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Knapp SJ, Cole GS, Pincot DDA, Dilla-Ermita CJ, Bjornson M, Famula RA, Gordon TR, Harshman JM, Henry PM, Feldmann MJ. Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance to Macrophomina in strawberry. HORTICULTURE RESEARCH 2024; 11:uhad289. [PMID: 38487295 PMCID: PMC10939388 DOI: 10.1093/hr/uhad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/17/2023] [Indexed: 03/17/2024]
Abstract
Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pathogen, began surfacing in California, Florida, and elsewhere. This disease has since become one of the most common causes of plant death and yield losses in strawberry. The Macrophomina problem emerged and expanded in the wake of the global phase-out of soil fumigation with methyl bromide and appears to have been aggravated by an increase in climate change-associated abiotic stresses. Here we show that sources of resistance to this pathogen are rare in gene banks and that the favorable alleles they carry are phenotypically unobvious. The latter were exposed by transgressive segregation and selection in populations phenotyped for resistance to Macrophomina under heat and drought stress. The genetic gains were immediate and dramatic. The frequency of highly resistant individuals increased from 1% in selection cycle 0 to 74% in selection cycle 2. Using GWAS and survival analysis, we found that phenotypic selection had increased the frequencies of favorable alleles among 10 loci associated with resistance and that favorable alleles had to be accumulated among four or more of these loci for an individual to acquire resistance. An unexpectedly straightforward solution to the Macrophomina disease resistance breeding problem emerged from our studies, which showed that highly resistant cultivars can be developed by genomic selection per se or marker-assisted stacking of favorable alleles among a comparatively small number of large-effect loci.
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Affiliation(s)
- Steven J Knapp
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christine Jade Dilla-Ermita
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal Street, CA 93905, USA
| | - Marta Bjornson
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Thomas R Gordon
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Julia M Harshman
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Peter M Henry
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal Street, CA 93905, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Shirai M, Eulgem T. Molecular interactions between the soilborne pathogenic fungus Macrophomina phaseolina and its host plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1264569. [PMID: 37780504 PMCID: PMC10539690 DOI: 10.3389/fpls.2023.1264569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Mentioned for the first time in an article 1971, the occurrence of the term "Macrophomina phaseolina" has experienced a steep increase in the scientific literature over the past 15 years. Concurrently, incidences of M. phaseolina-caused crop diseases have been getting more frequent. The high levels of diversity and plasticity observed for M. phasolina genomes along with a rich equipment of plant cell wall degrading enzymes, secondary metabolites and putative virulence effectors as well as the unusual longevity of microsclerotia, their asexual reproduction structures, make this pathogen very difficult to control and crop protection against it very challenging. During the past years several studies have emerged reporting on host defense measures against M. phaseolina, as well as mechanisms of pathogenicity employed by this fungal pathogen. While most of these studies have been performed in crop systems, such as soybean or sesame, recently interactions of M. phaseolina with the model plant Arabidopsis thaliana have been described. Collectively, results from various studies are hinting at a complex infection cycle of M. phaseolina, which exhibits an early biotrophic phase and switches to necrotrophy at later time points during the infection process. Consequently, responses of the hosts are complex and seem coordinated by multiple defense-associated phytohormones. However, at this point no robust and strong host defense mechanism against M. phaseolina has been described.
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Affiliation(s)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany & Plant Sciences, University of California at Riverside, Riverside, CA, United States
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Baggio JS, Cordova LG, Toledo BF, Noling JW, Peres NA. A reassessment of the fungicidal efficacy of 1,3-dichloropropene, chloropicrin, and metam potassium against Macrophomina phaseolina in strawberry. PEST MANAGEMENT SCIENCE 2022; 78:3416-3423. [PMID: 35544358 DOI: 10.1002/ps.6982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The effectiveness of metam potassium, 1,3-dichloropropene, chloropicrin, and different ratios of 1,3-dichloropropene and chloropicrin on the reduction of natural and artificial inoculum of Macrophomina phaseolina were investigated in laboratory and field experiments. Additionally, a multivariate meta-analysis with data from six field trials conducted in Florida from 2012 to 2018 was performed. RESULTS In small-plot field experiments using drip stakes, the highest rate (468 L ha-1 ) of metam potassium was most effective in controlling M. phaseolina in infected crowns buried at 15.2 cm from the point of fumigant injection, whereas none of the rates was able to reduce inoculum buried at 30.5 cm. In closed-container experiments, use of the highest rate of 1,3-dichloropropene (168 kg ha-1 ) resulted in the highest level of pathogen control. Different rates of chloropicrin also reduced inoculum when compared to the non-treated control. 1,3-dichloropropene + chloropicrin at different ratios were also highly effective in controlling M. phaseolina. Results from the meta-analysis of open-field experiments indicated that metam potassium and 1,3-dichloropropene + chloropicrin (63:35, v:v) treatments were significantly more effective in reducing M. phaseolina than the 1,3-dichloropropene + chloropicrin (39:60, v:v) treatment; however, metam potassium was not as effective at the side of the beds. CONCLUSION 1,3-dichloropropene alone and in mixture with chloropicrin were more effective in reducing inoculum of M. phaseolina than chloropicrin alone, indicating the fungicidal efficacy of 1,3-dichloropropene. Formulation with higher 1,3-dichloropropene concentration performed better than the formulation with higher chloropicrin concentration in field trials. Metam potassium was effective when applied at the highest rate, but with limited lateral movement perpendicular to the drip irrigation line. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Juliana S Baggio
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
- Syngenta Crop Protection, Professional Solutions, Vero Beach, FL, USA
| | - Leandro G Cordova
- Corteva Agriscience, Crop Protection Discovery & Development, Indianapolis, IN, USA
| | - Beatriz F Toledo
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
| | - Joseph W Noling
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, USA
| | - Natalia A Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, USA
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Cohen R, Elkabetz M, Paris HS, Gur A, Dai N, Rabinovitz O, Freeman S. Occurrence of Macrophomina phaseolina in Israel: Challenges for Disease Management and Crop Germplasm Enhancement. PLANT DISEASE 2022; 106:15-25. [PMID: 34649461 DOI: 10.1094/pdis-07-21-1390-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: 06/13/2023]
Abstract
Macrophomina phaseolina is a soil-borne fungal pathogen infecting many important crop plants. The fungus, which can survive on crop debris for a long period of time, causes charcoal rot disease by secreting a diverse array of cell-wall degrading enzymes and toxins. M. phaseolina thrives during periods of high temperatures and arid conditions, as typically occur in Israel and other countries with a Mediterranean climate. Crop losses due to charcoal rot can be expected to increase and spread to other countries in a warming global climate. Management of this pathogen is challenging, requiring an array of approaches for the various crop hosts. Approaches that have had some success in Israel include grafting of melons and watermelons on resistant squash rootstocks and soil application of fungicide to reduce disease incidence in melons, fumigation and alterations in planting date and mulching of strawberries, and alteration in irrigation regime of cotton. Elsewhere, these approaches, as well as soil amendments and addition of organisms that are antagonistic to M. phaseolina, have had success in some crop situations. Management through host resistance would be the most sustainable approach, but it requires identifying a resistant germplasm for each crop and introgressing the resistance into the leading cultivars. Resistance to charcoal rot is under complex genetic control in most crops, posing a great challenge for its introgression into elite germplasm. Moreover, fast, reliable methods of screening for resistance would have to be developed for each crop. The toothpick-inoculation method used by us holds great promise for selecting resistant germplasm for melons and possibly for sesame, but other methodologies have to be devised for each individual crop.
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Affiliation(s)
- Roni Cohen
- Department of Plant Pathology and Weed Research, Cucurbits Section, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Meital Elkabetz
- Department of Plant Pathology and Weed Research, Cucurbits Section, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Harry S Paris
- Department of Vegetable Sciences, Cucurbits Section, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Amit Gur
- Department of Vegetable Sciences, Cucurbits Section, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Nir Dai
- Department of Vegetable Sciences, The Volcani Center, Rishon LeZiyyon, Israel
| | - Onn Rabinovitz
- Northern Agriculture Research and Development, Migal Building, P. O. Box 831, Qiryat Shemona, Israel
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, The Volcani Center, Rishon LeZiyyon, Israel
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Baggio JS, Cordova LG, Seijo TE, Noling JW, Whitaker VM, Peres NA. Cultivar Selection Is an Effective and Economic Strategy for Managing Charcoal Rot of Strawberry in Florida. PLANT DISEASE 2021; 105:2071-2077. [PMID: 33428449 DOI: 10.1094/pdis-10-20-2250-re] [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: 06/12/2023]
Abstract
Macrophomina phaseolina, the causal agent of charcoal rot, is a soilborne pathogen that affects strawberry crowns leading to plant wilt and collapse. Disease management involves a combination of physical, cultural, and chemical methods. Field trials were conducted for 10 consecutive Florida seasons (2010-11 to 2019-20) to determine the susceptibility of strawberry cultivars to charcoal rot and the effect of cultivar selection on disease and to estimate the economic impact of cultivar selection on disease management. Six cultivars grown commercially in Florida were chosen and grouped as highly susceptible (HS) ('Strawberry Festival' and 'Treasure'), susceptible (S) ('Florida Radiance' and 'Florida Beauty'), and moderately resistant (MR) (Sensation 'Florida127' and Winterstar 'FL05-107') according to their susceptibility levels. After a primary analysis of the individual trials, a network meta-analysis was conducted to estimate and compare the final disease incidence and the disease progress rate of each susceptibility group. The economic impact of charcoal rot on strawberry production and gross revenue was estimated based on plant production functions, weekly fruit prices, and disease progress over time with parameters obtained via the meta-analytical models. Disease incidence was reduced by 91.5 and 77.3%, respectively, when the MR and S cultivar groups were adopted instead of the HS group. There was a 62.5% reduction in the disease incidence when the MR group was used instead of the S group. Significant differences in disease progress rates were also observed when the MR and S groups were adopted instead of the HS group. Therefore, the adoption of more resistant cultivars is an effective strategy when incorporated into a charcoal rot integrated management program and can significantly impact growers' revenue by reducing disease incidence, preventing yield loss, and, consequently, minimizing economic losses.
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Affiliation(s)
- Juliana S Baggio
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | | | - Teresa E Seijo
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Joseph W Noling
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850
| | - Vance M Whitaker
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
| | - Natalia A Peres
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598
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Baggio JS, Ruschel RG, Noling JW, Peres NA. Physical, Cultural, and Chemical Alternatives for Integrated Management of Charcoal Rot of Strawberry. PLANT DISEASE 2021; 105:295-304. [PMID: 32772832 DOI: 10.1094/pdis-04-20-0917-re] [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
Macrophomina phaseolina, the causal agent of charcoal rot in strawberry, induces plant wilting and collapse. The pathogen survives through the production of microsclerotia in the soil and in strawberry debris. However, its management is difficult, and the disease has become an increasing problem for the strawberry industry. Physical, cultural, and chemical alternatives for integrated management of charcoal rot were evaluated in laboratory and field trials during the 2017-18 and 2018-19 strawberry seasons. In a laboratory trial, M. phaseolina microsclerotia were subjected to heat treatment and germination was inhibited at 52, 56, 80, and 95°C after 30, 10, 1, and 0.5 min of exposure, respectively. In infected strawberry crowns, microsclerotial viability was reduced after 5 min, regardless of temperature, whereas in the field, reduction was observed after 1 min. In field trials, charcoal rot incidence of inoculated strawberry plants transplanted into white-striped plastic-mulched beds was reduced to 20.8%, compared with 60.8% for plants grown in the black plastic mulch. On commercial farms, crop residue removal from infested areas reduced the M. phaseolina population in the soil but did not decrease charcoal rot incidence. Moreover, M. phaseolina propagule densities in the soil and in strawberry debris was reduced by fumigant application at crop termination but surviving propagules allowed the population to increase over the summer. Furthermore, preplant fumigation with metam potassium reduced soil population and charcoal rot incidence. Overall, the adoption of integrated approaches such as physical, chemical, and/or cultural methods played a significant role in reducing M. phaseolina inoculum and contributed to control of the disease in areas with high disease pressure.
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Affiliation(s)
- Juliana S Baggio
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
| | - Rafaela G Ruschel
- São Paulo State University, College of Agricultural Sciences, Botucatu, SP 18610-034, Brazil
| | - Joseph W Noling
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850, U.S.A
| | - Natalia A Peres
- University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
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Holmes GJ, Mansouripour SM, Hewavitharana SS. Strawberries at the Crossroads: Management of Soilborne Diseases in California Without Methyl Bromide. PHYTOPATHOLOGY 2020; 110:956-968. [PMID: 32075499 DOI: 10.1094/phyto-11-19-0406-ia] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Strawberry production has historically been affected by soilborne diseases such as Verticillium wilt. This disease was a major limiting factor in strawberry production in California in the 1950s and was the main reason that preplant soil fumigation with methyl bromide (MB) was developed in the late 1950s. MB fumigation was so successful that over 90% of the commercial strawberry fruit production in California utilized this technique. However, MB was subsequently linked to ozone depletion, and its use was phased out in 2005. The California strawberry industry was awarded exemption to the full phase-out until 2016, when all MB use in strawberry fruit production was prohibited. MB use continues in strawberry nurseries under an exemption to prevent spread of nematodes and diseases on planting stock. This review examines the impact of the MB phase-out on the California strawberry industry and evaluates the outlook for the industry in the absence of one of the most effective tools for managing soilborne diseases. New soilborne diseases have emerged, and historically important soilborne diseases have reemerged. Registration of new fumigants has been difficult and replacement of MB with a new and effective alternative is unlikely in the foreseeable future. Thus, crop losses due to soilborne diseases are likely to increase. Host plant resistance to soilborne diseases has become a top priority for strawberry breeding programs, and cultivars are increasingly selected for their resistance to soilborne diseases. The intelligent integration of a variety of management tactics is necessary to sustain strawberry production in California.
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Affiliation(s)
- Gerald J Holmes
- Strawberry Center, California Polytechnic State University, San Luis Obispo, CA 93407
| | | | - Shashika S Hewavitharana
- Strawberry Center, California Polytechnic State University, San Luis Obispo, CA 93407
- Horticulture and Crop Science Department, California Polytechnic State University, San Luis Obispo, CA 93407
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Yu J, Baggio JS, Boyd NS, Freeman JH, Peres NA. Evaluation of ethanedinitrile (EDN) as a preplant soil fumigant in Florida strawberry production. PEST MANAGEMENT SCIENCE 2020; 76:1134-1141. [PMID: 31583808 DOI: 10.1002/ps.5626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Ethanedinitrile (EDN) has shown promising efficacy against weeds, plant-parasitic nematodes and soil-borne pathogens. Field experiments were conducted for three strawberry (Fragaria× ananassa D.) seasons in Balm and Dover, FL, USA to evaluate the control efficacy of EDN applied through drip tape on various weed species and the fungus Macrophomina phaseolina, the causal agent of charcoal rot of strawberry. RESULTS Results revealed that 224, 336, 448 or 560 kg ha-1 EDN, and 104 kg ha-1 1,3-dichloropropene (1,3-D) + 176 kg ha-1 chloropicrin (Pic) applied through drip tapes under totally impermeable film were safe for strawberry production, with no adverse effect on strawberry growth and yield. EDN rates at 224, 336, 448 and 560 kg ha-1 were highly efficacious and equally effective in reducing purple nutsedge (Cyperus rotundus L.) in two of three growing seasons. Compared with the efficacy on purple nutsedge, the evaluated EDN rates were generally less effective on various broadleaf and grass weeds emerging on the bare ground and planting holes, but at 560 kg ha-1 consistently exhibited similar levels of control as 1,3-D + Pic. For M. phaseolina, the evaluated EDN rates were more efficacious than 1,3-D + Pic and significantly reduced inoculum buried in different bed locations in plastic-mulched beds. CONCLUSION EDN has potential to be an efficacious tool for soil disinfestation and weed control in plasticulture strawberry production. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Jialin Yu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Gulf Coast Research and Education Center, University of Florida, Balm, FL, USA
| | - Juliana S Baggio
- Gulf Coast Research and Education Center, University of Florida, Balm, FL, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, University of Florida, Balm, FL, USA
| | - Josh H Freeman
- North Florida Research and Education Center, University of Florida, Quincy, FL, USA
| | - Natalia A Peres
- Gulf Coast Research and Education Center, University of Florida, Balm, FL, USA
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Burkhardt AK, Childs KL, Wang J, Ramon ML, Martin FN. Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts. BMC Genomics 2019; 20:802. [PMID: 31684862 PMCID: PMC6829926 DOI: 10.1186/s12864-019-6168-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/03/2019] [Indexed: 01/27/2023] Open
Abstract
Background Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts. Results We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes. Conclusions High-quality reference genomes of M. phaseolina have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.
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Affiliation(s)
- Alyssa K Burkhardt
- Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, California, USA.
| | - Kevin L Childs
- Department of Plant Biology and Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI, USA.
| | - Jie Wang
- Department of Plant Biology and Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI, USA
| | - Marina L Ramon
- Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, California, USA
| | - Frank N Martin
- Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, California, USA.
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Baggio JS, Cordova LG, Peres NA. Sources of Inoculum and Survival of Macrophomina phaseolina in Florida Strawberry Fields. PLANT DISEASE 2019; 103:2417-2424. [PMID: 31322978 DOI: 10.1094/pdis-03-19-0510-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Macrophomina phaseolina, the causal agent of charcoal rot, affects strawberry crowns, inducing plant collapse. The fungus survives in the soil through the production of microsclerotia and is usually controlled by preplant fumigation of soil. However, in the 2016 to 2017 Florida strawberry season, even after soil fumigation, about 30% plant mortality still occurred in plastic-covered beds that were used for a second season and where crop residue (mainly old strawberry crowns) was disposed of between beds. Therefore, this study was conducted to determine if M. phaseolina can survive on strawberry debris over summer in Florida and if so, verify whether strawberry debris might act as a source of inoculum for new transplants. Crowns from the previous season were collected from commercial farms where charcoal rot had been reported, and M. phaseolina was recovered from all samples. In a research field, infected crowns were buried in the soil at different depths and retrieved every 2 weeks during the summer. After 8 weeks, M. phaseolina could be recovered at all depths. Moreover, inoculation of strawberry plants by drenching the soil, dipping roots, or spraying leaves with a M. phaseolina microsclerotial suspension from pure cultures or infected crowns produced symptoms with differences in incubation periods depending on cultivar susceptibility. Furthermore, infected crowns disposed of in the aisles between beds or buried next to new transplants of cultivars Strawberry Festival, Florida Beauty, and Winterstar induced charcoal rot, with the level of aggressiveness depending on the cultivar susceptibility and inoculum placement in the field.
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Affiliation(s)
- Juliana S Baggio
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Leandro G Cordova
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Natalia A Peres
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
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Burkhardt A, Ramon ML, Smith B, Koike ST, Martin F. Development of Molecular Methods to Detect Macrophomina phaseolina from Strawberry Plants and Soil. PHYTOPATHOLOGY 2018; 108:1386-1394. [PMID: 29869955 DOI: 10.1094/phyto-03-18-0071-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Macrophomina phaseolina is a broad-host-range fungus that shows some degree of host preference on strawberry, and causes symptoms that include crown rot and root rot. Recently, this pathogen has affected strawberry production as fumigation practices have changed, leaving many growers in California and around the world in need of accurate, rapid diagnostic tools for M. phaseolina in soil and infected plants. This study uses next-generation sequencing and comparative genomics to identify a locus that is unique to isolates within a main genotype shared by a majority of isolates that infect strawberry. This locus was used to develop a quantitative single-tube nested TaqMan polymerase chain reaction assay which is able to quantify as little as 2 to 3 microsclerotia/g of soil with 100% genotype specificity. An isothermal assay using recombinase polymerase amplification was developed from the same locus and has been validated on over 200 infected strawberry plants with a diagnostic sensitivity of 93% and a diagnostic specificity of 99%. Together, this work demonstrates the value of using new approaches to identify loci for detection and provides valuable diagnostic tools that can be used to monitor soil and strawberry plant samples for M. phaseolina.
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Affiliation(s)
- Alyssa Burkhardt
- First, second, third, and fifth authors: Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service, Salinas, CA; and fourth author: TriCal Diagnostics, Hollister, CA
| | - Marina L Ramon
- First, second, third, and fifth authors: Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service, Salinas, CA; and fourth author: TriCal Diagnostics, Hollister, CA
| | - Brett Smith
- First, second, third, and fifth authors: Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service, Salinas, CA; and fourth author: TriCal Diagnostics, Hollister, CA
| | - Steven T Koike
- First, second, third, and fifth authors: Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service, Salinas, CA; and fourth author: TriCal Diagnostics, Hollister, CA
| | - Frank Martin
- First, second, third, and fifth authors: Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service, Salinas, CA; and fourth author: TriCal Diagnostics, Hollister, CA
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Baggio JS, Chamorro M, Cordova LG, Noling JW, Vallad GE, Peres NA. Effect of Formulations of Allyl Isothiocyanate on Survival of Macrophomina phaseolina from Strawberry. PLANT DISEASE 2018; 102:2212-2219. [PMID: 30222054 DOI: 10.1094/pdis-01-18-0172-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Management of Macrophomina phaseolina, causal agent of charcoal rot in many crops worldwide, including strawberry, has become more challenging since the phase out of methyl bromide (MeBr). The search for a fumigant equally effective as MeBr to control soilborne pathogens has been extensive. Allyl isothiocyanate (AITC), a biofumigant recently registered in the United States, was evaluated at different rates, formulations, fumigant combinations, and application methods in the fall of 2014 and 2015 at two research facilities in Balm and Dover, FL. The efficacy of treatments was determined by evaluating the survival of M. phaseolina inoculum on infested corn-cob litter buried in bags 7.6 and 20.3 cm deep in the center, and 7.6 cm deep in the side, of plastic mulched raised beds. The biofumigant was shown to be more or as effective in reducing populations of M. phaseolina in the soil compared with standard fumigants, such as chloropicrin and 1,3-dichloropropene with chloropicrin. Thus, AITC is a promising biofumigant alternative for managing charcoal rot of strawberry, particularly in organic production systems, and should be evaluated for the management of other soilborne pathogens.
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Affiliation(s)
- Juliana S Baggio
- University of Florida, Gulf Coast Research and Education Center, Wimauma, 33598
| | | | - Leandro G Cordova
- University of Florida, Gulf Coast Research and Education Center, Wimauma, 33598
| | - Joseph W Noling
- Citrus Research and Education Center, Lake Alfred, FL, 33850
| | - Gary E Vallad
- University of Florida, Gulf Coast Research and Education Center, Wimauma, 33598
| | - Natalia A Peres
- University of Florida, Gulf Coast Research and Education Center, Wimauma, 33598
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Zveibil A, Mor N, Gnayem N, Freeman S. Survival, Host-Pathogen Interaction, and Management of Macrophomina phaseolina on Strawberry in Israel. PLANT DISEASE 2012; 96:265-272. [PMID: 30731801 DOI: 10.1094/pdis-04-11-0299] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Crown and root rot of strawberry, caused by Macrophomina phaseolina, have become predominant soilborne diseases of strawberry in Israel over the past 5 years. In total, 151 isolates of the pathogen were isolated from infected strawberry plants of commercially grown cultivars in Israel onto a modified agar medium for the genus Macrophomina. Sclerotia viability declined more rapidly in soil maintained at 25°C or at soil temperatures fluctuating from 18 to 32°C under greenhouse conditions, compared with sclerotia viability in soil kept at 30°C. After 30 to 40 weeks of exposure in soil, inocula maintained at 25 or 30°C or at fluctuating temperatures in a greenhouse declined to negligible levels. A significant increase in plant mortality was observed in infested soils maintained at 30 versus 25°C, whereas water stress at 25 or 30°C did not affect plant mortality in M. phaseolina-infested soils. This demonstrated the importance of elevated soil temperature, not moisture stress, on plant mortality caused by M. phaseolina. Host specificity was not evident when strawberry plants were inoculated with each of seven Israeli isolates of M. phaseolina obtained from six other plant species, suggesting the importance of keeping strawberry crops out of rotation with other host crops of the pathogen. The soil fumigants methyl bromide (applied at 500 kg/ha) and metam sodium (730 liter/ha) caused 90 and 95% pathogen mortality in field experiments, respectively, indicating that fumigation may be an effective method of managing this pathogen in infested soils. The increase in prevalence of crown and root rot caused by M. phaseolina in strawberry crops in Israel may be related to the phase-out of methyl bromide.
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Affiliation(s)
- Aida Zveibil
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center
| | - Neta Mor
- Extension Service, Ministry of Agriculture and Rural Development
| | - Nabeel Gnayem
- Extension Service, Ministry of Agriculture and Rural Development
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet Dagan 50250, Israel
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Kaur S, Dhillon GS, Brar SK, Vallad GE, Chand R, Chauhan VB. Emerging phytopathogen Macrophomina phaseolina: biology, economic importance and current diagnostic trends. Crit Rev Microbiol 2012; 38:136-51. [PMID: 22257260 DOI: 10.3109/1040841x.2011.640977] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Macrophomina phaseolina (Tassi) Goid. is an important phytopathogenic fungus, infecting a large number of plant species and surviving for up to 15 years in the soil as a saprophyte. Although considerable research related to the biology and ecology of Macrophomina has been conducted, it continues to cause huge economic losses in many crops. Research is needed to improve the identification and characterization of genetic variability within their epidemiological and pathological niches. Better understanding of the variability within the pathogen population for traits that influence fitness and soil survival will certainly lead to improved management strategies for Macrophomina. In this context, the present review discusses various biological aspects and distribution of M. phaseolina throughout the world and their importance to different plant species. Accurate identification of the fungus has been aided with the use of nucleic acid-based molecular techniques. The development of PCR-based methods for identification and detection of M. phaseolina are highly sensitive and specific. Early diagnosis and accurate detection of pathogens is an essential step in plant disease management as well as quarantine. The progress in the development of various molecular tools used for the detection, identification and characterization of Macrophomina isolates were also discussed.
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Affiliation(s)
- Surinder Kaur
- Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University (BHU), Varanasi, India.
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Muchero W, Ehlers JD, Close TJ, Roberts PA. Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]. BMC Genomics 2011; 12:8. [PMID: 21208448 PMCID: PMC3025960 DOI: 10.1186/1471-2164-12-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 01/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Macrophomina phaseolina is an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [Vigna unguiculata (L) Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance to M. phaseolina and the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs). RESULTS Nine quantitative trait loci (QTLs), accounting for between 6.1 and 40.0% of the phenotypic variance (R2), were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (Glycine max) and Medicago truncatula, candidate resistance genes were found within mapped QTL intervals. QTL Mac-2 explained the largest percent R2 and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location of Mac-6 and Mac-7 QTLs with maturity-related senescence QTLs Mat-2 and Mat-1, respectively. Homologs of the ELF4 and FLK flowering genes were found in corresponding syntenic soybean regions. Only three Macrophomina resistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress and Macrophomina infection. CONCLUSION Effective sources of host resistance were identified in this study. QTL mapping and synteny analysis identified genomic loci harboring resistance factors and revealed candidate genes with potential for further functional genomics analysis.
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Affiliation(s)
- Wellington Muchero
- Nematology Dept., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA
- Current Address: Plant Systems Biology Group, Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
| | - Jeffrey D Ehlers
- Botany and Plant Sciences Dept., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA
| | - Timothy J Close
- Botany and Plant Sciences Dept., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA
| | - Philip A Roberts
- Nematology Dept., University of California-Riverside, 3401 Watkins Drive, Riverside, CA 92521, USA
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