1
|
Singh R, Caseys C, Kliebenstein DJ. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2024; 25:e13404. [PMID: 38037862 PMCID: PMC10788480 DOI: 10.1111/mpp.13404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity of B. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combat B. cinerea. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botrytis, species: cinerea. HOST RANGE B. cinerea infects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts of B. cinerea. GENETIC DIVERSITY This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PATHOGENICITY Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. DISEASE CONTROL STRATEGIES Efforts to control B. cinerea, being a high-diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.
Collapse
Affiliation(s)
- Ritu Singh
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
| | - Celine Caseys
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
| | | |
Collapse
|
2
|
Pearce TL, Scott JB, Wilson CR, Gent DH. Evolution of the Genetic Structure of the Didymella tanaceti Population During Development of Succinate Dehydrogenase Inhibitor Resistance. PHYTOPATHOLOGY 2023; 113:1946-1958. [PMID: 37129263 DOI: 10.1094/phyto-10-22-0385-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: 05/03/2023]
Abstract
Emergence of pathogens with decreased sensitivity to succinate dehydrogenase inhibitor fungicides is a global agronomical issue. Analysis of Didymella tanaceti isolates (n = 173), which cause tan spot of pyrethrum (Tanacetum cinerariifolium), collected prior to (2004 to 2005) and after (2009, 2010, 2012, and 2014) the commercial implementation of boscalid in Tasmanian pyrethrum fields identified that insensitivity developed over time and has become widespread. To evaluate temporal change, isolates were characterized for frequency of mutations in the succinate dehydrogenase (Sdh) B, C, and D subunits associated with boscalid resistance, mating type, and SSR genotype. All isolates from 2004 and 2005 exhibited wild-type (WT) Sdh alleles. Seven known Sdh substitutions were identified in isolates collected from 2009 to 2014. In 2009, 60.7% had Sdh substitutions associated with boscalid resistance in D. tanaceti. The frequency of WT isolates decreased over time, with no WT isolates identified in 2014. The frequency of the SdhB-H277Y genotype increased from 10.7 to 77.8% between 2009 and 2014. Genotypic evidence suggested that a shift in the population structure occurred between 2005 and 2009, with decreases in gene diversity (uh; 0.51 to 0.34), genotypic evenness (E5; 0.96 to 0.67), genotypic diversity (G; 9.3 to 6.8), and allele frequencies. No evidence was obtained to support the rapid spread of Sdh genotypes by clonal expansion of the population. Thus, insensitivity to boscalid has developed and become widespread within a diverse population within 4 years of usage. These results suggest that D. tanaceti can disperse insensitivity through repeated frequent mutation, sexual recombination, or a combination of both.
Collapse
Affiliation(s)
- Tamieka L Pearce
- Tasmanian Institute of Agriculture, College of Sciences and Engineering, University of Tasmania, Burnie, Tasmania 7320, Australia
| | - Jason B Scott
- Tasmanian Institute of Agriculture, College of Sciences and Engineering, University of Tasmania, Burnie, Tasmania 7320, Australia
| | - Calum R Wilson
- Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005
| | - David H Gent
- U.S. Department of Agriculture-Agriculture Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| |
Collapse
|
3
|
Wang X, Mattupalli C, Chastagner G, Tymon L, Wu Z, Jung S, Liu H, DeVetter LW. Physical characteristics of soil-biodegradable and nonbiodegradable plastic mulches impact conidial splash dispersal of Botrytis cinerea. PLoS One 2023; 18:e0285094. [PMID: 37155671 PMCID: PMC10166481 DOI: 10.1371/journal.pone.0285094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Botrytis cinerea causes gray mold disease of strawberry (Fragaria ×ananassa) and is a globally important pathogen that causes fruit rot both in the field and after harvest. Commercial strawberry production involves the use of plastic mulches made from non-degradable polyethylene (PE), with weedmat made from woven PE and soil-biodegradable plastic mulch (BDM) as emerging mulch technologies that may enhance sustainable production. Little is known regarding how these plastic mulches impact splash dispersal of B. cinerea conidia. The objective of this study was to investigate splash dispersal dynamics of B. cinerea when exposed to various plastic mulch surfaces. Mulch surface physical characteristics and conidial splash dispersal patterns were evaluated for the three mulches. Micrographs revealed different surface characteristics that have the potential to influence splash dispersal: PE had a flat, smooth surface, whereas weedmat had large ridges and BDM had an embossed surface. Both PE mulch and BDM were impermeable to water whereas weedmat was semi-permeable. Results generated using an enclosed rain simulator system showed that as the horizontal distance from the inoculum source increased, the number of splash dispersed B. cinerea conidia captured per plate decreased for all mulch treatments. More than 50% and approximately 80% of the total number of dispersed conidia were found on plates 10 and 16 cm away from the inoculum source across all treatments, respectively. A significant correlation between the total and germinated conidia on plates across all mulch treatments was detected (P<0.01). Irrespective of distance from the inoculum source, embossed BDM facilitated higher total and germinated splashed conidia (P<0.001) compared to PE mulch and weedmat (P = 0.43 and P = 0.23, respectively), indicating BDM's or embossed film's potential for enhancing B. cinerea inoculum availability in strawberry production under plasticulture. However, differences in conidial concentrations observed among treatments were low and may not be pathologically relevant.
Collapse
Affiliation(s)
- Xuechun Wang
- Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, Washington, United States of America
| | - Chakradhar Mattupalli
- Department of Plant Pathology, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, Washington, United States of America
| | - Gary Chastagner
- Department of Plant Pathology, Washington State University, Puyallup Research and Extension Center, Puyallup, Washington, United States of America
| | - Lydia Tymon
- Department of Plant Pathology, Washington State University, Puyallup Research and Extension Center, Puyallup, Washington, United States of America
| | - Zixuan Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Sunghwan Jung
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Hang Liu
- Department of Apparel, Merchandising, Design and Textiles, Washington State University, Pullman, Washington, United States of America
| | - Lisa Wasko DeVetter
- Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, Washington, United States of America
| |
Collapse
|
4
|
Naegele RP, Abdelsamad N, DeLong JA, Saito S, Xiao CL, Miles TD. Fungicide Resistance and Host Influence on Population Structure in Botrytis spp. from Specialty Crops in California. PHYTOPATHOLOGY 2022; 112:2549-2559. [PMID: 35801851 DOI: 10.1094/phyto-03-22-0070-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: 06/15/2023]
Abstract
Botrytis is an important genus of plant pathogens causing pre- and postharvest disease on diverse crops worldwide. This study evaluated Botrytis isolates collected from strawberry, blueberry, and table grape berries in California. Isolates were evaluated for resistance to eight different fungicides, and 60 amplicon markers were sequenced (neutral, species identification, and fungicide resistance associated) distributed across 15 of the 18 B. cinerea chromosomes. Fungicide resistance was common among the populations, with resistance to pyraclostrobin and boscalid being most frequent. Isolates from blueberry had resistance to the least number of fungicides, whereas isolates from strawberry had resistance to the highest number. Host and fungicide resistance-specific population structure explained 12 and 7 to 26%, respectively, of the population variability observed. Fungicide resistance was the major driver for population structure, with select fungicides explaining up to 26% and multiple fungicide resistance explaining 17% of the variability observed. Shared and unique significant single-nucleotide polymorphisms (SNPs) associated with host and fungicide (fluopyram, thiabendazole, pyraclostrobin, and fenhexamid) resistance-associated population structures were identified. Although overlap between host and fungicide resistance SNPs were detected, unique SNPs suggest that both host and fungicide resistance play an important role in Botrytis population structure.
Collapse
Affiliation(s)
- Rachel P Naegele
- U.S. Department of Agriculture-Agricultural Research Service, 9611 S. Riverbend Ave., Parlier, CA 93648
| | - Noor Abdelsamad
- U.S. Department of Agriculture-Agricultural Research Service, 9611 S. Riverbend Ave., Parlier, CA 93648
| | - Jeff A DeLong
- U.S. Department of Agriculture-Agricultural Research Service, 9611 S. Riverbend Ave., Parlier, CA 93648
| | - Seiya Saito
- U.S. Department of Agriculture-Agricultural Research Service, 9611 S. Riverbend Ave., Parlier, CA 93648
| | - Chang-Lin Xiao
- U.S. Department of Agriculture-Agricultural Research Service, 9611 S. Riverbend Ave., Parlier, CA 93648
| | - Timothy D Miles
- Michigan State University, Plant Pathology, 426 Auditorium Road, East Lansing, MI 48824
| |
Collapse
|
5
|
Makris G, Nikoloudakis N, Samaras A, Karaoglanidis GS, Kanetis LI. Under Pressure: A Comparative Study of Botrytis cinerea Populations from Conventional and Organic Farms in Cyprus and Greece. PHYTOPATHOLOGY 2022; 112:2236-2247. [PMID: 35671479 DOI: 10.1094/phyto-12-21-0510-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: 06/15/2023]
Abstract
The highly heterogeneous nature of Botrytis cinerea provides adaptive benefits to variable environmental regimes. Disentangling pathogen population structure in anthropogenic agroecosystems is crucial to designing more effective management schemes. Herein, we studied how evolutionary forces exerted in different farming systems, in terms of agrochemicals-input, shape B. cinerea populations. In total, 360 B. cinerea isolates were collected from conventional and organic, strawberry and tomato farms in Cyprus and Greece. The occurrence and frequency of sensitivities to seven botryticides were estimated. Results highlighted widespread fungicide resistance in conventional farms since only 15.5% of the isolates were sensitive. A considerable frequency of fungicide-resistant isolates was also detected in the organic farms (14.9%). High resistance frequencies were observed for boscalid (67.7%), pyraclostrobin (67.3%), cyprodinil (65.9%), and thiophanate-methyl (61.4%) in conventional farms, while high levels of multiple fungicide resistance were also evident. Furthermore, B. cinerea isolates were genotyped using a set of seven microsatellite markers (simple sequence repeat [SSR] markers). Index of association analyses (Ia and rBarD) suggest asexual reproduction of the populations, even though the mating-type idiomorphs were equally distributed, indicating frequency-dependent selection. Fungicide resistance was correlated with farming systems across countries and crops, while SSRs were able to detect population structure associated with resistance to thiophanate-methyl, pyraclostrobin, boscalid, and cyprodinil. The expected heterozygosity in organic farms was significantly higher than in conventional, suggesting the absence of selective pressure that may change the allelic abundance in organic farms. However, genetic variance among strawberry and tomato populations was high, ranking host specificity higher than other selection forces studied.
Collapse
Affiliation(s)
- Georgios Makris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Nikolaos Nikoloudakis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Anastasios Samaras
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Georgios S Karaoglanidis
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Loukas I Kanetis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| |
Collapse
|
6
|
Crandall SG, Spychalla J, Crouch UT, Acevedo FE, Naegele RP, Miles TD. Rotting Grapes Don't Improve with Age: Cluster Rot Disease Complexes, Management, and Future Prospects. PLANT DISEASE 2022; 106:2013-2025. [PMID: 35108071 DOI: 10.1094/pdis-04-21-0695-fe] [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: 06/14/2023]
Abstract
Cluster rots can be devastating to grape production around the world. There are several late-season rots that can affect grape berries, including Botrytis bunch rot, sour rot, black rot, Phomopsis fruit rot, bitter rot, and ripe rot. Tight-clustered varieties such as 'Pinot gris', 'Pinot noir', and 'Vignoles' are particularly susceptible to cluster rots. Symptoms or signs for these rots range from discolored berries or gray-brown sporulation in Botrytis bunch rot to sour rot, which smells distinctly of vinegar due to the presence of acetic acid bacteria. This review discusses the common symptoms and disease cycles of these different cluster rots. It also includes useful updates on disease diagnostics and management practices, including cultural practices in commercial vineyards and future prospects for disease management. By understanding what drives the development of different cluster rots, researchers will be able to identify new avenues for research to control these critical pathogens.
Collapse
Affiliation(s)
- Sharifa G Crandall
- Pennsylvania State University, Department of Plant Pathology & Environmental Microbiology, University Park, PA 16802
| | - Jamie Spychalla
- Pennsylvania State University, Department of Plant Pathology & Environmental Microbiology, University Park, PA 16802
| | - Uma T Crouch
- Pennsylvania State University, Department of Plant Pathology & Environmental Microbiology, University Park, PA 16802
| | - Flor E Acevedo
- Pennsylvania State University, Department of Entomology, University Park, PA 16802
| | - Rachel P Naegele
- United States Department of Agriculture-Agricultural Research Station, Parlier, CA 93648
| | - Timothy D Miles
- Michigan State University, Department of Plant, Soil and Microbial Sciences, East Lansing, MI 48824
| |
Collapse
|
7
|
Naegele RP, DeLong J, Alzohairy SA, Saito S, Abdelsamad N, Miles TD. Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach. Front Microbiol 2021; 12:660874. [PMID: 33959117 PMCID: PMC8093758 DOI: 10.3389/fmicb.2021.660874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022] Open
Abstract
As sequencing costs continue to decrease, new tools are being developed for assessing pathogen diversity and population structure. Traditional marker types, such as microsatellites, are often more cost effective than single-nucleotide polymorphism (SNP) panels when working with small numbers of individuals, but may not allow for fine scale evaluation of low or moderate structure in populations. Botrytis cinerea is a necrotrophic plant pathogen with high genetic variability that can infect more than 200 plant species worldwide. A panel of 52 amplicons were sequenced for 82 isolates collected from four Michigan vineyards representing 2 years of collection and varying fungicide resistance. A panel of nine microsatellite markers previously described was also tested across 74 isolates from the same population. A microsatellite and SNP marker analysis of B. cinerea populations was performed to assess the genetic diversity and population structure of Michigan vineyards, and the results from both marker types were compared. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and multiple fungicide resistance (MFR). Microsatellites were also able to differentiate population structure associated with another fungicide, fluopyram, while SNPs were able to additionally differentiate structure based on year. For both methods, AMOVA results were similar, with microsatellite results explaining a smaller portion of the variation compared with the SNP results. The SNP-based markers presented here were able to successfully differentiate population structure similar to microsatellite results. These SNP markers represent new tools to discriminate B. cinerea isolates within closely related populations using multiple targeted sequences.
Collapse
Affiliation(s)
- Rachel P Naegele
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Jeff DeLong
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Safa A Alzohairy
- Small Fruit and Hop Pathology Laboratory, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Seiya Saito
- Commodity Protection and Quality Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Noor Abdelsamad
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Timothy D Miles
- Small Fruit and Hop Pathology Laboratory, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| |
Collapse
|