Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa)
Abstract Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is one of the most damaging diseases of strawberry worldwide. Mefenoxam is one of the major fungicides currently used to manage PhCR. However, the emergence and spread of resistant isolates have made controlling the pathogen in t...
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Nature Portfolio
2023-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-34271-z |
| _version_ | 1797832173458292736 |
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| author | Marcus V. Marin Juliana S. Baggio Youngjae Oh Hyeondae Han Saket Chandra Nan-Yi Wang Seonghee Lee Natalia A. Peres |
| author_facet | Marcus V. Marin Juliana S. Baggio Youngjae Oh Hyeondae Han Saket Chandra Nan-Yi Wang Seonghee Lee Natalia A. Peres |
| author_sort | Marcus V. Marin |
| collection | DOAJ |
| description | Abstract Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is one of the most damaging diseases of strawberry worldwide. Mefenoxam is one of the major fungicides currently used to manage PhCR. However, the emergence and spread of resistant isolates have made controlling the pathogen in the field problematic. In the present study, using whole genome sequencing analysis, mutations associated with mefenoxam-resistant isolates were identified in six different genomic regions of P. cactorum. The 95.54% reads from a sensitive isolate pool and 95.65% from a resistant isolate pool were mapped to the reference genome of P. cactorum P414. Four point mutations were in coding regions while the other two were in noncoding regions. The genes harboring mutations were functionally unknown. All mutations present in resistant isolates were confirmed by sanger sequencing of PCR products. For the rapid diagnostic assay, SNP-based high-resolution melting (HRM) markers were developed to differentiate mefenoxam-resistant P. cactorum from sensitive isolates. The HRM markers R3-1F/R3-1R and R2-1F/R2-1R were suitable to differentiate both sensitive and resistant profiles using clean and crude DNA extraction. None of the mutations associated with mefenoxam resistance found in this study were in the RNA polymerase subunit genes, the hypothesized target of this compound in oomycetes. Our findings may contribute to a better understanding of the mechanisms of resistance of mefenoxam in oomycetes since serves as a foundation to validate the candidate genes as well as contribute to the monitoring of P. cactorum populations for the sustainable use of this product. |
| first_indexed | 2024-04-09T14:03:31Z |
| format | Article |
| id | doaj.art-9b691a7e365e43a7bc689f5a9e82c72d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T14:03:31Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9b691a7e365e43a7bc689f5a9e82c72d2023-05-07T11:10:17ZengNature PortfolioScientific Reports2045-23222023-05-0113111210.1038/s41598-023-34271-zIdentification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa)Marcus V. Marin0Juliana S. Baggio1Youngjae Oh2Hyeondae Han3Saket Chandra4Nan-Yi Wang5Seonghee Lee6Natalia A. Peres7Department of Plant Pathology, University of FloridaGulf Coast Research and Education Center, University of FloridaGulf Coast Research and Education Center, University of FloridaGulf Coast Research and Education Center, University of FloridaSchool of Biotechnology, National Institute of Technology CalicutGulf Coast Research and Education Center, University of FloridaGulf Coast Research and Education Center, University of FloridaDepartment of Plant Pathology, University of FloridaAbstract Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is one of the most damaging diseases of strawberry worldwide. Mefenoxam is one of the major fungicides currently used to manage PhCR. However, the emergence and spread of resistant isolates have made controlling the pathogen in the field problematic. In the present study, using whole genome sequencing analysis, mutations associated with mefenoxam-resistant isolates were identified in six different genomic regions of P. cactorum. The 95.54% reads from a sensitive isolate pool and 95.65% from a resistant isolate pool were mapped to the reference genome of P. cactorum P414. Four point mutations were in coding regions while the other two were in noncoding regions. The genes harboring mutations were functionally unknown. All mutations present in resistant isolates were confirmed by sanger sequencing of PCR products. For the rapid diagnostic assay, SNP-based high-resolution melting (HRM) markers were developed to differentiate mefenoxam-resistant P. cactorum from sensitive isolates. The HRM markers R3-1F/R3-1R and R2-1F/R2-1R were suitable to differentiate both sensitive and resistant profiles using clean and crude DNA extraction. None of the mutations associated with mefenoxam resistance found in this study were in the RNA polymerase subunit genes, the hypothesized target of this compound in oomycetes. Our findings may contribute to a better understanding of the mechanisms of resistance of mefenoxam in oomycetes since serves as a foundation to validate the candidate genes as well as contribute to the monitoring of P. cactorum populations for the sustainable use of this product.https://doi.org/10.1038/s41598-023-34271-z |
| spellingShingle | Marcus V. Marin Juliana S. Baggio Youngjae Oh Hyeondae Han Saket Chandra Nan-Yi Wang Seonghee Lee Natalia A. Peres Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) Scientific Reports |
| title | Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) |
| title_full | Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) |
| title_fullStr | Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) |
| title_full_unstemmed | Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) |
| title_short | Identification of sequence mutations in Phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry (F. × ananassa) |
| title_sort | identification of sequence mutations in phytophthora cactorum genome associated with mefenoxam resistance and development of a molecular assay for the mutant detection in strawberry f ananassa |
| url | https://doi.org/10.1038/s41598-023-34271-z |
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