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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [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: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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Kumar R, Chander Y, Verma A, Tripathi BN, Barua S, Kumar N. TA novel HRM-based gap-qRT-PCR for identification and quantitation of the vaccine and field strain(s) of lumpy skin disease virus. J Immunol Methods 2023:113521. [PMID: 37392930 DOI: 10.1016/j.jim.2023.113521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Lumpy skin disease (LSD) has become the most important animal health problem in India due to high morbidity, mortality and production losses. A homologous live-attenuated LSD vaccine (Lumpi-ProVacInd) was recently developed by using a local LSD virus (LSDV) strain (LSDV/2019/India/Ranchi) in India which is likely to replace the existing practice of vaccinating cattle with goatpox vaccine. It is essential to differentiate the vaccine and field strains, if a live-attenuated vaccine has been used for control and eradication of the disease, particularly in endemic areas. As compared to the prevailing vaccine and field/virulent strains, the Indian vaccine strain (Lumpi-ProVacInd) has a unique deletion of 801 nucleotides in its inverted terminal repeat (ITR) region. We exploited this unique feature and developed a novel high resolution melting-based gap quantitative real-time PCR (HRM-gap-qRT-PCR) for rapid identification and quantitation of the vaccine and field strain(s) of LSDV.
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Affiliation(s)
- Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India; Animal Science Division, Indian Council of Agricultural Research, New Delhi, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India.
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Marin MV, Baggio JS, Oh Y, Han H, Chandra S, Wang NY, Lee S, Peres NA. 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). Sci Rep 2023; 13:7385. [PMID: 37149656 PMCID: PMC10164155 DOI: 10.1038/s41598-023-34271-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/26/2023] [Indexed: 05/08/2023] Open
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.
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Affiliation(s)
- Marcus V Marin
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A
| | - Juliana S Baggio
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A
- Department of Horticultural Science, Chungbuk National University, Cheongju, South Korea
| | - Hyeondae Han
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A
| | - Saket Chandra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, India
| | - Nan-Yi Wang
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A..
- Horticultural Science Department, University of Florida, Gainesville, FL, 32611, U.S.A..
| | - Natalia A Peres
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A..
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, U.S.A..
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Wang NY, Gama AB, Marin MV, Peres NA. Development of a Multiplex High-Throughput Diagnostic Assay for the Detection of Strawberry Crown Rot Diseases Using High-Resolution Melting Analysis. PHYTOPATHOLOGY 2021; 111:1470-1483. [PMID: 33754805 DOI: 10.1094/phyto-12-20-0556-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rapid and accurate disease diagnosis is a prerequisite for an effective disease management program in strawberry production. In Florida, Colletotrichum spp., Phytophthora spp., and Macrophomina phaseolina are the primary microorganisms causing strawberry crown rot. Even though the diseases can be caused by different pathogens, symptoms are indistinguishable and equally devastating. To inform strawberry growers in a timely fashion of diagnostic results for effective deployment of chemical control practices, we developed a multiplex high-resolution melting (HRM) assay to rapidly and accurately detect the abovementioned pathogens. The multiplex HRM assays using three predesigned primer pairs showed high specificity for individual species by generating specific melting peaks without cross-reaction between primers or with other common strawberry pathogens. The amplification limit of the assay was 1 pg of Colletotrichum and Phytophthora and 100 pg of M. phaseolina DNA per 10-μl reaction. However, the presence of different melting peaks was observed in mixed DNA samples and was concentration and target DNA dependent. A crude DNA extraction protocol was developed to allow high-throughput screening by minimizing the inhibitory effects. Moreover, we applied the HRM assay to 522 plant samples and found high correlations between conventional pathogen isolation and HRM and between singleplex and multiplex assays. Altogether, this multiplex HRM assay is specific, cost effective, and reliable for the timely detection of strawberry crown rot pathogens.
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Affiliation(s)
- Nan-Yi Wang
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Andre Bueno Gama
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Marcus Vinicius Marin
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
| | - Natalia A Peres
- Gulf Coast Research and Education Center, Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL 33598
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Dehbashi S, Tahmasebi H, Alikhani MY, Keramat F, Arabestani MR. Distribution of Class B and Class A β-Lactamases in Clinical Strains of Pseudomonas aeruginosa: Comparison of Phenotypic Methods and High-Resolution Melting Analysis (HRMA) Assay. Infect Drug Resist 2020; 13:2037-2052. [PMID: 32636657 PMCID: PMC7335274 DOI: 10.2147/idr.s255292] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background There are various phenotypic methods for identifying class B and class A β-lactamase enzymes in Pseudomonas aeruginosa. The purpose of this study was to compare the sensitivity and specificity of different phenotypic methods with HRMA assay to detect β-lactamase-producing P. aeruginosa strains. Methods Eighty-eight of P. aeruginosa isolates were collected from different specimens. Conventional double-disk test (DDT) and EDTA-imipenem microbiological (EIM) were performed to detect ESBL and MBL-producing strains, respectively. Meanwhile, the Modified Hodge test and Carba-NP test were performed on all carbapenem-resistant strains. HRMA method and sensitivity and specificity of primers were determined based on the melt curve temperature range. In all comparisons, PCR was considered as the gold standard. Results Of the 402 isolates collected from different clinical specimens, 88 isolates of P. aeruginosa were identified. However, 43 strains were (48.88%) ESBL-producing, and 7 strains (7.95%) were MBL-producing. Also, using the Modified Hodge test and Carba-NP method, 11 (12.5%) and 19 (21.59%) strains were carbapenemase-producing, respectively. The results of the HRMA test revealed that genes coding for bla SHV, bla TEM, bla KPC, bla IMP, bla VIM, and bla GES were detected in 44.31%, 22.72%, 13.63%, 14.7%, 5.6%, and 2.27% of P. aeruginosa isolates. Nonetheless, for bla KPC and bla GES genes, sensitivity and specificity of the Carba-NP test were 90.47%, 94.87%, and 83.36%, 94.80%, respectively. However, sensitivity and specificity of MHT was 91.66%, 98.70%, and 77.77%, 96.42%, respectively. For bla SHV and bla TEM genes, sensitivity and specificity of DDT were 95.55%, 95.55%, and 86%, 83.50%, respectively. However, sensitivity and specificity of EMI were 77.77%, 97.59%, and 91.66%, 97.43% for bla VIM and bla IMP, respectively. Conclusion The HRMA is a powerful, accurate, closed-tube, rapid method for detecting β-lactamase genes in P. aeruginosa. The high sensitivity and specificity of this method, along with phenotypic tests, play a useful role in increasing the predictive value of clinical reports.
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Affiliation(s)
- Sanaz Dehbashi
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamed Tahmasebi
- Microbiology Department, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Yousef Alikhani
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Fariba Keramat
- Brucellosis Research Center, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Reza Arabestani
- Microbiology Department, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Nutrition Health Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Chatzidimopoulos M, Ganopoulos I, Moraitou-Daponta E, Lioliopoulou F, Ntantali O, Panagiotaki P, Vellios EK. High-Resolution Melting (HRM) Analysis Reveals Genotypic Differentiation of Venturia inaequalis Populations in Greece. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Su Z, Zhang X, Zhao J, Wang W, Shang L, Ma S, Adzavon YM, Lu F, Weng M, Han X, Yang L, Zhao Q, Zhao P, Xie F, Ma X. Combination of Suspension Array and Mycelial Growth Assay for Detecting Multiple-Fungicide Resistance in Botrytis cinerea in Hebei Province in China. PLANT DISEASE 2019; 103:1213-1219. [PMID: 30964418 DOI: 10.1094/pdis-07-18-1269-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To provide a high-throughput, efficient, and accurate method to monitor multiple-fungicide resistance of Botrytis cinerea in the field, we used the suspension array, sequencing, and mycelial growth assay in our research. Discriminating-dose bioassays for detecting carbendazim, diethofencarb, boscalid, and iprodione resistance (CarR, DieR, BosR, and IprR, respectively) were used to analyze 257 isolates collected from Hebei Province in China during 2016 and 2017. High resistance frequencies to carbendazim (100%), diethofencarb (92.08%), and iprodione (86.59%) were detected. BosR isolates accounted for 11.67% of the total. In addition, 103 isolates were randomly selected for phenotype and genotype detection. The high-throughput suspension array was utilized to detect eight genotypes simultaneously, including BenA-E198, BenA-198A, SdhB-H272, SdhB-272Y, BcOS1-I365, BcOS1-365S, erg27-F412, and erg27-412S, which were associated with resistance toward carbendazim or diethofencarb, boscalid, iprodione, and fenhexamid (FenR), respectively. Most of the benzimidazole-resistant isolates (81.55%) possessed the E198V mutation in the BenA gene. Ninety-three isolates with dual resistance to carbendazim and diethofencarb showed the E198V/K mutation. All BosR isolates carried the H272R mutation in the SdhB gene. The I365S and Q369P+N373S (66.99%) mutations in the BcOS1 gene were more frequently observed. No mutation was detected in the erg27 gene in Hebei isolates. There were 13 resistance profile phenotypes. Phenotypes with triple resistance were the most common (83.50%), and CarRDieRBosSIprRFenS was the major type. CarR isolates that carried E198V/K/A were all highly resistant (HR) and only one F200Y mutant was moderately resistant (MR) to carbendazim. Isolates that possessed E198V/K were MR or HR to diethofencarb. BosR isolates that possessed H272R mutation were lowly resistant (LR). IprR isolates were all LR or MR. The distribution of half maximal effective concentrations of CarR isolates with E198V/K mutations and IprR isolates with Q369P+N373S mutations significantly increased from 2016 to 2017. Combined with our observations, a combination method of the high-throughput suspension array and the mycelial growth assay was suggested to accurately monitor multiple resistance of B. cinerea in the field.
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Affiliation(s)
- Zehua Su
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Xin Zhang
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
- 2 College of Applied Sciences, Beijing University of Technology, Beijing 100124, China; and
| | - Jianjiang Zhao
- 3 Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Wenqiao Wang
- 3 Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Lei Shang
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Shengnan Ma
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Yao Mawulikplimi Adzavon
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Fen Lu
- 3 Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Mantian Weng
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiuying Han
- 3 Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Lei Yang
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Qinghui Zhao
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Pengxiang Zhao
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Fei Xie
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
| | - Xuemei Ma
- 1 College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
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Forcelini BB, Lee S, Oliveira MS, Peres NA. Development of High-Throughput SNP Genotyping Assays for Rapid Detection of Strawberry Colletotrichum Species and the G143A Mutation. PHYTOPATHOLOGY 2018; 108:1501-1508. [PMID: 29996698 DOI: 10.1094/phyto-04-18-0128-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Colletotrichum spp. cause major diseases of strawberry and disease management depends on the species present. However, species identification based on symptoms and spore morphology is difficult. Therefore, development of molecular techniques for trustworthy and high-throughput identification of Colletotrichum spp. is vital for the accurate diagnosis. A high-resolution melting (HRM) assay was developed for simultaneous identification and differentiation of Colletotrichum spp. from fungal colonies or from symptomatic strawberry tissue. HRM markers were designed based on the internal transcribed spacer region of Colletotrichum acutatum and C. gloeosporioides from strawberry, and accurately identified and differentiated the two species. In addition, for the rapid detection of a single-nucleotide polymorphism (SNP) in the cytochrome b (cytb) gene of C. acutatum and C. gloeosporioides associated with resistance to quinone-outside inhibitor fungicides, an endpoint SNP genotyping analysis was developed. The HRM and endpoint SNP genotyping assays are useful methods that can be implemented in plant diagnostic clinics for the rapid and accurate identification of Colletotrichum spp. and detection of the G143A mutation in the cytb gene of C. acutatum and C. gloeosporioides.
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Affiliation(s)
- Bruna B Forcelini
- Gulf Coast Research and Education Center, University of Florida, Wimauma 33598
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma 33598
| | - Michelle S Oliveira
- Gulf Coast Research and Education Center, University of Florida, Wimauma 33598
| | - Natalia A Peres
- Gulf Coast Research and Education Center, University of Florida, Wimauma 33598
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Contreras RA, Pizarro M, Köhler H, Sáez CA, Zúñiga GE. Copper stress induces antioxidant responses and accumulation of sugars and phytochelatins in Antarctic Colobanthus quitensis (Kunth) Bartl. Biol Res 2018; 51:48. [PMID: 30428921 PMCID: PMC6234666 DOI: 10.1186/s40659-018-0197-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/07/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In field, C. quitensis is subjected to many abiotic extreme environmental conditions, such as low temperatures, high UV-B, salinity and reduced water potentials, but not metal or metalloid high concentrations in soil, however, other members of Caryophyllaceae family have tolerance to high concentrations of metals, this is the case of Silene genre. In this work, we hypothesize that C. quitensis have the same mechanisms of Silene to tolerate metals, involving accumulation and induction of antioxidant systems, sugar accumulation and the induction of thiols such as phytochelatins to tolerate. RESULTS The results showing an effective antioxidant defensive machinery involving non-enzymatic antioxidants such as phenolics, GSH and ascorbic acid, in another hand, GSH-related oligomers (phytochelatins) and sugars was induced as a defensive mechanism. CONCLUSIONS Colobanthus quitensis exhibits certain mechanisms to tolerate copper in vitro demonstrating its plasticity to tolerate several abiotic stress conditions.
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Affiliation(s)
- Rodrigo A. Contreras
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, L.B. O’Higgins #3363, Estación Central, Santiago, Chile
| | - Marisol Pizarro
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, L.B. O’Higgins #3363, Estación Central, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile
| | - Hans Köhler
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, L.B. O’Higgins #3363, Estación Central, Santiago, Chile
| | - Claudio A. Sáez
- Laboratory of Aquatic Environmental Research (LACER), Center of Advanced Studies, Universidad de Playa Ancha, Viña del Mar, Chile
| | - Gustavo E. Zúñiga
- Laboratorio de Fisiología y Biotecnología Vegetal, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, L.B. O’Higgins #3363, Estación Central, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile
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Baggio JS, Peres NA, Amorim L. Sensitivity of Botrytis cinerea Isolates from Conventional and Organic Strawberry Fields in Brazil to Azoxystrobin, Iprodione, Pyrimethanil, and Thiophanate-Methyl. PLANT DISEASE 2018; 102:1803-1810. [PMID: 30125196 DOI: 10.1094/pdis-08-17-1221-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Botrytis fruit rot, caused by Botrytis cinerea, is one of the most important strawberry diseases worldwide, and fungicide applications are often used to manage the disease in commercial production. Isolates of B. cinerea were collected from conventional and organic strawberry fields in four Brazilian States from 2013 to 2015 and their sensitivity to the main single-site mode-of action fungicides used in Brazil was tested. Resistance to azoxystrobin, iprodione, pyrimethanil, and thiophanate-methyl was found and values for effective concentration that inhibited mycelial growth by 50% were higher than 71.9, 1.2, 5.0, and 688 µg/ml, respectively, regardless the production system. Resistance to these fungicides was observed in 87.5, 76.6, 23.4, and 92.2% of isolates from conventional fields and 31.4, 22.9, 14.3, and 51.4% of isolates from organic fields, respectively. Moreover, frequencies of isolates with multiple fungicide resistance to the four active ingredients were 20.6 and 2.8% whereas 6.3 and 27.8% were sensitive to the four fungicides for conventional and organic areas, respectively. Molecular analyses of the cytochrome b, β-tubulin, and bos1 genes revealed the presence of G143A; E198A; and I365 N/S, Q369P, or N373S mutations, respectively, in resistant isolates of B. cinerea. Field rates of fungicides sprayed preventively to inoculated strawberry fruit failed to control disease caused by the respective resistant isolates.
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Affiliation(s)
- Juliana S Baggio
- Departamento de Fitopatologia, ESALQ, University of Sao Paulo, CEP 13418-900, Piracicaba, SP, Brazil
| | - Natalia A Peres
- Gulf Coast Research and Education Center, University of Florida, Wimauma
| | - Lilian Amorim
- Departmento de Fitopatologia, ESALQ, University of São Paulo, CEP 13418-900 Piracicaba, SP, Brazil
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Trends and Challenges in Pesticide Resistance Detection. TRENDS IN PLANT SCIENCE 2016; 21:834-853. [PMID: 27475253 DOI: 10.1016/j.tplants.2016.06.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 06/06/2023]
Abstract
Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides while maintaining pesticide efficacy. This goal requires monitoring the emergence and development of resistance to pesticides in crop pests. To this end, various methods for resistance diagnosis have been developed for different groups of pests. This review provides an overview of biological, biochemical, and molecular methods that are currently used to detect and quantify pesticide resistance. The agronomic, technical, and economic advantages and drawbacks of each method are considered. Emerging technologies are also described, with their associated challenges and their potential for the detection of resistance mechanisms likely to be selected by current and future plant protection methods.
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Zhang X, Xie F, Lv B, Zhao P, Ma X. Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea. Front Microbiol 2016; 7:1482. [PMID: 27708631 PMCID: PMC5030824 DOI: 10.3389/fmicb.2016.01482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/06/2016] [Indexed: 11/14/2022] Open
Abstract
A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea. Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene (BenA), H272 and 272Y of the Succinate dehydrogenase iron–sulfur subunit gene (SdhB), I365 and 365S of the putative osmosensor histidine kinase gene (BcOS1), and F412 and 412S of the 3-ketoreductase gene (erg27). This assay was first established and optimized with eight plasmid templates containing the DNA sequence variants BenA-E198, BenA-198A, SdhB-H272, SdhB-272Y, BcOS1-I365, BcOS1-365S, erg27-F412, and erg27-412S. Results indicated that none of the probes showed cross-reactivity with one another. The minimum limit of detection for these genotypes was one copy per test. Four mutant plasmids were mixed with 10 ng/μL wild-type genomic DNA in different ratios. Detection sensitivity of mutant loci was 0.45% for BenA-E198A, BcOS1-I365S, and erg27-F412S, and was 4.5% for SdhB-H272Y. A minimum quantity of 0.1 ng of genomic DNA was necessary to obtain reliable results. This is the first reported assay that can simultaneously detect mutations in BenA, SdhB, BcOS1, and erg27.
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Affiliation(s)
- Xin Zhang
- College of Life Science and Bioengineering, Beijing University of Technology Beijing, China
| | - Fei Xie
- College of Life Science and Bioengineering, Beijing University of Technology Beijing, China
| | - Baobei Lv
- College of Life Science and Bioengineering, Beijing University of Technology Beijing, China
| | - Pengxiang Zhao
- College of Life Science and Bioengineering, Beijing University of Technology Beijing, China
| | - Xuemei Ma
- College of Life Science and Bioengineering, Beijing University of Technology Beijing, China
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