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Zhang C, Zhao T, Li J, Liu X, Wang W, Huang X, Liu Y, Sun Y, Wei P. Ultrasensitive and on-site diagnosis of rice bakanae disease based on CRISPR-LbCas12a coupled with LAMP. PEST MANAGEMENT SCIENCE 2024. [PMID: 39183634 DOI: 10.1002/ps.8390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/20/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Rice bakanae disease (RBD) has longstanding challenges impacted rice production, which is predominantly induced by Fusarium fujikuroi Nirenberg. Early diagnosis of F. fujikuroi is important to control RBD and improve quality and quantity of rice production. This study presents a novel on-site diagnosis platform combined with CRISPR/LbCas12a and LAMP to detect F. fujikuroi. RESULTS LAMP amplification of TEF1-α, a characteristic gene of F. fujikuroi were performed, followed with trans-cleavage reaction of LbCas12a, cleaving the single-stranded DNA reporter, which is modified by the terminal fluorophore and quencher groups, producing fluorescence signal. The platform was confirmed with high specificity and sensitivity (LOD <1 aM). Furthermore, we designed a lateral flow strip experiment based on the trans-cleavage activity of LbCas12a, which was identified with similar sensitivity and specificity to the fluorescence detection method. CONCLUSION In summary, this study achieved a platform with remarkable sensitivity and specificity for F. fujikuroi detection and provide potential for on-site and ultrasensitive diagnostic tools for RBD. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chao Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Tianyue Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Jianhang Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xiaoshuang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Wenting Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
| | - Xuanda Huang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Yu Liu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Yang Sun
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Pengcheng Wei
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui Province, People's Republic of China
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Avenot HF, Jaime-Frias R, Travadon R, Holland LA, Lawrence DP, Trouillas FP. Development of PCR-Based Assays for Rapid and Reliable Detection and Identification of Canker-Causing Pathogens from Symptomatic Almond Trees. PHYTOPATHOLOGY 2022; 112:1710-1722. [PMID: 35240867 DOI: 10.1094/phyto-08-21-0351-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Trunk and scaffold canker diseases (TSCDs) of almond cause significant yield and tree losses and reduce the lifespan of orchards. In California, several pathogens cause TSCDs, including Botryosphaeriaceae, Ceratocystis destructans, Eutypa lata, Collophorina hispanica, Pallidophorina paarla, Cytospora, Diaporthe, and Phytophthora spp. Field diagnosis of TSCDs is challenging because symptom delineation among the diseases is not clear. Accurate diagnosis of the causal species requires detailed examination of symptoms and subsequent isolation on medium and identification using morphological criteria and subsequent confirmation using molecular tools. The process is time-consuming and difficult, particularly as morphological characteristics are variable and overlap among species. To facilitate diagnosis of TSCD, we developed PCR assays using 23 species-specific primers designed by exploiting sequence differences in the translation elongation factor, β-tubulin, or internal transcribed spacer gene. Using genomic DNA from pure cultures of each fungal and oomycete species, each primer pair successfully amplified a single DNA fragment from the target pathogen but not from selected nontarget pathogens or common endophytes. Although 10-fold serial dilution of fungal DNA extracted from either pure cultures or infected wood samples detected as little as 0.1 pg of DNA sample, consistent detection required 10 ng of pathogen DNA from mycelial samples or from wood chips or drill shavings from artificially or naturally infected almond wood samples with visible symptoms. The new PCR assay represents an improved tool for diagnostic laboratories and will be critical to implement effective disease surveillance and control measures.
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Affiliation(s)
- Herve F Avenot
- Kearney Agricultural Research & Extension Center, Parlier, CA 93648
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Rosa Jaime-Frias
- Kearney Agricultural Research & Extension Center, Parlier, CA 93648
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Leslie A Holland
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706
| | - Daniel P Lawrence
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Florent P Trouillas
- Kearney Agricultural Research & Extension Center, Parlier, CA 93648
- Department of Plant Pathology, University of California, Davis, CA 95616
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Mu K, Ren X, Yang H, Zhang T, Yan W, Yuan F, Wu J, Kang Z, Han D, Deng R, Zeng Q. CRISPR-Cas12a-Based Diagnostics of Wheat Fungal Diseases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7240-7247. [PMID: 35578739 DOI: 10.1021/acs.jafc.1c08391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fusarium head blight (FHB) of wheat, mainly caused by Fusarium graminearum (F. graminearum) infection, reduces crop yield and contaminates grain with mycotoxins. We report a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based nucleic acid assay for an early and rapid diagnosis of wheat FHB. Guide RNA (gRNA) was screened for highly specific recognition of polymerase chain reaction (PCR) amplicon of the internal transcribed spacer (ITS) region and the transcription elongation factor 1α (EF1α) of F. graminearum. The trans-activation of Cas12a protein cleaves the single-stranded DNA probes with the terminal fluorophore and quencher groups, thus allowing us to report the presence of ITS and EF1α of F. graminearum. Owing to the dual recognition process through PCR primers and gRNA hybridization, the approach realized specific discrimination of F. graminearum from other pathogenic fungi. It also allowed us to detect as low as 1 fg/μL total DNA from F. graminearum, which is sufficient to diagnose a 4 day F. graminearum infection. CRISPR-Cas12a-based nucleic acid assay promises the molecular diagnosis of crop diseases and broadens the application of CRISPR tools.
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Affiliation(s)
- Keqing Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Weiyi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Xianyang 712100, China
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Grinbergs D, Chilian J, Hahn C, Reyes M, Isla M, France A, Børve J. Silverleaf (Chondrostereum purpureum) Effects on Japanese Plum (Prunus salicina). PLANTS 2021; 10:plants10122777. [PMID: 34961248 PMCID: PMC8709163 DOI: 10.3390/plants10122777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022]
Abstract
Silverleaf is an important fungal trunk disease of fruit crops, such as Japanese plum (Prunus salicina). It is known that infection by Chondrostereum purpureum results in discolored wood, “silvered” foliage, and tree decline. However, effects on fruit yield and quality have not been assessed. Therefore, the objectives of this study were to determine C. purpureum pathogenicity on P. salicina and the effects on physiology, fruit yield, and quality, in Chile, in 2019 and 2020. Wood samples from affected plum trees were collected in the Chilean plum productive area. Fungi were isolated by plating wood sections from the necrosis margin on culture media. Morphological and molecular characteristics of the isolates corresponded to C. purpureum (98%). Representative isolates were inoculated from healthy plum plants and after 65-d incubation, wood necrotic lesions and silver leaves were visible. Fungi were reisolated, fulfilling Koch’s postulates. To determine Silverleaf effects, xylem water potential and fruit yield and quality were measured in healthy and Silverleaf-diseased plum trees ‘Angeleno’. Water potential was altered in diseased trees, and fruit yield was reduced by 51% (2019) and by 41% (2020) compared to fruit from healthy trees. Moreover, cover-colour, equatorial-diameter, and weight were reduced, and fruit were softer, failing to meet the criteria to be properly commercialized and exported to demanding markets.
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Affiliation(s)
- Daina Grinbergs
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
- Correspondence: (D.G.); (J.C.); Tel.: +56-42-2206-832 (D.G. & J.C.)
| | - Javier Chilian
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
- Correspondence: (D.G.); (J.C.); Tel.: +56-42-2206-832 (D.G. & J.C.)
| | - Carla Hahn
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
| | - Marisol Reyes
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
| | - Mariana Isla
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
| | - Andrés France
- Laboratorio de Fitopatología de Frutales INIA Quilamapu, Instituto de Investigaciones Agropecuarias, INIA, Av. Vicente Méndez 515, Chillán 3780000, Chile; (C.H.); (M.R.); (M.I.); (A.F.)
| | - Jorunn Børve
- Norwegian Institute of Bioeconomy Research, NIBIO, P.O. Box 115, 1431 Ås, Norway;
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Grinbergs D, Chilian J, Padilla N, Reyes M, France A, Moya-Elizondo E, Gerding M. Endophytic Microorganisms Associated with Reversion of Silverleaf Disease Symptoms in Apple. PHYTOPATHOLOGY 2021; 111:1541-1550. [PMID: 33591814 DOI: 10.1094/phyto-12-20-0548-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Silverleaf is caused by the fungus Chondrostereum purpureum, which produces wood necrosis and foliar silvering in woody plants. Field observations and studies in apple have shown the reversion of foliar symptoms. Because plants were clones and received identical agronomical management, it was hypothesized that reversion is driven by endophytic microbiota. Thus, the objectives of this study were to compare healthy, diseased, and reverted plants with respect to their physiology, endophytic microbial communities, antagonistic ability of their endophytes against C. purpureum, and defense genes expression. Water potential, stomatal conductance, chlorophyll content, and fluorescence were measured. Endophytic bacterial and fungal DNA were analyzed by denaturing gradient gel electrophoresis, and community richness and similarity were calculated. Wood cores were collected and bacterial and fungal endophytes were isolated and confronted with C. purpureum-virulent strains in dual-culture assays. Defense genes expression was measured by quantitative PCR. Results indicated that there were no differences in physiological parameters between healthy and reverted plants, except for fluorescence, and both type of plants differed from diseased ones. Bacterial and fungal community richness was similar in healthy and reverted plants and higher than in diseased ones. Endophytes from reverted and healthy plants showed high antagonism to C. purpureum. Furthermore, nonexpressor of pathogenesis-related gene 1 expression was upregulated in reverted plants, whereas phenylalanine ammonia lyase and polygalacturonase-inhibiting protein genes showed higher values in diseased plants. Overall, physiological, molecular, and microbial characteristics were similar between healthy and reverted plants, and both differed from diseased ones. Therefore, reversion of symptoms is associated with changes in the endophytic microbiota, which seems to be a promising source of biological control agents against C. purpureum.
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Affiliation(s)
- D Grinbergs
- Instituto de Investigaciones Agropecuarias, INIA, Chillán, Chile
- Universidad de Concepción, Chillán, Chile
| | - J Chilian
- Instituto de Investigaciones Agropecuarias, INIA, Chillán, Chile
| | - N Padilla
- Universidad de Concepción, Chillán, Chile
| | - M Reyes
- Instituto de Investigaciones Agropecuarias, INIA, Chillán, Chile
| | - A France
- Instituto de Investigaciones Agropecuarias, INIA, Chillán, Chile
| | | | - M Gerding
- Universidad de Concepción, Chillán, Chile
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