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Karim MM, Usman HM, Tan Q, Hu JJ, Fan F, Hussain R, Luo CX. Fungicide resistance in Colletotrichum fructicola and Colletotrichum siamense causing peach anthracnose in China. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 203:106006. [PMID: 39084801 DOI: 10.1016/j.pestbp.2024.106006] [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: 05/14/2024] [Revised: 06/24/2024] [Accepted: 06/29/2024] [Indexed: 08/02/2024]
Abstract
Peach is one of the popular and economically important fruit crops in China. Peach cultivation is hampered due to attacks of anthracnose disease, causing significant economic losses. Colletotrichum fructicola and Colletotrichum siamense belong to the Colletotrichum gloeosporioides species complex and are considered major pathogens of peach anthracnose. Application of different groups of fungicides is a routine approach for controlling this disease. However, fungicide resistance is a significant drawback in managing peach anthracnose nowadays. In this study, 39 isolates of C. fructicola and 41 isolates of C. siamense were collected from different locations in various provinces in China. The sensitivity of C. fructicola and C. siamense to some commonly used fungicides, i.e., carbendazim, iprodione, fluopyram, and propiconazole, was determined. All the isolates of C. fructicola collected from Guangdong province showed high resistance to carbendazim, whereas isolates collected from Guizhou province were sensitive. In C. siamense, isolates collected from Hebei province showed moderate resistance, while those from Shandong province were sensitive to carbendazim. On the other hand, all the isolates of C. fructicola and C. siamense showed high resistance to the dicarboximide (DCF) fungicide iprodione and succinate dehydrogenase inhibitor (SDHI) fungicide fluopyram. However, they are all sensitive to the demethylation inhibitor (DMI) fungicide propiconazole. Positive cross-resistance was observed between carbendazim and benomyl as they are members of the same methyl benzimidazole carbamate (MBC) group. While no correlation of sensitivity was observed between different groups of fungicides. No significant differences were found in each fitness parameter between carbendazim-resistant and sensitive isolates in both species. Molecular characterization of the β-tubulin 2 (TUB2) gene revealed that in C. fructicola, the E198A point mutation was the determinant for the high resistance to carbendazim, while the F200Y point mutation was linked with the moderate resistance to carbendazim in C. siamense. Based on the results of this study, DMI fungicides, e.g., propiconazole or prochloraz could be used to control peach anthracnose, especially at locations where the pathogens have already developed the resistance to carbendazim and other fungicides.
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Affiliation(s)
- Mohammad Mazharul Karim
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Plant Pathology Division, Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh
| | - Hafiz Muhammad Usman
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Qin Tan
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Jie Hu
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Fan
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Rafakat Hussain
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao-Xi Luo
- National Key Laboratory for Germplasm Innovation Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Zhang Q, Meng Y, Zhao W, Wang Q, Wang X, Xue L, Xu X, Chen C. Bipolaris fujianensis sp. nov., an Emerging Pathogen of Sapling Shoot Blight on Chinese Fir, and Its Sensitivity to Fungicides. PLANT DISEASE 2024; 108:1025-1032. [PMID: 38085971 DOI: 10.1094/pdis-07-23-1254-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: 04/18/2024]
Abstract
Chinese fir is an extremely important economic tree species in southern China. In recent years, 74.5% of Chinese fir saplings suffered from shoot blight in Shunchang County, Nanping City, Fujian Province, China. Seventeen isolates were collected from rotten shoots, and their pathogenicity was confirmed following Koch's postulates. The five pathogenic isolates were identified as belonging to the genus Bipolaris based on morphological characteristics, including septate and geniculate conidiophores, smooth to slightly verruculose conidiogenous nodes, dematiaceous phragmospore conidia, oblong or fusiform conidia, and slightly protruding or truncate hilum on conidia, but the number of pseudosepta (3 to 11, mostly 5 to 8) and the size of conidia ([22.81 to 116.13] × [9.16 to 26.58] μm) are different from those of the known species of Bipolaris. A phylogenetic analysis based on ITS, GAPDH, and Tef1-α sequences determined that the five strains belong to a new species of Bipolaris, and the name Bipolaris fujianensis sp. nov. is proposed. The fungicide sensitivity of the pathogen strain Cfsb3 was further evaluated using eight fungicides. Flusilazole, difenoconazole, tebuconazole, and propiconazole exhibited high toxicity to Cfsb3, and the effective concentration inhibiting 50% (EC50) of mycelial growth was 0.08, 0.20, 0.34, and 0.36 μg/ml, respectively, for these four fungicides. Flusilazole, difenoconazole, and iprodione inhibited B. fujianensis by 100% on detached Chinese fir shoots at their recommended concentrations, but azoxystrobin and thiram were ineffective. In conclusion, this study reported an emerging pathogen of Chinese fir sapling shoot blight and proposed triazole and dicarboximide fungicides for disease control.
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Affiliation(s)
- Qinghua Zhang
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuhan Meng
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenbao Zhao
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qianqian Wang
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoting Wang
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lili Xue
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaochen Xu
- Forestry College of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunli Chen
- Fujian Yangkou State-Owned Forest Farm, Nanping 353299, China
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Cembrowska-Lech D, Krzemińska A, Miller T, Nowakowska A, Adamski C, Radaczyńska M, Mikiciuk G, Mikiciuk M. An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture. BIOLOGY 2023; 12:1298. [PMID: 37887008 PMCID: PMC10603917 DOI: 10.3390/biology12101298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.
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Affiliation(s)
- Danuta Cembrowska-Lech
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland;
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
| | - Adrianna Krzemińska
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
- Institute of Biology, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland;
| | - Tymoteusz Miller
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
| | - Anna Nowakowska
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland;
| | - Cezary Adamski
- Institute of Biology, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland;
| | | | - Grzegorz Mikiciuk
- Department of Horticulture, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland;
| | - Małgorzata Mikiciuk
- Department of Bioengineering, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland;
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Hu JJ, Liu D, Cai MZ, Zhou Y, Yin WX, Luo CX. One-Pot Assay for Rapid Detection of Benzimidazole Resistance in Venturia carpophila by Combining RPA and CRISPR/Cas12a. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1381-1390. [PMID: 36624936 DOI: 10.1021/acs.jafc.2c06549] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
High resistance to benzimidazole fungicides in Venturia carpophila is caused by the point mutation E198K of the β-tubulin (TUB2) gene. Traditional methods for detection of fungicide resistance are time-consuming, which are routinely based on tedious operation, reliance on expensive equipment, and specially trained people. Therefore, it is important to establish efficient methods for field detection of benzimidazole resistance in V. carpophila to make suitable management strategies and ensure food safety. Based on recombinase polymerase amplification (RPA) combined with CRISPR/Cas12a, a rapid one-pot assay ORCas12a-BRVc (one-pot RPA-CRISPR/Cas12 platform) was established for the detection of benzimidazole resistance in V. carpophila. The ORCas12a-BRVc assay enabled one-pot detection by adding components at the bottom and wall of the tube separately, solving the problems of aerosol contamination and decreased sensitivity caused by competing DNA substrates between Cas12a cleavage and RPA amplification. The ORCas12a-BRVc assay could accomplish the detection with a minimum of 7.82 × 103 fg μL-1 V. carpophila genomic DNA in 45 min at 37 °C. Meanwhile, this assay showed excellent specificity due to the specific recognition ability of the Cas12a-crRNA complex. Further, we combined a method that could rapidly extract DNA from V. carpophila within 2 min with the ORCas12a-BRVc to achieve more rapid and simple detection of V. carpophila with benzimidazole resistance in fields. The ORCas12a-BRVc assay has the advantages of simplicity, rapidity, high sensitivity, high specificity, and ease of operation without the need for precision instruments and the need to isolate and culture pathogens. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in fungicide resistance detection and can be used for monitoring of resistant populations in fields, providing guidance on making suitable management strategies for peach scab.
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Affiliation(s)
- Jia-Jie Hu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Duo Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Min-Zheng Cai
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Wei-Xiao Yin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao-Xi Luo
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Zhou Y, Chaisiri C, Luo M, Fan F, Wang YF, Yin LF, Yin WX, Luo CX. Genetic diversity of Venturia carpophila populations from different hosts and geographic regions in China. Front Microbiol 2022; 13:985691. [PMID: 36590415 PMCID: PMC9800423 DOI: 10.3389/fmicb.2022.985691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Venturia carpophila, the causal agent of scab disease of peach, mume, and apricot, is widely distributed around the world. Scab of stone fruits is an important disease in China. However, little is known about the population biology and genetic diversity of the V. carpophila. To better understand the genetic diversity and population structure of V. carpophila, 186 single-spore isolates from different hosts and geographic regions were obtained and analyzed by using 31 simple sequence repeat (SSR) markers. This included 156 isolates from peach spanning 14 provinces, 15 isolates from mume and 15 isolates from apricot in Huazhong Agricultural University (HZAU). Diversity analysis with SSR markers showed a low incidence of polymorphisms within mume isolates (32.59% of markers), but a higher incidence of polymorphisms within peach isolates (42.96%) and apricot isolates (57.04%). Within peach isolates, Nei's average gene diversity ranged from 0.07 for Hebei population to 0.18 for Hubei population. AMOVA analysis revealed that 13% of the observed genetic diversity was partitioned among the geographic populations, while 40% of the observed genetic diversity was partitioned among the host populations. Other analyses (PCoA, STRUCTURE, DAPC, MSN, and UPGMA) indicated that the Chinese V. carpophila populations could be clustered into three distinct genetic groups, which correspond to the host boundaries of peach, mume and apricot. The genetic identity of V. carpophila isolates throughout the range is dependent on hosts, but not geographic regions.
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Affiliation(s)
- Yang Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China,Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mei Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Fan
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Fu Wang
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang-Fen Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China,Experimental Teaching Center of Crop Science, Huazhong Agricultural University, Wuhan, China
| | - Wei-Xiao Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Chao-Xi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China,*Correspondence: Chao-Xi Luo,
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Mao Y, Zhao B, Cao Z, Shen J, Xu S, Wu J, Li T, Wang J, Statsyuk N, Shcherbakova L, Zhou M, Duan Y. Risk assessment and molecular mechanism of Fusarium incarnatum resistance to phenamacril. PEST MANAGEMENT SCIENCE 2022; 78:3394-3403. [PMID: 35514230 DOI: 10.1002/ps.6967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 04/03/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cucumber fruit rot (CFR) caused by Fusarium incarnatum is a devastating fungal disease in cucumber. In recent years, CFR has occurred frequently, resulting in serious yield and quality losses in China. Phenamacril exhibits a specific antifungal activity against Fusarium species. However, no data for phenamacril against F. incarnatum is available. RESULTS The sensitivity of 80 F. incarnatum strains to phenamacril was determined. The half maximal effective concentration (EC50 ) values ranged from 0.1134 to 0.3261 μg mL-1 with a mean EC50 value of 0.2170 ± 0.0496 μg mL-1 . A total of seven resistant mutants were obtained from 450 mycelial plugs by phenamacril-taming on potato dextrose agar (PDA) plates with 10 μg mL-1 of phenamacril, and the resistant frequency was 1.56%. Phenamacril-resistant mutants showed decreased mycelial growth, conidiation and virulence as compared with the corresponding wild-type strains, indicating that phenamacril resistance suffered a fitness penalty in F. incarnatum. In addition, using sequence analysis, the point mutations of S217P or I424S were discovered in Fimyosin-5 (the target of phenamacril). The site-directed mutagenesis of the S217P, P217S, I424S and S424I substitutions were constructed to reveal the relationship between the point mutations and phenamacril resistance. The results strongly demonstrated that the mutations of S217P and I424S in Fimyosin-5 conferred phenamacril-resistance in F. incarnatum. CONCLUSION Phenamacril-resistant mutants were easily induced and their resistance level was high. The S217P or I424S substitutions in Fimyosin-5 conferring phenamacril resistance were detected and futherly verified by transformation assay with site-directed mutagenesis. Thus, we proposed that the resistance development of F. incarnatum to phenamacril is high risk. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yushuai Mao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Baoquan Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhiguo Cao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jinghan Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Shaohua Xu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jian Wu
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tao Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Natalia Statsyuk
- All-Russian Research Institute of Phytopathology, Moscow, Russia
| | | | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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