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Zhang YD, Ji XB, Zong J, Dai XF, Klosterman SJ, Subbarao KV, Zhang DD, Chen JY. Functional analysis of the mating type genes in Verticillium dahliae. BMC Biol 2024; 22:108. [PMID: 38714997 PMCID: PMC11077750 DOI: 10.1186/s12915-024-01900-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Populations of the plant pathogenic fungus Verticillium dahliae display a complex and rich genetic diversity, yet the existence of sexual reproduction in the fungus remains contested. As pivotal genes, MAT genes play a crucial role in regulating cell differentiation, morphological development, and mating of compatible cells. However, the functions of the two mating type genes in V. dahliae, VdMAT1-1-1, and VdMAT1-2-1, remain poorly understood. RESULTS In this study, we confirmed that the MAT loci in V. dahliae are highly conserved, including both VdMAT1-1-1 and VdMAT1-2-1 which share high collinearity. The conserved core transcription factor encoded by the two MAT loci may facilitate the regulation of pheromone precursor and pheromone receptor genes by directly binding to their promoter regions. Additionally, peptide activity assays demonstrated that the signal peptide of the pheromone VdPpg1 possessed secretory activity, while VdPpg2, lacked a predicted signal peptide. Chemotactic growth assays revealed that V. dahliae senses and grows towards the pheromones FO-a and FO-α of Fusarium oxysporum, as well as towards VdPpg2 of V. dahliae, but not in response to VdPpg1. The findings herein also revealed that VdMAT1-1-1 and VdMAT1-2-1 regulate vegetative growth, carbon source utilization, and resistance to stressors in V. dahliae, while negatively regulating virulence. CONCLUSIONS These findings underscore the potential roles of VdMAT1-1-1 and VdMAT1-2-1 in sexual reproduction and confirm their involvement in various asexual processes of V. dahliae, offering novel insights into the functions of mating type genes in this species.
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Affiliation(s)
- Ya-Duo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Bin Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Juan Zong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o United States Agricultural Research Station, Salinas, CA, USA.
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Chen JY, Klosterman SJ, Hu XP, Dai XF, Subbarao KV. Key Insights and Research Prospects at the Dawn of the Population Genomics Era for Verticillium dahliae. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:31-51. [PMID: 33891830 DOI: 10.1146/annurev-phyto-020620-121925] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species.Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae.
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Affiliation(s)
- Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; ,
| | - Steven J Klosterman
- Agricultural Research Service, United States Department of Agriculture, Salinas, California 93905, USA;
| | - Xiao-Ping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China;
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; ,
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, California 93905, USA;
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LeBlanc N, Cubeta MA, Crouch JA. Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood. PHYTOPATHOLOGY 2021; 111:184-193. [PMID: 33048629 DOI: 10.1094/phyto-06-20-0219-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species Calonectria pseudonaviculata has remained genetically isolated from its European-limited sister species C. henricotiae, while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 C. pseudonaviculata isolates from four continents and 1,017 SNPs in 13 C. henricotiae isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in C. pseudonaviculata identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two C. pseudonaviculata genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation.
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Affiliation(s)
- Nicholas LeBlanc
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
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4
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Bautista-Jalón LS, Frenkel O, Tsror Lahkim L, Malcolm GM, Gugino BK, Lebiush S, Hazanovsky M, Milgroom MG, Del Mar Jiménez-Gasco M. Genetic Differentiation of Verticillium dahliae Populations Recovered from Symptomatic and Asymptomatic Hosts. PHYTOPATHOLOGY 2021; 111:149-159. [PMID: 33079020 DOI: 10.1094/phyto-06-20-0230-fi] [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: 06/11/2023]
Abstract
Verticillium dahliae is a soilborne fungal pathogen affecting many economically important crops that can also infect weeds and rotational crops with no apparent disease symptoms. The main research goal was to test the hypothesis that V. dahliae populations recovered from asymptomatic rotational crops and weed species are evolutionarily and genetically distinct from symptomatic hosts. We collected V. dahliae isolates from symptomatic and asymptomatic hosts growing in fields with histories of Verticillium wilt of potato in Israel and Pennsylvania (United States), and used genotyping-by-sequencing to analyze the evolutionary history and genetic differentiation between populations of different hosts. A phylogeny inferred from 26,934 single-nucleotide polymorphisms (SNPs) in 126 V. dahliae isolates displayed a highly clonal structure correlated with vegetative compatibility groups, and isolates grouped in lineages 2A, 2B824, 4A, and 4B, with 77% of the isolates in lineage 4B. The lineages identified in this study were differentiated by host of origin; we found 2A, 2B824, and 4A only in symptomatic hosts but isolates from asymptomatic hosts (weeds, oat, and sorghum) grouped exclusively within lineage 4B, and were genetically indistinguishable from 4B isolates sampled from symptomatic hosts (potato, eggplant, and avocado). Using coalescent analysis of 158 SNPs of lineage 4B, we inferred a genealogy with clades that correlated with geographic origin. In contrast, isolates from asymptomatic and symptomatic hosts shared some of the same haplotypes and were not differentiated. We conclude that asymptomatic weeds and rotational hosts may be potential reservoirs for V. dahliae populations of lineage 4B, which are pathogenic to many cultivated hosts.
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Affiliation(s)
- Laura S Bautista-Jalón
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Volcani Center, Rishon Lezion 7528809, Israel
| | - Leah Tsror Lahkim
- Department of Plant Pathology and Weed Research, Gilat Center, M.P. Negev, 8531100, Israel
| | - Glenna M Malcolm
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Sara Lebiush
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Marina Hazanovsky
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
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Dung JKS. Verticillium Wilt of Mint in the United States of America. PLANTS 2020; 9:plants9111602. [PMID: 33218083 PMCID: PMC7698963 DOI: 10.3390/plants9111602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022]
Abstract
Verticillium wilt, caused by the fungus Verticillium dahliae, is the most important and destructive disease of mint (Mentha spp.) in the United States (U.S.). The disease was first observed in commercial mint fields in the Midwestern U.S. in the 1920s and, by the 1950s, was present in mint producing regions of the U.S. Pacific Northwest. Verticillium wilt continues to be a major limiting factor in commercial peppermint (Mentha x piperita) and Scotch spearmint (Mentha x gracilis) production, two of the most important sources of mint oil in the U.S. The perennial aspect of U.S. mint production, coupled with the soilborne, polyetic nature of V. dahliae, makes controlling Verticillium wilt in mint a challenge. Studies investigating the biology and genetics of the fungus, the molecular mechanisms of virulence and resistance, and the role of soil microbiota in modulating host-pathogen interactions are needed to improve our understanding of Verticillium wilt epidemiology and inform novel disease management strategies. This review will discuss the history and importance of Verticillium wilt in commercial U.S. mint production, as well as provide a format to highlight past and recent research advances in an effort to better understand and manage the disease.
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Affiliation(s)
- Jeremiah K S Dung
- Central Oregon Agricultural Research and Extension Center, Department of Botany and Plant Pathology, Oregon State University, Madras, OR 97741, USA
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Wheeler DL, Johnson DA. Verticillium isaacii is a Pathogen and Endophyte of Potato and Sunflower in the Columbia Basin of Washington. PLANT DISEASE 2019; 103:3150-3153. [PMID: 31596689 DOI: 10.1094/pdis-04-19-0779-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The objective of this research was to test the hypothesis that Verticillium isaacii causes diseases of sunflower and potato plants. Two sunflower genotypes and one potato cultivar were inoculated with five V. isaacii isolates and three pathogenic V. dahliae isolates. Biomass, disease expression, and stem colonization were quantified. Overt wilt symptoms were observed on both sunflower genotypes and potato plants inoculated with a subset of the V. isaacii isolates. Biomass of both sunflower genotypes was not affected by V. isaacii infection. Tuber yields either decreased in response to infection by one V. isaacii isolate or were not affected by infection. Stems of sunflower and potato plants were infected by at least four of the five V. isaacii isolates. A new disease of sunflower and potato is documented. Evidence that V. isaacii exhibits different lifestyles including pathogenicity and endophytism is presented. Finally, this research documents variation in fungal lifestyles that can exist in samples from a single field.
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Affiliation(s)
- David Linnard Wheeler
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT
| | - Dennis A Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA
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7
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Dung JKS, Knaus BJ, Fellows HLS, Grünwald NJ, Vining KJ. Genetic Diversity of Verticillium dahliae Isolates From Mint Detected with Genotyping by Sequencing. PHYTOPATHOLOGY 2019; 109:1966-1974. [PMID: 31246137 DOI: 10.1094/phyto-12-18-0475-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Verticillium wilt is the most important disease threatening the commercial production of mint grown for essential oil. An important long-term goal for mint breeders is the production of cultivars with resistance to Verticillium wilt. Before that can be accomplished, a better understanding of the genetic variation within and among populations of Verticillium dahliae is needed. We characterized the extent of phenotypic and genetic diversity present in contemporary and archival populations of V. dahliae from mint fields in Oregon and other production regions of the United States using genotyping by sequencing, PCR assays for mating type and pathogenic race, vegetative compatibility group (VCG) tests, and aggressiveness assays. We report that the population in the Pacific Northwest can be described as one common genetic group and four relatively rare genetic groups. Eighty-three percent of the isolates belonged to VCG2B, and all isolates possessed the MAT1-2 idiomorph and were characterized as pathogenic race 2. These results indicate low levels of genetic diversity and a negligible risk of sexual recombination in populations of this host-adapted pathogen population. Knowledge of the genetic structure of V. dahliae in the Pacific Northwest will inform breeders about the diversity of pathogenicity factors that may need to be considered in their breeding programs.
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Affiliation(s)
- Jeremiah K S Dung
- Central Oregon Agricultural Research and Extension Center, Madras, OR 97741
| | - Brian J Knaus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Henry L S Fellows
- Department of Horticulture, Oregon State University, Corvallis, OR 97331
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97331
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331
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8
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Wheeler DL, Johnson DA. Does Coinoculation with Different Verticillium dahliae Genotypes Affect the Host or Fungus? PHYTOPATHOLOGY 2019; 109:780-786. [PMID: 30614378 DOI: 10.1094/phyto-11-18-0430-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Inferences about Verticillium dahliae are often deduced from experiments where hosts are inoculated with one isolate. The assumption that the outcomes from these experiments scale with V. dahliae diversity is untested. The objectives of this research were to test the hypotheses that (i) coinoculation with combinations of isolates affects plant biomass, disease expression, and fungal colonization; and (ii) hosts select for the specific isolates. Potato, mustard, and barley plants were coinoculated with seven combinations of three isolates. Genotypes recovered from infected plants were genotyped with microsatellite markers. Disease expression and fungal colonization but not plant biomass of potato was affected by coinoculation (F = 7.07, P < 0.0001; F = 2.36, P = 0.0427) and depended on the isolates with which plants were inoculated. One genotype was disproportionately selected for by all hosts. Putative heterokaryons were recovered from mustard plants coinoculated with isolates of different vegetative compatibility groups (VCG). These results support the assumption that mixed infections have marginal impacts on plant biomass but challenge the assumption that they do not affect disease expression and fungal colonization. Finally, this research provides evidence that plants select for specific V. dahliae genotypes and isolates from different VCGs can anastomose in planta.
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Wheeler DL, Dung JKS, Johnson DA. From pathogen to endophyte: an endophytic population of Verticillium dahliae evolved from a sympatric pathogenic population. THE NEW PHYTOLOGIST 2019; 222:497-510. [PMID: 30372525 DOI: 10.1111/nph.15567] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/18/2018] [Indexed: 05/27/2023]
Abstract
The fungus Verticillium dahliae causes wilts of several hundred plant species, including potato and mint. Verticillium spp. also colonize sympatric hosts such as mustards and grasses as endophytes. The evolutionary history of and interactions between pathogenic and endophytic of this fungus are unknown. Verticillium dahliae isolates recovered from sympatric potato, mint, mustard and grasses were characterized genotypically with microsatellite markers and phenotypically for pathogenicity. The evolutionary history of pathogenic and endophytic populations was reconstructed and gene flow between populations quantified. Verticillium dahliae was recovered from all hosts. Endophytic populations were genetically and genotypically similar to but marginally differentiated from the potato population, from which they evolved. Bidirectional migration was detected between these populations and endophytic isolates were pathogenic to potato and behaved as endophytes in mustard and barley. Verticillium dahliae colonizes plants as both endophytes and pathogens. A historical host-range expansion together with endophytic and pathogenic capabilities are likely to have enabled infection of and gene flow between asymptomatic and symptomatic host populations despite minor differentiation. The ability of hosts to harbor asymptomatic infections and the stability of asymptomatic infections over time warrants investigation to elucidate the mechanisms involved in the maintenance of endophytism and pathogenesis.
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Affiliation(s)
| | - Jeremiah Kam Sung Dung
- Department of Botany and Plant Pathology, Oregon State University, Madras, OR, 97741, USA
| | - Dennis Allen Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
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10
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Baroudy F, Putman AI, Habib W, Puri KD, Subbarao KV, Nigro F. Genetic Diversity of Verticillium dahliae Populations From Olive and Potato in Lebanon. PLANT DISEASE 2019; 103:656-667. [PMID: 30823856 DOI: 10.1094/pdis-03-18-0420-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Verticillium dahliae is widely distributed in potato and olive fields in Lebanon, causing serious economic losses. However, little is known about the inoculum source, population structure, and genetic diversity of the pathogen or the mechanisms of dissemination within Lebanon. To understand the population structure, a total of 203 isolates sampled from olive (n = 78) and potato (n = 125) were characterized for species, mating type, and race, and the genetic relationships were delineated using 13 microsatellite markers. All isolates except one from potato were V. dahliae, with 55.1 and 12.1% race 1, and 43.6 and 83.1% race 2 in olive and potato, respectively. The genetic structure of the studied population was best described by two large and two small clusters. Membership in the two large clusters was determined by the presence or absence of the effector gene Ave1. Furthermore, genetic structure was moderately associated with the host of origin but was weakly associated with the geographic origin. All but four isolates represented by three multilocus haploid genotypes were MAT1-2. This study identified a clear lack of gene flow between virulence genotypes of V. dahliae despite the proximity of these cropping systems and the wide distribution of genetic diversity among hosts and geographic regions in Lebanon.
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Affiliation(s)
- Farah Baroudy
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Alexander I Putman
- 3 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A.; and
| | - Wassim Habib
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Krishna D Puri
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Krishna V Subbarao
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Franco Nigro
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
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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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Wheeler DL, Scott J, Dung JKS, Johnson DA. Evidence of a trans-kingdom plant disease complex between a fungus and plant-parasitic nematodes. PLoS One 2019; 14:e0211508. [PMID: 30759127 PMCID: PMC6373923 DOI: 10.1371/journal.pone.0211508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/15/2019] [Indexed: 11/23/2022] Open
Abstract
Disease prediction tools improve management efforts for many plant diseases. Prediction and downstream prevention demand information about disease etiology, which can be complicated for some diseases, like those caused by soilborne microorganisms. Fortunately, the availability of machine learning methods has enabled researchers to elucidate complex relationships between hosts and pathogens without invoking difficult-to-satisfy assumptions. The etiology of a destructive plant disease, Verticillium wilt of mint, caused by the fungus Verticillium dahliae was reevaluated with several supervised machine learning methods. Specifically, the objective of this research was to identify drivers of wilt in commercial mint fields, describe the relationships between these drivers, and predict wilt. Soil samples were collected from commercial mint fields. Wilt foci, V. dahliae, and plant-parasitic nematodes that can exacerbate wilt were quantified. Multiple linear regression, a generalized additive model, random forest, and an artificial neural network were fit to the data, validated with 10-fold cross-validation, and measures of explanatory and predictive performance were compared. All models selected nematodes within the genus Pratylenchus as the most important predictor of wilt. The fungus after which this disease is named, V. dahliae, was the fourth most important predictor of wilt, after crop age and cultivar. All models explained around 50% of the total variation (R2 ≤ 0.46), and exhibited comparable predictive error (RMSE ≤ 1.21). Collectively, these models revealed that the quantitative relationships between two pathogens, mint cultivars and age are required to explain wilt. The ascendance of Pratylenchus spp. in predicting symptoms of a disease assumed to primarily be caused by V. dahliae exposes the underestimated contribution of these nematodes to wilt. This research provides a foundation on which predictive forecasting tools can be developed for mint growers and reminds us of the lessons that can be learned by revisiting assumptions about disease etiology.
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Affiliation(s)
- David Linnard Wheeler
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
| | - Jeness Scott
- Department of Botany and Plant Pathology, Oregon State University, Madras, OR, United States of America
| | - Jeremiah Kam Sung Dung
- Department of Botany and Plant Pathology, Oregon State University, Madras, OR, United States of America
| | - Dennis Allen Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
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Rafiei V, Banihashemi Z, Bautista-Jalon LS, Del Mar Jiménez-Gasco M, Turgeon BG, Milgroom MG. Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers. PHYTOPATHOLOGY 2018; 108:780-788. [PMID: 29318912 DOI: 10.1094/phyto-11-17-0360-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B824; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.
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Affiliation(s)
- Vahideh Rafiei
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
| | - Ziaeddin Banihashemi
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
| | - Laura S Bautista-Jalon
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
| | - Maria Del Mar Jiménez-Gasco
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
| | - B Gillian Turgeon
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
| | - Michael G Milgroom
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran; third and fourth authors: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park 16802; and fifth and sixth authors: School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York 14853
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Weiland JE, Benedict C, Zasada IA, Scagel CR, Beck BR, Davis A, Graham K, Peetz A, Martin RR, Dung JKS, Gaige AR, Thiessen L. Late-summer Disease Symptoms in Western Washington Red Raspberry Fields Associated with Co-Occurrence of Phytophthora rubi, Verticillium dahliae, and Pratylenchus penetrans, but not Raspberry bushy dwarf virus. PLANT DISEASE 2018; 102:938-947. [PMID: 30673387 DOI: 10.1094/pdis-08-17-1293-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sixty percent of the $109 million processed red raspberry industry of the United States occurs in northern Washington State. In 2012, late-summer symptoms of vascular wilt and root disease were observed in many raspberry plantings. These symptoms were initially attributed to Verticillium dahliae. However, diagnostic tests for the pathogen were often contradictory and other soilborne pathogens (Phytophthora rubi and Pratylenchus penetrans) or Raspberry bushy dwarf virus (RBDV) might also have been involved. Therefore, a survey was conducted in 2013 and 2014 to (i) establish the incidence and soil population levels of V. dahliae in red raspberry production fields, (ii) compare among diagnostic methods and laboratories for detecting and quantifying V. dahliae from raspberry field soil, and (iii) assess which pathogens are associated with late-summer disease symptoms of raspberry. Plant and soil samples were collected from 51 disease sites and 20 healthy sites located in 24 production fields. Samples were analyzed for the presence and quantity of each pathogen using traditional plating and extraction methods (V. dahliae, P. rubi, and P. penetrans), quantitative polymerase chain reaction (qPCR) (V. dahliae and P. rubi), and enzyme-linked immunosorbent assay (RBDV). Results showed that V. dahliae was present in 88% of the production fields and that detection of the pathogen differed by method and by laboratory: qPCR detected V. dahliae in the soil from approximately three times as many sites (51 of 71 total sites) as by plating on NP10 semi-selective medium (15 of 71 total sites). Soil populations of V. dahliae were slightly greater at disease sites, but the pathogen was detected with similar frequency from healthy sites and it was rarely isolated from diseased plants (4%). P. rubi, P. penetrans, and RBDV were also common in production fields (79, 91, and 53% of fields, respectively). Both P. rubi (soil and root samples) and P. penetrans (root populations only), but not RBDV, were more frequently found at disease sites than healthy sites, and the amount of P. rubi detected by qPCR was greater from disease sites than healthy sites. In addition, P. rubi was isolated from 27% of the symptomatic plants located at disease sites. Regardless of detection method, V. dahliae, P. rubi, and P. penetrans, either with or without RBDV, were more likely to co-occur at disease sites (73%) than healthy sites (35%), suggesting that a soilborne disease complex is present in raspberry production fields. Results indicate that P. rubi is the primary pathogen most strongly associated with late-summer symptoms of disease, but root populations of P. penetrans and higher soil populations of V. dahliae may also be of concern. Therefore, disease control methods should focus on all three soilborne pathogens.
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Affiliation(s)
- Jerry E Weiland
- United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Horticultural Crops Research Laboratory, Corvallis, OR 97330
| | - Chris Benedict
- Washington State University Whatcom County Extension, Bellingham 98225
| | | | | | - Bryan R Beck
- USDA-ARS, Horticultural Crops Research Laboratory
| | - Anne Davis
- USDA-ARS, Horticultural Crops Research Laboratory
| | - Kim Graham
- USDA-ARS, Horticultural Crops Research Laboratory
| | - Amy Peetz
- USDA-ARS, Horticultural Crops Research Laboratory
| | | | - Jeremiah K S Dung
- Oregon State University, Department of Botany and Plant Pathology, Corvallis 97331
| | - Andres Reyes Gaige
- Oregon State University, Department of Botany and Plant Pathology, Corvallis 97331
| | - Lindsey Thiessen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis 97331
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Martín-Sanz A, Rueda S, García-Carneros AB, González-Fernández S, Miranda-Fuentes P, Castuera-Santacruz S, Molinero-Ruiz L. Genetics, Host Range, and Molecular and Pathogenic Characterization of Verticillium dahliae From Sunflower Reveal Two Differentiated Groups in Europe. FRONTIERS IN PLANT SCIENCE 2018; 9:288. [PMID: 29593756 PMCID: PMC5855324 DOI: 10.3389/fpls.2018.00288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/19/2018] [Indexed: 05/13/2023]
Abstract
Verticillium wilt and leaf mottle of sunflower, caused by the fungus Verticillium dahliae (Vd) has become a major constraint to sunflower oil production in temperate European countries. Information about Vd from sunflower is very scarce despite genetics, molecular traits and pathogenic abilities of fungal strains affecting many other crops being widely known. Understanding and characterizing the diversity of Vd populations in those countries where sunflowers are frequent and severely affected by the fungus are essential for efficient breeding for resistance. In this study, we have analyzed genetic, molecular and pathogenic traits of Vd isolates affecting sunflower in European countries. When their genetics was investigated, almost all the isolates from France, Italy, Spain, Argentina, and Ukraine were assigned to vegetative compatibility group (VCG) 2B. In Bulgaria, Turkey, Romania, and Ukraine, some isolates were assigned to VCG6, but some others could not be assigned to any VCG. Genotyping markers used for Vd affecting crops other than sunflower showed that all the isolates were molecularly identified as race 2 and that markers of defoliating (D) and non-defoliating (ND) pathotypes distinguished two well-differentiated clusters, one (E) grouping those isolates from Eastern Europe and the other (W) all those from the Western Europe and Argentina. All the isolates in cluster W were VCG2B, while the isolates in cluster E belonged to an unknown VCG or to VCG6. When the host range was investigated in the greenhouse, the fungus was highly pathogenic to artichoke, showing the importance of farming alternatives in the management of Verticillium attacks. Sunflower genotypes were inoculated with a selection of isolates in two experiments. Two groups were identified, one including the isolates from Western Europe, Argentina, and Ukraine, and the other including isolates from Bulgaria, Romania, and Turkey. Three pathogenic races were differentiated: V1, V2-EE (Eastern Europe) and V2-WE (Western Europe). Similarly, three differentials are proposed for race identification: HA 458 (universal susceptible), HA 89 (resistant to V2-EE, susceptible to V2-WE) and INRA2603 (susceptible to V2-EE, resistant to V2-WE). The diversity found in Vd affecting sunflower must be taken into account in the search for resistance to the pathogen for European environments of sunflower production.
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Affiliation(s)
| | - Sandra Rueda
- Pioneer Hi-Bred International, Inc., La Rinconada, Spain
| | - Ana B. García-Carneros
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Sara González-Fernández
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Pedro Miranda-Fuentes
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Sandra Castuera-Santacruz
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
| | - Leire Molinero-Ruiz
- Department of Crop Protection, Institute for Sustainable Agriculture, Spanish National Research Council, Córdoba, Spain
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Frederick ZA, Cummings TF, Johnson DA. Susceptibility of Weedy Hosts from Pacific Northwest Potato Production Systems to Crop-Aggressive Isolates of Verticillium dahliae. PLANT DISEASE 2017; 101:1500-1506. [PMID: 30678582 DOI: 10.1094/pdis-01-17-0055-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Verticillium wilt, caused by Verticillium dahliae, is a disease of dicotyledonous crops such as potato and has a wide host range and persistent, long-term survival structures called microsclerotia that can persist in soil for up to 14 years. Some V. dahliae isolates are particularly aggressive on a specific plant host while retaining the ability to infect a wide range of other hosts. Weeds can serve as hosts for V. dahliae but whether they serve as sources of inoculum for aggressive isolates of V. dahliae to crop hosts is unknown. The goal of this research was to quantify V. dahliae microsclerotia obtained from 16 weeds which were grown in the greenhouse. Potting medium was infested with one of eight V. dahliae isolates from potato, mint, sugar beet, sunflower, tomato, and watermelon. The isolates from mint and potato were aggressive on the host from which they were originally isolated. All 16 weeds were infected by at least one V. dahliae isolate, although the number of microsclerotia produced from some infections was relatively low (≤5 microsclerotia/g of dry plant). Black nightshade yielded greater numbers of microsclerotia of the V. dahliae potato isolate than any other isolate in three of four trials in the greenhouse (second trial false discovery rate, adjusted P ≤ 0.0158; third trial, P ≤ 0.0264; and fourth trial, P ≤ 0.0193). Litchi tomato yielded greater numbers of microsclerotia of the V. dahliae potato isolate than any other isolate in one of four trials (first trial, P ≤ 0.0149). A V. dahliae isolate from tomato yielded greater numbers of microsclerotia in large crabgrass and wild oat in a second trial (P ≤ 0.0158). Weeds, depending on the species, grown during and between potato crop rotations may increase the number of microsclerotia of the potato-aggressive isolates of V. dahliae.
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Affiliation(s)
- Z A Frederick
- Department of Plant Pathology, Washington State University, Pullman 99164
| | - T F Cummings
- Department of Plant Pathology, Washington State University, Pullman 99164
| | - D A Johnson
- Department of Plant Pathology, Washington State University, Pullman 99164
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17
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Frederick ZA, Cummings TF, Brown CR, Quick RA, Johnson DA. Evaluation of Solanum sisymbriifolium as a Potential Inoculum Source of Verticillium dahliae and Colletotrichum coccodes. PLANT DISEASE 2017; 101:1300-1305. [PMID: 30682946 DOI: 10.1094/pdis-07-16-1077-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Solanum sisymbriifolium, the litchi tomato, is a perennial herbaceous plant from South America that is used as a trap crop to reduce soilborne populations of the pale cyst nematode Globodera pallida, an important potato pathogen. Possible interactions of soilborne potato pathogens Verticillium dahliae and Colletotrichum coccodes with litchi tomato are unknown, yet important for potato production if litchi tomato is to be planted as a trap crop. The goal of this research was to quantitatively assess if litchi tomato is a potential inoculum source for C. coccodes and V. dahliae by comparing colony forming units (CFU) observed in litchi tomato to susceptible and resistant potato cultivars. The potato cvs. Alturas (P = 0.0003), Ranger Russet (P = 0.0193), and Russet Norkotah (P = 0.0022) produced more CFUs of the potato pathotype of V. dahliae than litchi tomato the first of two years of greenhouse trials. Significantly more CFUs of the potato pathotype of V. dahliae were quantified from stems and roots of only cv. Russet Norkotah compared with litchi tomato (P = 0.0001) in the second year. The CFUs for C. coccodes varied between litchi tomato and the potato cvs., perhaps due to varying levels of resistance since litchi tomato is from a selected intermated seed source. Based on these data, the effect of litchi tomato in rotation with potato is likely to have limited effect on the proliferation of V. dahliae or C. coccodes populations in the soil when compared with a susceptible potato cultivar.
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Affiliation(s)
- Z A Frederick
- Department of Plant Pathology, Washington State University, Pullman, 99164
| | - T F Cummings
- Department of Plant Pathology, Washington State University, Pullman, 99164
| | - C R Brown
- United States Department of Agriculture, Agricultural Research Service, Prosser, WA 99350
| | - R A Quick
- United States Department of Agriculture, Agricultural Research Service, Prosser, WA 99350
| | - D A Johnson
- Department of Plant Pathology, Washington State University, Pullman, 99164
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18
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Milgroom MG, Del Mar Jiménez-Gasco M, Olivares-García C, Jiménez-Díaz RM. Clonal Expansion and Migration of a Highly Virulent, Defoliating Lineage of Verticillium dahliae. PHYTOPATHOLOGY 2016; 106:1038-46. [PMID: 27050569 DOI: 10.1094/phyto-11-15-0300-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We used a population genomics approach to test the hypothesis of clonal expansion of a highly fit genotype in populations of Verticillium dahliae. This fungal pathogen has a broad host range and can be dispersed in contaminated seed or other plant material. It has a highly clonal population structure, with several lineages having nearly worldwide distributions in agricultural crops. Isolates in lineage 1A are highly virulent and cause defoliation in cotton, okra, and olive (denoted 1A/D), whereas those in other lineages cause wilting but not defoliation (ND). We tested whether the highly virulent lineage 1A/D could have spread from the southwestern United States to the Mediterranean basin, as predicted from historical records. We found 187 single-nucleotide polymorphisms (SNPs), determined by genotyping by sequencing, among 91 isolates of lineage 1A/D and 5 isolates in the closely related lineage 1B/ND. Neighbor-joining and maximum-likelihood analyses on the 187 SNPs showed a clear divergence between 1A/D and 1B/ND haplotypes. Data for only 77 SNPs were obtained for all 96 isolates (no missing data); lineages 1A/D and 1B/ND differed by 27 of these 77 SNPs, confirming a clear divergence between the two lineages. No evidence of recombination was detected within or between these two lineages. Phylogenetic and genealogical analyses resulted in five distinct subclades of 1A/D isolates that correlated closely with geographic origins in the Mediterranean basin, consistent with the hypothesis that the D pathotype was introduced at least five times in independent founder events into this region from a relatively diverse source population. The inferred ancestral haplotype was found in two isolates sampled before 1983 from the southwestern United States, which is consistent with historical records that 1A/D originated in North America. The five subclades coalesce with the ancestral haplotype at the same time, consistent with a hypothesis of rapid population expansion in the source population during the emergence of 1A/D as a severe pathogen of cotton in the United States.
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Affiliation(s)
- Michael G Milgroom
- First author: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853; second author: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802; and third and fourth authors: College of Agriculture and Forestry (ETSIAM), University of Córdoba, and Institute for Sustainable Agriculture (IAS), CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, P.O. Box 4084, 14080, Córdoba, Spain
| | - María Del Mar Jiménez-Gasco
- First author: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853; second author: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802; and third and fourth authors: College of Agriculture and Forestry (ETSIAM), University of Córdoba, and Institute for Sustainable Agriculture (IAS), CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, P.O. Box 4084, 14080, Córdoba, Spain
| | - Concepción Olivares-García
- First author: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853; second author: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802; and third and fourth authors: College of Agriculture and Forestry (ETSIAM), University of Córdoba, and Institute for Sustainable Agriculture (IAS), CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, P.O. Box 4084, 14080, Córdoba, Spain
| | - Rafael M Jiménez-Díaz
- First author: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853; second author: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802; and third and fourth authors: College of Agriculture and Forestry (ETSIAM), University of Córdoba, and Institute for Sustainable Agriculture (IAS), CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, P.O. Box 4084, 14080, Córdoba, Spain
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Wheeler DL, Johnson DA. Verticillium dahliae Infects, Alters Plant Biomass, and Produces Inoculum on Rotation Crops. PHYTOPATHOLOGY 2016; 106:602-13. [PMID: 26828231 DOI: 10.1094/phyto-07-15-0174-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Verticillium wilt, caused by Verticillium dahliae, reduces yields of potato and mint. Crop rotation is a potential management tactic for Verticillium wilt; however, the wide host range of V. dahliae may limit the effectiveness of this tactic. The hypothesis that rotation crops are infected by V. dahliae inoculum originating from potato and mint was tested by inoculation of mustards, grasses, and Austrian winter pea with eight isolates of V. dahliae. Inoculum density was estimated from plants and soil. Typical wilt symptoms were not observed in any rotation crop but plant biomass of some crops was reduced, not affected, or increased by infection of specific isolates. Each isolate was host-specific and infected a subset of the rotation crops tested but microsclerotia from at least one isolate were observed on each rotation crop. Some isolates were host-adapted and differentially altered plant biomass or produced differential amounts of inoculum on rotation crops like arugula and Austrian winter pea, which supported more inoculum of specific isolates than potato. Evidence of asymptomatic and symptomatic infection and differential inoculum formation of V. dahliae on rotation crops presented here will be useful in designing rotations for management of Verticillium wilt.
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Affiliation(s)
- D L Wheeler
- Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - D A Johnson
- Department of Plant Pathology, Washington State University, Pullman 99164-6430
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20
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Gao W, Long L, Xu L, Lindsey K, Zhang X, Zhu L. Suppression of the homeobox gene HDTF1 enhances resistance to Verticillium dahliae and Botrytis cinerea in cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:503-13. [PMID: 26407676 DOI: 10.1111/jipb.12432] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 09/21/2015] [Indexed: 05/21/2023]
Abstract
Development of pathogen-resistant crops, such as fungus-resistant cotton, has significantly reduced chemical application and improved crop yield and quality. However, the mechanism of resistance to cotton pathogens such as Verticillium dahliae is still poorly understood. In this study, we characterized a cotton gene (HDTF1) that was isolated following transcriptome profiling during the resistance response of cotton to V. dahliae. HDTF1 putatively encodes a homeodomain transcription factor, and its expression was found to be down-regulated in cotton upon inoculation with V. dahliae and Botrytis cinerea. To characterise the involvement of HDTF1 in the response to these pathogens, we used virus-induced gene silencing (VIGS) to generate HDTF1-silenced cotton. VIGS reduction in HDTF1 expression significantly enhanced cotton plant resistance to both pathogens. HDTF1 silencing resulted in activation of jasmonic acid (JA)-mediated signaling and JA accumulation. However, the silenced plants were not altered in the accumulation of salicylic acid (SA) or the expression of marker genes associated with SA signaling. These results suggest that HDTF1 is a negative regulator of the JA pathway, and resistance to V. dahliae and B. cinerea can be engineered by activation of JA signaling.
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Affiliation(s)
- Wei Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lu Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Li Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Keith Lindsey
- Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, University of Durham, Durham, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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21
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Short DPG, Gurung S, Gladieux P, Inderbitzin P, Atallah ZK, Nigro F, Li G, Benlioglu S, Subbarao KV. Globally invading populations of the fungal plant pathogen Verticillium dahliae are dominated by multiple divergent lineages. Environ Microbiol 2015; 17:2824-40. [PMID: 25630463 DOI: 10.1111/1462-2920.12789] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 11/28/2022]
Abstract
The spread of aggressive fungal pathogens into previously non-endemic regions is a major threat to plant health and food security. Analyses of the spatial and genetic structure of plant pathogens offer valuable insights into their origin, dispersal mechanisms and evolution, and have been useful to develop successful disease management strategies. Here, we elucidated the genetic diversity, population structure and demographic history of worldwide invasion of the ascomycete Verticillium dahliae, a soil-borne pathogen, using a global collection of 1100 isolates from multiple plant hosts and countries. Seven well-differentiated genetic clusters were revealed through discriminant analysis of principal components (DAPC), but no strong associations between these clusters and host/geographic origin of isolates were found. Analyses of clonal evolutionary relationships among multilocus genotypes with the eBURST algorithm and analyses of genetic distances revealed that genetic clusters represented several ancient evolutionary lineages with broad geographic distribution and wide host range. Comparison of different scenarios of demographic history using approximate Bayesian computations revealed the branching order among the different genetic clusters and lineages. The different lineages may represent incipient species, and this raises questions with respect to their evolutionary origin and the factors allowing their maintenance in the same areas and same hosts without evidence of admixture between them. Based on the above findings and the biology of V. dahliae, we conclude that anthropogenic movement has played an important role in spreading V. dahliae lineages. Our findings have implications for the development of management strategies such as quarantine measures and crop resistance breeding.
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Affiliation(s)
- Dylan P G Short
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Suraj Gurung
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Pierre Gladieux
- Ecologie Systematique Evolution, CNRS, Université Paris Sud, Orsay, F-91405, France
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Zahi K Atallah
- Department of Advanced Technology, Hartnell College, Salinas, CA, 93905, USA
| | - Franco Nigro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Bari, 70126, Italy
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
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23
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Milgroom MG, Jiménez-Gasco MDM, Olivares García C, Drott MT, Jiménez-Díaz RM. Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. PLoS One 2014; 9:e106740. [PMID: 25181515 PMCID: PMC4152335 DOI: 10.1371/journal.pone.0106740] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/09/2014] [Indexed: 11/18/2022] Open
Abstract
Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.
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Affiliation(s)
- Michael G. Milgroom
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Concepción Olivares García
- College of Agriculture and Forestry, University of Córdoba, and Institute for Sustainable Agriculture, CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
| | - Milton T. Drott
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Rafael M. Jiménez-Díaz
- College of Agriculture and Forestry, University of Córdoba, and Institute for Sustainable Agriculture, CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
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Jiménez-Gasco MDM, Malcolm GM, Berbegal M, Armengol J, Jiménez-Díaz RM. Complex molecular relationship between vegetative compatibility groups (VCGs) in Verticillium dahliae: VCGs do not always align with clonal lineages. PHYTOPATHOLOGY 2014; 104:650-659. [PMID: 24328492 DOI: 10.1094/phyto-07-13-0180-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Verticillium wilts caused by the soilborne fungus Verticillium dahliae are among the most challenging diseases to control. Populations of this pathogen have been traditionally studied by means of vegetative compatibility groups (VCGs) under the assumption that VCGs comprise genetically related isolates that correlate with clonal lineages. We aimed to resolve the phylogenetic relationships among VCGs and their subgroups based on sequences of the intergenic spacer region (IGS) of the ribosomal DNA and six anonymous polymorphic sequences containing single-nucleotide polymorphisms (VdSNPs). A collection of 68 V. dahliae isolates representing the main VCGs and subgroups (VCGs 1A, 1B, 2A, 2B, 3, 4A, 4B, and 6) from different geographic origins and hosts was analyzed using the seven DNA regions. Maximum parsimony (MP) phylogenies inferred from IGS and VdSNP sequences showed five and six distinct clades, respectively. Phylogenetic analyses of individual and combined data sets indicated that certain VCG subgroups (e.g., VCGs 1A and 1B) are closely related and share a common ancestor; however, other subgroups (e.g., VCG 4B) are more closely related to members of a different VCG (e.g., VCG 2A) than to subgroups of the same VCG (VCG 4B). Furthermore, MP analyses indicated that VCG 2B is polyphyletic, with isolates placed in at least three distinct phylogenetic lineages based on IGS sequences and two lineages based on VdSNP sequences. Results from our study suggest the existence of main VCG lineages that contain VCGs 1A and 1B; VCGs 2A and 4B; and VCG 4A, for which both phylogenies agree; and the existence of other VCGs or VCG subgroups that seem to be genetically heterogeneous or show discrepancies in their phylogenetic placement: VCG 2B, VCG 3, and VCG 6. These results raise important caveats regarding the interpretation of VCG analyses: genetic homogeneity and close evolutionary relationship between members of a VCG should not be assumed.
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Gurung S, Short DPG, Atallah ZK, Subbarao KV. Clonal expansion of Verticillium dahliae in lettuce. PHYTOPATHOLOGY 2014; 104:641-9. [PMID: 24476528 DOI: 10.1094/phyto-10-13-0282-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Few studies in population biology have documented how structure and diversity of pathogens evolve over time at local scales. With the historical samples of Verticillium dahliae available from lettuce, we investigated the structure and diversity of this pathogen in time and space. Three hundred twenty-nine V. dahliae isolates from lettuce fields collected over 18 years were characterized with polymorphic microsatellite markers and polymerase chain reaction tests for race and mating type. Genetic variation within and among commercial lettuce fields in a single season was also investigated using an additional 146 isolates. Sixty-two haplotypes (HTs) were observed among the 329 isolates. A single HT was frequently observed over multiple years and locations (61.40%). Genetic diversity, allelic richness, and private allelic richness suggested a relatively recent clonal expansion. Race 1 (93.63%) and MAT1-2-1 (99.69%) were overwhelmingly represented among the isolates. Linkage disequilibrium was significant (P < 0.001) for all populations, suggesting limited sexual recombination in the sampled populations from lettuce. Populations from 2006, 2009, and 2010 had higher numbers of unique HTs, implying a recent introduction of novel HTs. We conclude that V. dahliae population from lettuce evaluated in this study is expanding clonally, consistent with an asexually reproducing pathogen, and the movement of clonal genotypes locally occurs over time.
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