brewer MT, Rath M, Li HX. Genetic Diversity and Population Structure of Cucurbit Gummy Stem Blight Fungi Based on Microsatellite Markers. PHYTOPATHOLOGY 2015; 105:815-824. [PMID: 25710205 DOI: 10.1094/phyto-10-14-0282-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Combining population genetics with epidemiology provides insight into the population biology of pathogens, which could lead to improved management of plant diseases. Gummy stem blight, caused by three closely related species of Stagonosporopsis-Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), S. citrulli, and S. caricae-is a devastating disease of cucurbits worldwide. Sources of inoculum for epidemics, mechanisms of dispersal, and the mating system of these species are not well understood. To improve our knowledge of gummy stem blight epidemiology, we developed 18 polymorphic microsatellite markers by combining microsatellite motif enrichment with next-generation sequencing. When tested on 46 isolates from diverse cucurbit hosts and regions, the markers were robust for the dominant and widely distributed S. citrulli. Within this species, we found no population structure based on broad-scale geographic region or host of origin. Using the microsatellites, a rapid polymerase chain reaction-based method was developed to distinguish the three morphologically similar species causing gummy stem blight. To better understand dispersal, reproduction, and fine-scale genetic diversity of S. citrulli within and among watermelon fields, 155 isolates from two field populations in Georgia, United States were genotyped with the 18 microsatellite loci. Although dominant and widespread clones were detected, we found relatively high genotypic diversity and recombinant genotypes consistent with outcrossing. Significant population genetic structure between the two field populations demonstrated that there is regional geographic structure and limited dispersal among fields. This study provides insight into the fine-scale genetic diversity and reproductive biology of the gummy stem blight pathogen S. citrulli in the field.
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Affiliation(s)
| | - Manisha Rath
- Department of Plant Pathology, University of Georgia, Athens
| | - Hao-Xi Li
- Department of Plant Pathology, University of Georgia, Athens
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Brar S, Tsui CKM, Dhillon B, Bergeron MJ, Joly DL, Zambino PJ, El-Kassaby YA, Hamelin RC. Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen. PLoS One 2015; 10:e0127916. [PMID: 26010250 PMCID: PMC4444259 DOI: 10.1371/journal.pone.0127916] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/20/2015] [Indexed: 11/19/2022] Open
Abstract
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.
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Affiliation(s)
- Simren Brar
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Clement K. M. Tsui
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marie-Josée Bergeron
- Natural Resources Canada, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - David L. Joly
- Département de Biologie, Université de Moncton, Moncton, New Brunswick, Canada
| | - P. J. Zambino
- USDA Forest Service, Coeur d'Alene Field Office, Coeur d'Alene, Idaho, United States of America
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Natural Resources Canada, Laurentian Forestry Centre, Quebec City, Quebec, Canada
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Vaghefi N, Ades PK, Hay FS, Pethybridge SJ, Ford R, Taylor PW. Identification of the MAT1 locus in Stagonosporopsis tanaceti, and exploring its potential for sexual reproduction in Australian pyrethrum fields. Fungal Biol 2015; 119:408-19. [DOI: 10.1016/j.funbio.2014.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/01/2014] [Indexed: 11/26/2022]
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Burchhardt KM, Cubeta MA. Population Structure of the Blueberry Pathogen Monilinia vaccinii-corymbosi in the United States. PHYTOPATHOLOGY 2015; 105:533-541. [PMID: 25338172 DOI: 10.1094/phyto-03-14-0074-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The fungus Monilinia vaccinii-corymbosi causes disease of blueberry (Vaccinium section Cyanococcus) shoots, flowers, and fruit. The objective of our research was to examine the population biology and genetics of M. vaccinii-corymbosi in the United States. A total of 480 samples of M. vaccinii-corymbosi were collected from 18 blueberry fields in 10 states; one field in Georgia, Massachusetts, Maine, Michigan, Mississippi, New Jersey, New York, Oregon, and Washington and nine fields in North Carolina. Analysis with 10 microsatellite markers revealed 247 unique multilocus haplotypes (MLHs), with 244 MLHs detected within 11 fields in the Northeast, Northwest, Midwest, and Southeast and three MLHs detected within seven fields in the Southeast United States. Genetic similarity and low genetic diversity of M. vaccinii-corymbosi isolates from the seven fields in the Southeast United States suggested the presence of an expansive, self-fertile population. Tests for linkage disequilibrium within 10 fields that contained ≥12 MLHs supported random mating in six fields and possible inbreeding and/or self-fertilization in four fields. Analysis of molecular variance, discriminate analysis of principal components, and Bayesian cluster analysis provided evidence for population structure and restricted gene flow among fields. This research represents the first comprehensive investigation of the genetic diversity and structure of field populations of M. vaccinii-corymbosi.
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Affiliation(s)
- Kathleen M Burchhardt
- Department of Plant Pathology, North Carolina State University, Campus Box 7567, Raleigh 27695-001
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41
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Vaghefi N, Hay FS, Ades PK, Pethybridge SJ, Ford R, Taylor PWJ. Rapid Changes in the Genetic Composition of Stagonosporopsis tanaceti Population in Australian Pyrethrum Fields. PHYTOPATHOLOGY 2015; 105:358-369. [PMID: 25226524 DOI: 10.1094/phyto-08-14-0212-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel set of microsatellite markers were developed and employed for geographical and temporal population analyses of Stagonosporopsis tanaceti, the cause of ray blight of pyrethrum in Australia. Genotyping of 407 isolates, using 13 markers, suggested an asexual mode of reproduction with significant linkage disequilibrium and high levels of clonality. Low geographical differentiation and widespread distribution of a few multilocus genotypes (MLGs), in the absence of airborne ascospores, suggested the role of human-mediated movement of seed as a major means of long-distance pathogen dispersal. The genetic composition of S. tanaceti was stable for a decade then changed rapidly in only 2 years. Bayesian clustering analyses and minimum spanning networks determined only two major clonal lineages in and prior to 2010. However, in 2012, a previously unobserved cluster of MLGs was detected, which significantly increased in frequency and displaced the historically dominant MLGs by 2013. This rapid change in the genetic composition of S. tanaceti could indicate a second introduction then a selective sweep, or strong selection pressures from recently introduced fungicides or pyrethrum varieties. These results may have serious implications for durability of management strategies for this disease.
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Short DPG, Gurung S, Koike ST, Klosterman SJ, Subbarao KV. Frequency of Verticillium Species in Commercial Spinach Fields and Transmission of V. dahliae from Spinach to Subsequent Lettuce Crops. PHYTOPATHOLOGY 2015; 105:80-90. [PMID: 25098494 DOI: 10.1094/phyto-02-14-0046-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Verticillium wilt caused by V. dahliae is a devastating disease of lettuce in California (CA). The disease is currently restricted to a small geographic area in central coastal CA, even though cropping patterns in other coastal lettuce production regions in the state are similar. Infested spinach seed has been implicated in the introduction of V. dahliae into lettuce fields but direct evidence linking this inoculum to wilt epidemics in lettuce is lacking. In this study, 100 commercial spinach fields in four coastal CA counties were surveyed to evaluate the frequency of Verticillium species recovered from spinach seedlings and the area under spinach production in each county was assessed. Regardless of the county, V. isaacii was the most frequently isolated species from spinach followed by V. dahliae and, less frequently, V. klebahnii. The frequency of recovery of Verticillium species was unrelated to the occurrence of Verticillium wilt on lettuce in the four counties but was related to the area under spinach production in individual counties. The transmission of V. dahliae from infested spinach seeds to lettuce was investigated in microplots. Verticillium wilt developed on lettuce following two or three plantings of Verticillium-infested spinach, in independent experiments. The pathogen recovered from the infected lettuce from microplots was confirmed as V. dahliae by polymerase chain reaction assays. In a greenhouse study, transmission of a green fluorescence protein-tagged mutant strain of V. dahliae from spinach to lettuce roots was demonstrated, after two cycles of incorporation of infected spinach residue into the soil. This study presents conclusive evidence that V. dahliae introduced via spinach seed can cause Verticillium wilt in lettuce.
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Bergua M, Luis-Arteaga M, Escriu F. Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain. PHYTOPATHOLOGY 2014; 104:1241-1250. [PMID: 24779352 DOI: 10.1094/phyto-11-13-0309-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions--P1, P2, movement protein (MP), and coat protein (CP)--revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.
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Walker AS, Gladieux P, Decognet V, Fermaud M, Confais J, Roudet J, Bardin M, Bout A, C. Nicot P, Poncet C, Fournier E. Population structure and temporal maintenance of the multihost fungal pathogenBotrytis cinerea: causes and implications for disease management. Environ Microbiol 2014; 17:1261-74. [DOI: 10.1111/1462-2920.12563] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/04/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Anne-Sophie Walker
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Pierre Gladieux
- CNRS, UMR 8079 Ecologie Systématique Evolution; Bâtiment 360 Orsay F-91405 France
- University of Paris-Sud; Orsay F-91405 France
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
| | - Véronique Decognet
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Marc Fermaud
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Johann Confais
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Jean Roudet
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Marc Bardin
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Alexandre Bout
- INRA, UMR 1355 ISA, TEAPEA; Sophia-Antipolis F-06903 France
| | - Philippe C. Nicot
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | | | - Elisabeth Fournier
- INRA, UMR BGPI; TA A 54/K; Campus International de Baillarguet Montpellier F-34398 France
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Zanardo LG, Silva FN, Lima ATM, Milanesi DF, Castilho-Urquiza GP, Almeida AMR, Zerbini FM, Carvalho CM. Molecular variability of cowpea mild mottle virus infecting soybean in Brazil. Arch Virol 2014; 159:727-37. [PMID: 24142270 DOI: 10.1007/s00705-013-1879-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/03/2013] [Indexed: 11/26/2022]
Abstract
Molecular variability was assessed for 18 isolates of cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexiviridae) found infecting soybean in various Brazilian states (Bahia, Goiás, Maranhão, Mato Grosso, Minas Gerais, Pará) in 2001 and 2010. A variety of symptoms was expressed in soybean cv. CD206, ranging from mild (crinkle/blistering leaves, mosaic and vein clearing) to severe (bud blight, dwarfing, leaf and stem necrosis). Recombination analysis revealed only one CPMMV isolate to be recombinant. Pairwise comparisons and phylogenetic analysis were performed for partial genomes (ORF 2 to the 3' terminus) and for each ORF individually (ORFs 2 to 6), showing the isolates to be distinct. The topology of the phylogenetic tree could be related to symptoms, but not to the year of collection or geographical origin. Additionally, the phylogenetic analysis supported the existence of two distinct strains of the virus, designated CPMMV-BR1 and CPMMV-BR2, with molecular variations between them.
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Affiliation(s)
- L G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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Ali S, Gladieux P, Rahman H, Saqib MS, Fiaz M, Ahmad H, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogenPuccinia striiformisf.sp.tritici. Mol Ecol 2014; 23:603-17. [DOI: 10.1111/mec.12629] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/30/2013] [Accepted: 12/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sajid Ali
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; The University of Agriculture; Peshawar 25000 Pakistan
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Pierre Gladieux
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720-3102 USA
- Ecologie, Systématique et Evolution; UMR8079; Univ Paris-Sud; 91405 Orsay France
- Ecologie, Systématique et Evolution; UMR8079; CNRS; 91405 Orsay France
| | - Hidayatur Rahman
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | - Muhammad S. Saqib
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | | | | | - Marc Leconte
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
| | | | | | - Mogens S. Hovmøller
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Jérôme Enjalbert
- INRA UMR 320 Génétique Végétale; Ferme du Moulon; 91190 Gif sur Yvette France
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Combining field epidemiological information and genetic data to comprehensively reconstruct the invasion history and the microevolution of the sudden oak death agent Phytophthora ramorum (Stramenopila: Oomycetes) in California. Biol Invasions 2013; 15:2281-2297. [PMID: 24078788 PMCID: PMC3782357 DOI: 10.1007/s10530-013-0453-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 03/18/2013] [Indexed: 11/27/2022]
Abstract
Understanding the migration patterns of invasive organisms is of paramount importance to predict and prevent their further spread. Previous attempts at reconstructing the entire history of the sudden oak death (SOD) epidemic in California were limited by: (1) incomplete sampling; (2) the inability to include infestations caused by a single genotype of the pathogen; (3) collapsing of non-spatially contiguous yet genetically similar samples into large meta-samples that confounded the coalescent analyses. Here, we employ an intensive sampling coverage of 832 isolates of Phytopthora ramorum (the causative agent of SOD) from 60 California forests, genotyped at nine microsatellite loci, to reconstruct its invasion. By using age of infestation as a constraint on coalescent analyses, by dividing genetically indistinguishable meta-populations into highly-resolved sets of spatially contiguous populations, and by using Bruvo genetic distances for most analyses, we reconstruct the entire history of the epidemic and convincingly show infected nursery plants are the original source for the entire California epidemic. Results indicate that multiple human-mediated introductions occurred in most counties and that further disease sources were represented by large wild infestations. The study also identifies minor introductions, some of them relatively recent, linked to infected ornamental plants. Finally, using archival isolates collected soon after the discovery of the pathogen in California, we corroborate that the epidemic is likely to have resulted form 3 to 4 core founder individuals evolved from a single genotype. This is probably the most complete reconstruction ever completed for an invasion by an exotic forest pathogen, and the approach here described may be useful for the reconstruction of invasions by any clonally reproducing organism with a relatively limited natural dispersal range.
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Rampersad SN. Genetic structure of Colletotrichum gloeosporioides sensu lato isolates infecting papaya inferred by multilocus ISSR markers. PHYTOPATHOLOGY 2013; 103:182-189. [PMID: 23294406 DOI: 10.1094/phyto-07-12-0160-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Colletotrichum gloeosporioides sensu lato is widely distributed throughout temperate and tropical regions and causes anthracnose disease in numerous plant species. Development of effective disease management strategies is dependent on, among other factors, an understanding of pathogen genetic diversity and population stratification at the intraspecific level. For 132 isolates of C. gloeosporioides sensu lato collected from papaya in Trinidad, inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 121 polymorphic loci from five ISSR primers selected from an initial screen of 22 ISSR primers. The mean percentage of polymorphic loci was 99.18%. Bayesian cluster analysis inferred three genetic subpopulations, where group 1 consisted exclusively of isolates collected in the southern part of Trinidad whereas groups 2 and 3, although genetically distinct, were mixtures of isolates collected from both the northern and southern parts of Trinidad. Principal coordinates analysis and unweighted pair-group method with arithmetic mean phylogeny were concordant with Bayesian cluster analysis and supported subdivision into the three subpopulations. Overall, the total mean gene diversity was 0.279, the mean within-population gene diversity was 0.2161, and genetic differentiation for the Trinidad population was 0.225. Regionally, northern isolates had a lower gene diversity compared with southern isolates. Nei's gene diversity was highest for group 1 (h = 0.231), followed by group 2 (h = 0.215) and group 3 (h = 0.202). Genotypic diversity was at or near maximum for all three subpopulations after clone correction. Pairwise estimates of differentiation indicated high and significant genetic differentiation among the inferred subpopulations (Weir's θ of 0.212 to 0.325). Pairwise comparisons among subpopulations suggested restricted gene flow between groups 1 and 2 and groups 1 and 3 but not between groups 2 and 3. The null hypothesis of random mating was rejected for all three inferred subpopulations. These results suggest that pathogen biology and epidemiology as well as certain evolutionary factors may play an important role in population substructuring of C. gloeosporioides sensu lato isolates infecting papaya in Trinidad.
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Affiliation(s)
- Sephra N Rampersad
- The University of the West Indies, Development of Life Sciences, St. Augustine, Trinidad and Tobago.
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XHAARD CONSTANCE, BARRÈS BENOÎT, ANDRIEUX AXELLE, BOUSSET LYDIA, HALKETT FABIEN, FREY PASCAL. Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Mol Ecol 2012; 21:2383-98. [DOI: 10.1111/j.1365-294x.2012.05556.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bolton MD, Secor GA, Rivera V, Weiland JJ, Rudolph K, Birla K, Rengifo J, Campbell LG. Evaluation of the potential for sexual reproduction in field populations of Cercospora beticola from USA. Fungal Biol 2012; 116:511-21. [PMID: 22483049 DOI: 10.1016/j.funbio.2012.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 02/04/2023]
Abstract
Cercospora leaf spot, caused by the hemibiotrophic fungal pathogen Cercospora beticola, is the most economically damaging foliar disease of sugarbeet worldwide. Although most C. beticola populations display characteristics reminiscent of sexual recombination, no teleomorph has been described. To assess whether populations in northern United States have characteristics consistent with sexual reproduction, 1024 isolates collected over a 3-y period were analyzed for frequency and distribution of mating type genes. After clone correction, an approximately equal distribution of mating types was found for each sampling year. Mating type frequency was also assessed in individual lesions. Lesions always consisted of isolates with a single mating type and microsatellite haplotype, but both mating types and up to five microsatellite haplotypes could be found on an individual leaf. The MAT1-1-1 and MAT1-2-1 genes were sequenced from 28 MAT1-1 and 28 MAT1-2 isolates, respectively. Three MAT1-1-1 nucleotide haplotypes were identified that encoded a single amino acid sequence. For MAT1-2-1, five nucleotide haplotypes were identified that encoded four protein variants. MAT1-1-1 and MAT1-2-1 gene expression analyses were conducted on plants inoculated with either or both mating types. MAT1-1-1 expression remained low, but MAT1-2-1 spiked during late stages of colonization. A segment of the MAT1-2-1 coding sequence was also found in MAT1-1 isolates. Taken together, these results suggest that C. beticola has the potential for sexual reproduction.
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Affiliation(s)
- Melvin D Bolton
- United States Department of Agriculture - Agricultural Research Service, Northern Crops Science Laboratory, Fargo, ND 58102-2765, USA.
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