1
|
Shang J, Feng H, Wang Y, Wang Y, Zhang X, Zhang Z. Preparation and Application of Polyclonal Antibodies for the Rapid Detection of Actinidia Chlorotic Ringspot-Associated Virus. Viruses 2024; 16:1600. [PMID: 39459933 DOI: 10.3390/v16101600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 09/16/2024] [Accepted: 10/09/2024] [Indexed: 10/28/2024] Open
Abstract
Actinidia chlorotic ringspot-associated virus (AcCRaV, Emaravirus actinidiae) is prevalent in Chinese kiwifruit, leading to substantial yield reduction. The intricate nature of symptoms presents diagnostic challenges, underscoring the necessity for a rapid and accurate detection method that facilitates effective control. In this investigation, AcCRaV isolates from key kiwi-producing regions in Sichuan province were collected and analyzed, with representative strains chosen as experimental materials. Primers targeting the nucleoprotein gene of AcCRaV were designed, and their codon usage was optimized to enhance performance. Various serological methods utilizing polyclonal antibodies were developed, including ELISA, dot immunobinding assay, and AcCRaV-specific gold immunochromatographic bands (AcCRaV-GICS). Field samples exhibited high specificity and sensitivity when tested using these methods. Furthermore, the results obtained from a large number of field samples are consistent with those derived from RT-PCR analysis, further validating the applicability of our approach. A detection method capable of handling a large volume of field samples infected with AcCRaV is currently lacking; thus, our system construction provides an important reference for addressing this gap.
Collapse
Affiliation(s)
- Jing Shang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Feng
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxuan Wang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yunan Wang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao Zhang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhouyu Zhang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
2
|
Zhou C, Zheng M, Du X, Cao Z, Wu J, Zhu J, Nie C. Construction of a full-length infectious cDNA clone of zucchini tigre mosaic virus infecting snake gourd and genetic diversity analysis based on complete genome sequences of ZTMV isolates. Arch Virol 2024; 169:220. [PMID: 39387940 DOI: 10.1007/s00705-024-06152-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/27/2024] [Indexed: 10/15/2024]
Abstract
Zucchini tigre mosaic virus (ZTMV) is a positive-sense single-stranded RNA virus belonging to the genus Potyvirus. In this study, a full-length infectious cDNA clone of a ZTMV strain infecting snake gourd (Trichosanthes cucumerina var. anguina L.) was constructed and shown to infect snake gourd, chieh-qua, zucchini, ridge gourd, and bitter melon. The complete genome sequence of ZTMV-FS7 (PP291701) showed the highest nucleotide sequence similarity to ZTMV-TW (86.2% identity). Genetic diversity analysis of 12 ZTMV isolates showed that the P1 gene had the highest variability. Selection pressure analysis indicated that all of the ZTMV genes were under negative selection. However, some sites, particularly within the P1 gene, were under positive selection.
Collapse
Affiliation(s)
- Cuiji Zhou
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Mingwei Zheng
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Xianfeng Du
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Ziqi Cao
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Jialin Wu
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Junhao Zhu
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Chengrong Nie
- Department of Horticulture, Foshan University, Foshan, Guangdong, 528225, P. R. China.
| |
Collapse
|
3
|
Gauthier K, Strauch CJ, Bonse S, Bauer P, Heidler C, Niehl A. Detection and Quantification of Soil-Borne Wheat Mosaic Virus, Soil-Borne Cereal Mosaic Virus and Japanese Soil-Borne Wheat Mosaic Virus by ELISA and One-Step SYBR Green Real-Time Quantitative RT-PCR. Viruses 2024; 16:1579. [PMID: 39459913 DOI: 10.3390/v16101579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 10/01/2024] [Accepted: 10/05/2024] [Indexed: 10/28/2024] Open
Abstract
Furoviruses are bipartite viruses causing mosaic symptoms and stunting in cereals. Infection with these viruses can lead to severe crop losses. The virus species Furovirus tritici with soil-borne wheat mosaic virus (SBWMV), Furovirus cerealis with soil-borne cereal mosaic virus (SBCMV) and Furovirus japonicum with Japanese soil-borne wheat mosaic virus (JSBWMV) and French barley mosaic virus (FBMV) as members are biologically and genetically closely related. Here, we develop SYBR green-based real-time quantitative RT-PCR assays to detect and quantify the RNA1 and RNA2 of the three virus species. Using experimental data in combination with Tm-value prediction and analysis of primer and amplicon sequences, we determine the capacity of our method to discriminate between the different viruses and evaluate its genericity to detect different isolates within the same virus species. We demonstrate that our method is suitable for discriminating between the different virus species and allows for the detection of different virus isolates. However, JSBWMV RNA1 primers may amplify SBWMV samples, bearing a risk for false positive detection with this primer. We also test the efficiency of polyclonal antibodies to detect the different viruses by ELISA and suggest that ELISA may be applied as a first screening to identify the virus. The real-time qRT-PCR assays developed provide the possibility to screen for quantitative disease resistance against SBCMV, SBWMV and JSBWMV. Moreover, with our method, we hope to promote research to unravel yet unresolved questions with respect to furovirus-host interaction concerning host range and resistance as well as regarding the role of multipartite genomes.
Collapse
Affiliation(s)
- Kevin Gauthier
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
- Agroscope, Department of Plant Breeding, Route de Duillier 60, 1260 Nyon, Switzerland
| | - Claudia Janina Strauch
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
| | - Sabine Bonse
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
| | - Petra Bauer
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
| | - Carolin Heidler
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
| | - Annette Niehl
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Brunswick, Germany
| |
Collapse
|
4
|
Gryzunov N, Morozov SY, Suprunova T, Samarskaya V, Spechenkova N, Yakunina S, Kalinina NO, Taliansky M. Genomes of Alphanucleorhabdovirus Physostegiae Isolates from Two Different Cultivar Groups of Solanum melongena. Viruses 2024; 16:1538. [PMID: 39459872 DOI: 10.3390/v16101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/13/2024] [Accepted: 09/27/2024] [Indexed: 10/28/2024] Open
Abstract
Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus-PhCMoV), and their minus-sense RNA genomes have the typical gene order 3'-nucleocapsid (N)-X protein (X)-phosphoprotein (P)-Y protein (Y)-matrix protein (M)-glycoprotein (G)-polymerase (L)-5' observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown.
Collapse
Affiliation(s)
- Nikita Gryzunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sergey Yu Morozov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Viktoriya Samarskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sofiya Yakunina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalia O Kalinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Michael Taliansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| |
Collapse
|
5
|
Adero J, Wokorach G, Stomeo F, Yao N, Machuka E, Njuguna J, Byarugaba DK, Kreuze J, Yencho GC, Otema MA, Yada B, Kitavi M. Next Generation Sequencing and Genetic Analyses Reveal Factors Driving Evolution of Sweetpotato Viruses in Uganda. Pathogens 2024; 13:833. [PMID: 39452705 PMCID: PMC11510311 DOI: 10.3390/pathogens13100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 10/26/2024] Open
Abstract
Sweetpotato (Ipomoea batatas L.) is an essential food crop globally, especially for farmers facing resource limitations. Like other crops, sweetpotato cultivation faces significant production challenges due to viral infections. This study aimed to identify and characterize viruses affecting sweetpotato crops in Uganda, mostly those associated with sweetpotato virus disease (SPVD). Infected leaf samples were collected from farmers' fields in multiple districts spanning three regions in Uganda. MiSeq, a next-generation sequencing platform, was used to generate reads from the viral nucleic acid. The results revealed nine viruses infecting sweetpotato crops in Uganda, with most plants infected by multiple viral species. Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. The sweet potato virus C carried more codons under positive diversifying selection than the closely related sweet potato feathery mottle virus, particularly in the P1 gene. This study provides valuable insights into the viral species infecting sweetpotato crops, infection severity, and the evolution of sweet potato viruses in Uganda.
Collapse
Affiliation(s)
- Joanne Adero
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Godfrey Wokorach
- Department of Biology, Faculty of Science, Muni University, Arua P.O. Box 725, Uganda;
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Nasser Yao
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Eunice Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Denis K. Byarugaba
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Jan Kreuze
- International Potato Centre, CIP Headquarters Lima, Avenida La Molina 1895, La Molina Apartado Postal 1558, Lima 15024, Peru;
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, 214 Kilgore Hall, P.O. Box 7609, Raleigh, NC 27695, USA;
| | - Milton A. Otema
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
| | - Benard Yada
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
| | - Mercy Kitavi
- International Potato Centre, SSA Regional Office, Nairobi P.O. Box 25171, Kenya
| |
Collapse
|
6
|
He WZ, Zhao L, Sun K, Feng Z, Zhou G, Rao Q. Transcriptomic profiling reveals the complex interaction between a bipartite begomovirus and a cucurbitaceous host plant. BMC Genomics 2024; 25:876. [PMID: 39294575 PMCID: PMC11409788 DOI: 10.1186/s12864-024-10781-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 09/09/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Begomoviruses are major constraint in the production of many crops. Upon infection, begomoviruses may substantially modulate plant biological processes. While how monopartite begomoviruses interact with their plant hosts has been investigated extensively, bipartite begomoviruses-plant interactions are understudied. Moreover, as one of the major groups of hosts, cucurbitaceous plants have been seldom examined in the interaction with begomoviruses. RESULTS We profiled the zucchini transcriptomic changes induced by a bipartite begomovirus squash leaf curl China virus (SLCCNV). We identified 2275 differentially-expressed genes (DEGs), of which 1310 were upregulated and 965 were downregulated. KEGG enrichment analysis of the DEGs revealed that many pathways related to primary and secondary metabolisms were enriched. qRT-PCR verified the transcriptional changes of twelve selected DEGs induced by SLCCNV infection. Close examination revealed that the expression levels of all the DEGs of the pathway Photosynthesis were downregulated upon SLCCNV infection. Most DEGs in the pathway Plant-pathogen interaction were upregulated, including some positive regulators of plant defenses. Moreover, the majority of DEGs in the MAPK signaling pathway-plant were upregulated. CONCLUSION Our findings indicates that SLCCNV actively interact with its cucurbitaceous plant host by suppressing the conversion of light energy to chemical energy and inducing immune responses. Our study not only provides new insights into the interactions between begomoviruses and host plants, but also adds to our knowledge on virus-plant interactions in general.
Collapse
Affiliation(s)
- Wen-Ze He
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Zhejiang A&F University, Hangzhou, 311300, China
| | - Li Zhao
- Hangzhou Agricultural Technology Extension Center, Hangzhou, 310058, China
| | - Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Zhen Feng
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Zhejiang A&F University, Hangzhou, 311300, China
| | - Gen Zhou
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Zhejiang A&F University, Hangzhou, 311300, China
| | - Qiong Rao
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Zhejiang A&F University, Hangzhou, 311300, China.
| |
Collapse
|
7
|
Zhang AL, Hao M, Shi Z, Gao Z, Xu Y, Liu Z. Combining Thermotherapy with Shoot Tip Culture or Cryotherapy for Improved Virus Eradication from In Vitro Actinidia macrosperma. PLANT DISEASE 2024:PDIS03240546RE. [PMID: 38853335 DOI: 10.1094/pdis-03-24-0546-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In recent years, kiwifruit viral diseases have become increasingly prevalent in kiwifruit-producing regions of China, significantly impacting both the yield and quality of kiwifruit. This has emerged as a significant constraint on the healthy and sustainable development of the kiwifruit industry. The use of virus-free propagation materials has been proven the most effective strategy for controlling plant viral diseases. In the present study, shoot tip culture, shoot tip cryotherapy, and their combinations with thermotherapy were established to eradicate Actinidia virus A (AcVA), Actinidia virus B (AcVB), and Actinidia chlorotic ringspot-associated virus (AcCRaV) from Actinidia macrosperma. Additionally, the impact of shoot tip size on virus eradication was evaluated. Among the three confirmed viruses, regardless of the procedure, AcVB was the easiest to eradicate, followed by AcVA and AcCRaV. Combining thermotherapy with shoot tip culture or cryotherapy resulted in a higher virus-free frequency (up to 27.3 and 50%, respectively) than shoot tip culture or cryotherapy alone (0 to 20%). Notably, the combination of thermotherapy and 0.5- to 1-mm shoot tip cryotherapy was shown to be the most effective protocol for virus eradication from A. macrosperma, which produced 50% of regenerated shoots free from all the tested viruses. To the best of our knowledge, this is the first report on virus elimination from kiwifruit infected with multiple viruses based on conventional shoot tip culture and shoot tip cryotherapy.
Collapse
Affiliation(s)
- A-Ling Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Yangling 712100, Shaanxi, China
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Mingxing Hao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhimin Shi
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhixiong Gao
- Yangling Molo Ecological Agriculture Co., Ltd., Yangling 712100, Shaanxi, China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Yangling 712100, Shaanxi, China
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhande Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| |
Collapse
|
8
|
Juárez ID, Kurouski D. Contemporary applications of vibrational spectroscopy in plant stresses and phenotyping. FRONTIERS IN PLANT SCIENCE 2024; 15:1411859. [PMID: 39345978 PMCID: PMC11427297 DOI: 10.3389/fpls.2024.1411859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/08/2024] [Indexed: 10/01/2024]
Abstract
Plant pathogens, including viruses, bacteria, and fungi, cause massive crop losses around the world. Abiotic stresses, such as drought, salinity and nutritional deficiencies are even more detrimental. Timely diagnostics of plant diseases and abiotic stresses can be used to provide site- and doze-specific treatment of plants. In addition to the direct economic impact, this "smart agriculture" can help minimizing the effect of farming on the environment. Mounting evidence demonstrates that vibrational spectroscopy, which includes Raman (RS) and infrared spectroscopies (IR), can be used to detect and identify biotic and abiotic stresses in plants. These findings indicate that RS and IR can be used for in-field surveillance of the plant health. Surface-enhanced RS (SERS) has also been used for direct detection of plant stressors, offering advantages over traditional spectroscopies. Finally, all three of these technologies have applications in phenotyping and studying composition of crops. Such non-invasive, non-destructive, and chemical-free diagnostics is set to revolutionize crop agriculture globally. This review critically discusses the most recent findings of RS-based sensing of biotic and abiotic stresses, as well as the use of RS for nutritional analysis of foods.
Collapse
Affiliation(s)
- Isaac D. Juárez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Interdisciplinary Faculty of Toxicology, Texas A&M University,
College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Interdisciplinary Faculty of Toxicology, Texas A&M University,
College Station, TX, United States
| |
Collapse
|
9
|
Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
Collapse
Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
| |
Collapse
|
10
|
Anbazhagan P, Parameswari B, Anitha K, Chaitra GV, Bajaru B, Rajashree A, Mangrauthia SK, Yousuf F, Chalam VC, Singh GP. Advances in plant pathogen detection: integrating recombinase polymerase amplification with CRISPR/Cas systems. 3 Biotech 2024; 14:214. [PMID: 39211481 PMCID: PMC11349965 DOI: 10.1007/s13205-024-04055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Plant pathogens are causing substantial economic losses and thus became a significant threat to global agriculture. Effective and timely detection methods are prerequisite for combating the damages caused by the plant pathogens. In the realm of plant pathogen detection, the isothermal amplification techniques, e.g., recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), have emerged as a fast, precise, and most sensitive alternative to conventional PCR but they often comprise high rates of non-specific amplification and operational complexity. In recent advancements, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease Cas systems, particularly Cas12, have emerged as powerful tools for highly sensitive, specific, and rapid pathogen detection. Exploiting the collateral activities of Cas12, which selectively cleaves single-stranded DNA (ssDNA), novel detection platforms have been developed. The mechanism employs the formation of a triple complex molecule comprising guide RNA, Cas12 enzyme, and the substrate target nucleotide sequence. Upon recognition of the target, Cas12 indiscriminately cleaves the DNA strand, leading to the release of fluorescence from the cleaved ssDNA reporter. Integration of isothermal amplification methods with CRISPR/Cas12 enables one-step detection assays, facilitating rapid pathogen identification within 30 min at a single temperature. This integrated RPA-CRISPR/Cas12a approach eliminates the need for RNA extraction and cDNA conversion, allowing direct use of crude plant sap as a template. With an affordable fluorescence visualization system, this portable method achieves 100-fold greater sensitivity than conventional techniques. This review summarizes recent advances in RPA-CRISPR/Cas12a for detecting plant pathogens, covering primer design, field-level portability, and enhanced sensitivity.
Collapse
Affiliation(s)
- P. Anbazhagan
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - B. Parameswari
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - K. Anitha
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - G. V. Chaitra
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - Bhaskar Bajaru
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - A. Rajashree
- ICAR-National Bureau of Plant Genetic Resources Regional Station, Hyderabad, Telangana 500030 India
| | - S. K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - Faisal Yousuf
- ICAR-Indian Institute of Rice Research, Hyderabad, Telangana 500030 India
| | - V. Celia Chalam
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012 India
| | - G. P. Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012 India
| |
Collapse
|
11
|
Massman C, Rivedal HM, Dorman SJ, Tanner KC, Fredrickson C, Temple TN, Fisk S, Helgerson L, Hayes PM. Yellow Dwarf Virus Resistance in Barley: Phenotyping, Remote Imagery, and Virus-Vector Characterization. PHYTOPATHOLOGY 2024; 114:2084-2095. [PMID: 38916923 DOI: 10.1094/phyto-10-23-0394-kc] [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: 06/26/2024]
Abstract
Yellow dwarf viruses (YDVs) spread by aphids are some of the most economically important barley (Hordeum vulgare) virus-vector complexes worldwide. Detection and control of these viruses are critical components in the production of barley, wheat, and numerous other grasses of agricultural importance. Genetic control of plant diseases is often preferable to chemical control to reduce the environmental and economic cost of foliar insecticides. Accordingly, the objectives of this work were to (i) screen a barley population for resistance to YDVs under natural infection using phenotypic assessment of disease symptoms, (ii) implement drone imagery to further assess resistance and test its utility as a disease screening tool, (iii) identify the prevailing virus and vector types in the experimental environment, and (iv) perform a genome-wide association study to identify genomic regions associated with measured traits. Significant genetic differences were found in a population of 192 barley inbred lines regarding their YDV symptom severity, and symptoms were moderately to highly correlated with grain yield. The YDV severity measured with aerial imaging was highly correlated with on-the-ground estimates (r = 0.65). Three aphid species vectoring three YDV species were identified with no apparent genotypic influence on their distribution. A quantitative trait locus impacting YDV resistance was detected on chromosome 2H, albeit undetected using aerial imaging. However, quantitative trait loci for canopy cover and mean normalized difference vegetation index were successfully mapped using the drone. This work provides a framework for utilizing drone imagery in future resistance breeding efforts for YDVs in cereals and grasses, as well as in other virus-vector disease complexes.
Collapse
Affiliation(s)
- Chris Massman
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Hannah M Rivedal
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - Seth J Dorman
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - K Christy Tanner
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Chance Fredrickson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Todd N Temple
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| |
Collapse
|
12
|
Chen Y, Zhong J, Lu M, Yang C. Transient Expression Vector Construction, Subcellular Localisation, and Evaluation of Antiviral Potential of Flagellin BP8-2. Molecules 2024; 29:3876. [PMID: 39202955 PMCID: PMC11357009 DOI: 10.3390/molecules29163876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/04/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
This study used the DNA of Bacillus amyloliquefaciens Ba168 as a template to amplify the flagellin BP8-2 gene and ligate it into the fusion expression vector pCAMBIA1300-35S-EGFP after digestion for the construction of the expression vector pCAMBIA1300-EGFP-BP8-2. Next, using Nicotiana benthamiana as receptor material, transient expression was carried out under the mediation of Agrobacterium tumefaciens C58C1. Finally, the transient expression and subcellular localisation of flagellin BP8-2 protein were analysed using the imaging of co-transformed GFP under laser confocal microscopy. The results showed that flagellin BP8-2 was localised in the cell membrane and nucleus, and the RT-PCR results showed that the BP8-2 gene could be stably expressed in tobacco leaf cells. Furthermore, there was stronger antiviral activity against tobacco mosaic virus (TMV) infection in Nicotiana glutinosa than in BP8-2 and ningnanmycin, with an inhibitory effect of 75.91%, protective effect of 77.45%, and curative effect of 68.15%. TMV movement and coat protein expression were suppressed, and there was a high expression of PR-1a, PAL, and NPR1 in BP8-2-treated tobacco leaf. These results suggest that flagellin BP8-2 inhibits TMV by inducing resistance. Moreover, BP8-2 has low toxicity and is easily biodegradable and eco-friendly. These results further enrich our understanding of the antiviral mechanisms of proteins and provide alternatives for controlling viral diseases in agriculture.
Collapse
Affiliation(s)
- Yahan Chen
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.Z.); (C.Y.)
| | - Jianxin Zhong
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.Z.); (C.Y.)
| | - Meihuan Lu
- Microbial Resources of Research Center, Microbiology Institute of Shaanxi, Xi’an 710043, China;
| | - Chengde Yang
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.Z.); (C.Y.)
| |
Collapse
|
13
|
Kanapiya A, Amanbayeva U, Tulegenova Z, Abash A, Zhangazin S, Dyussembayev K, Mukiyanova G. Recent advances and challenges in plant viral diagnostics. FRONTIERS IN PLANT SCIENCE 2024; 15:1451790. [PMID: 39193213 PMCID: PMC11347306 DOI: 10.3389/fpls.2024.1451790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
Accurate and timely diagnosis of plant viral infections plays a key role in effective disease control and maintaining agricultural productivity. Recent advances in the diagnosis of plant viruses have significantly expanded our ability to detect and monitor viral pathogens in agricultural crops. This review discusses the latest advances in diagnostic technologies, including both traditional methods and the latest innovations. Conventional methods such as enzyme-linked immunosorbent assay and DNA amplification-based assays remain widely used due to their reliability and accuracy. However, diagnostics such as next-generation sequencing and CRISPR-based detection offer faster, more sensitive and specific virus detection. The review highlights the main advantages and limitations of detection systems used in plant viral diagnostics including conventional methods, biosensor technologies and advanced sequence-based techniques. In addition, it also discusses the effectiveness of commercially available diagnostic tools and challenges facing modern diagnostic techniques as well as future directions for improving informed disease management strategies. Understanding the main features of available diagnostic methodologies would enable stakeholders to choose optimal management strategies against viral threats and ensure global food security.
Collapse
Affiliation(s)
- Aizada Kanapiya
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Ulbike Amanbayeva
- Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
| | - Zhanar Tulegenova
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
- Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
| | - Altyngul Abash
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Sayan Zhangazin
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Kazbek Dyussembayev
- Department of Biotechnology and Microbiology, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
- Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
| | - Gulzhamal Mukiyanova
- Laboratory of Biodiversity and Genetic Resources, National Center for Biotechnology, Astana, Kazakhstan
- Scientific Center "Agrotechnopark", Shakarim University, Semey, Kazakhstan
| |
Collapse
|
14
|
Martínez-Fajardo C, Navarro-Simarro P, Morote L, Rubio-Moraga Á, Mondéjar-López M, Niza E, Argandoña J, Ahrazem O, Gómez-Gómez L, López-Jiménez AJ. Exploring the viral landscape of saffron through metatranscriptomic analysis. Virus Res 2024; 345:199389. [PMID: 38714217 PMCID: PMC11101869 DOI: 10.1016/j.virusres.2024.199389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/09/2024]
Abstract
Saffron (Crocus sativus L.), a historically significant crop valued for its nutraceutical properties, has been poorly explored from a phytosanitary perspective. This study conducted a thorough examination of viruses affecting saffron samples from Spanish cultivars, using high-throughput sequencing alongside a systematic survey of transcriptomic datasets from Crocus sativus at the Sequence Read Archive. Our analysis unveiled a broad diversity and abundance, identifying 17 viruses across the 52 analyzed libraries, some of which were highly prevalent. This includes known saffron-infecting viruses and previously unreported ones. In addition, we discovered 7 novel viruses from the Alphaflexiviridae, Betaflexiviridae, Potyviridae, Solemoviridae, and Geminiviridae families, with some present in libraries from various locations. These findings indicate that the saffron-associated virome is more complex than previously reported, emphasizing the potential of phytosanitary analysis to enhance saffron productivity.
Collapse
Affiliation(s)
- Cristian Martínez-Fajardo
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Pablo Navarro-Simarro
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Lucía Morote
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Ángela Rubio-Moraga
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - María Mondéjar-López
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Enrique Niza
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Facultad de Farmacia. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Javier Argandoña
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - Oussama Ahrazem
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Facultad de Farmacia. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Alberto José López-Jiménez
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain.
| |
Collapse
|
15
|
Li Z, Qin J, Zhu Y, Zhou M, Zhao N, Zhou E, Wang X, Chen X, Cui X. Occurrence, distribution, and genetic diversity of faba bean viruses in China. Front Microbiol 2024; 15:1424699. [PMID: 38962134 PMCID: PMC11219563 DOI: 10.3389/fmicb.2024.1424699] [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: 04/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024] Open
Abstract
With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.
Collapse
Affiliation(s)
- Zongdi Li
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Jiachao Qin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Yuxiang Zhu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Mimi Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Na Zhao
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Enqiang Zhou
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Xuejun Wang
- Department of Economic Crops, Yanjiang Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Nantong, Jiangsu, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| | - Xiaoyan Cui
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, Jiangsu, China
| |
Collapse
|
16
|
Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
Collapse
Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| |
Collapse
|
17
|
Vlasava NB, Michener DC, Kharytonchyk S, Cortés-Ortiz L. Co-Infection of Tobacco Rattle and Cycas Necrotic Stunt Viruses in Paeonia lactiflora: Detection Strategies, Potential Origins of Infection, and Implications for Paeonia Germplasm Conservation. Viruses 2024; 16:893. [PMID: 38932185 PMCID: PMC11209033 DOI: 10.3390/v16060893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Increasing reports of tobacco rattle virus (TRV) and cycas necrotic stunt virus (CNSV) in herbaceous Paeonia worldwide highlight the importance of conserving the genetic resources of this economically important ornamental and medicinal crop. The unknown origin(s) of infection, differential susceptibility of peony cultivars to these viruses, and elusive disease phenotypes for CNSV in peonies make early detection and management challenging. Here, we report the presence of TRV and CNSV in plants of the University of Michigan living peony collection in the United States and a molecular characterization of their strains. Using sequences of the TRV 194 K RNA polymerase gene, we confirmed TRV infections in seven symptomatic plants (1.07% of all plants in the collection). Using newly developed primers, we recovered sequences of the CNSV RdRp gene and the polyprotein 1 gene region from nine out of twelve samples analyzed, including three from symptomless plants. Four of the nine plants had TRV and CNSV co-infections and showed more severe disease symptoms than plants only infected with TRV. Phylogenetic analyses of isolates from the University of Michigan living peony collection and publicly available isolates point to multiple origins of TRV and CNSV infections in this collection. This is the first report of TRV/CNSV co-infection and of a symptomatic detection of CNSV on cultivated P. lactiflora.
Collapse
Affiliation(s)
- Nastassia B. Vlasava
- Matthaei Botanical Gardens and Nichols Arboretum, University of Michigan, Ann Arbor, MI 48105, USA;
- Central Botanical Garden, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - David C. Michener
- Matthaei Botanical Gardens and Nichols Arboretum, University of Michigan, Ann Arbor, MI 48105, USA;
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| |
Collapse
|
18
|
González-Pérez E, Chiquito-Almanza E, Villalobos-Reyes S, Canul-Ku J, Anaya-López JL. Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding. Viruses 2024; 16:888. [PMID: 38932180 PMCID: PMC11209215 DOI: 10.3390/v16060888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.
Collapse
Affiliation(s)
| | - Elizabeth Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
| | | | | | - José Luis Anaya-López
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
| |
Collapse
|
19
|
Ali S, Tyagi A, Mir ZA. Plant Immunity: At the Crossroads of Pathogen Perception and Defense Response. PLANTS (BASEL, SWITZERLAND) 2024; 13:1434. [PMID: 38891243 PMCID: PMC11174815 DOI: 10.3390/plants13111434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Plants are challenged by different microbial pathogens that affect their growth and productivity. However, to defend pathogen attack, plants use diverse immune responses, such as pattern-triggered immunity (PTI), effector-triggered immunity (ETI), RNA silencing and autophagy, which are intricate and regulated by diverse signaling cascades. Pattern-recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat (NLR) receptors are the hallmarks of plant innate immunity because they can detect pathogen or related immunogenic signals and trigger series of immune signaling cascades at different cellular compartments. In plants, most commonly, PRRs are receptor-like kinases (RLKs) and receptor-like proteins (RLPs) that function as a first layer of inducible defense. In this review, we provide an update on how plants sense pathogens, microbe-associated molecular patterns (PAMPs or MAMPs), and effectors as a danger signals and activate different immune responses like PTI and ETI. Further, we discuss the role RNA silencing, autophagy, and systemic acquired resistance as a versatile host defense response against pathogens. We also discuss early biochemical signaling events such as calcium (Ca2+), reactive oxygen species (ROS), and hormones that trigger the activation of different plant immune responses. This review also highlights the impact of climate-driven environmental factors on host-pathogen interactions.
Collapse
Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Zahoor Ahmad Mir
- Department of Plant Science and Agriculture, University of Manitoba, Winnipeg, MB R2M 0TB, Canada;
| |
Collapse
|
20
|
Sandra N, Mandal B. Emerging evidence of seed transmission of begomoviruses: implications in global circulation and disease outbreak. FRONTIERS IN PLANT SCIENCE 2024; 15:1376284. [PMID: 38807782 PMCID: PMC11130427 DOI: 10.3389/fpls.2024.1376284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024]
Abstract
Begomoviruses (family Geminiviridae) are known for causing devastating diseases in fruit, fibre, pulse, and vegetable crops throughout the world. Begomoviruses are transmitted in the field exclusively through insect vector whitefly (Bemisia tabaci), and the frequent outbreaks of begomoviruses are attributed largely due to the abundance of whitefly in the agri-ecosystem. Begomoviruses being phloem-borne were known not be transmitted through seeds of the infected plants. The recent findings of seed transmission of begomoviruses brought out a new dimension of begomovirus perpetuation and dissemination. The first convincing evidence of seed transmission of begomoviruses was known in 2015 for sweet potato leaf curl virus followed by several begomoviruses, like bhendi yellow vein mosaic virus, bitter gourd yellow mosaic virus, dolichos yellow mosaic virus, mungbean yellow mosaic virus, mungbean yellow mosaic India virus, pepper yellow leaf curl Indonesia virus, tomato leaf curl New Delhi virus, tomato yellow leaf curl virus, tomato yellow leaf curl Sardinia virus, and okra yellow mosaic Mexico virus. These studies brought out two perspectives of seed-borne nature of begomoviruses: (i) the presence of begomovirus in the seed tissues derived from the infected plants but no expression of disease symptoms in the progeny seedlings and (ii) the seed infection successfully transmitted the virus to cause disease to the progeny seedlings. It seems that the seed transmission of begomovirus is a feature of a specific combination of host-genotype and virus strain, rather than a universal phenomenon. This review comprehensively describes the seed transmitted begomoviruses reported in the last 9 years and the possible mechanism of seed transmission. An emphasis is placed on the experimental results that proved the seed transmission of various begomoviruses, factors affecting seed transmission and impact of begomovirus seed transmission on virus circulation, outbreak of the disease, and management strategies.
Collapse
Affiliation(s)
- Nagamani Sandra
- Seed Pathology Laboratory, Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
21
|
Belete MT, Kim SE, Gudeta WF, Igori D, Kwon JA, Lee SH, Moon JS. Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis. Virol J 2024; 21:86. [PMID: 38622686 PMCID: PMC11017662 DOI: 10.1186/s12985-024-02361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.
Collapse
Affiliation(s)
- Mesele Tilahun Belete
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Amhara Agricultural Research Institute, Plant Biotechnology Research Division, Bahir Dar, Ethiopia
| | - Se Eun Kim
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Workitu Firmosa Gudeta
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jeong A Kwon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 98411, Republic of Korea.
| | - Jae Sun Moon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
22
|
Zaheer U, Munir F, Salum YM, He W. Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 2024; 12:e17115. [PMID: 38560454 PMCID: PMC10979746 DOI: 10.7717/peerj.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
Collapse
Affiliation(s)
- Uroosa Zaheer
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Faisal Munir
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yussuf Mohamed Salum
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiyi He
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| |
Collapse
|
23
|
Nourinejhad Zarghani S, Monavari M, Nourinejhad Zarghani A, Nouri S, Ehlers J, Hamacher J, Bandte M, Büttner C. Quantifying Plant Viruses: Evolution from Bioassay to Infectivity Dilution Curves along the Model of Tobamoviruses. Viruses 2024; 16:440. [PMID: 38543805 PMCID: PMC10974926 DOI: 10.3390/v16030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 05/23/2024] Open
Abstract
This review describes the development of the bioassay as a means of quantifying plant viruses, with particular attention to tobamovirus. It delves into various models used to establish a correlation between virus particle concentration and the number of induced local lesions (the infectivity dilution curve), including the Poisson, Furumoto and Mickey, Kleczkowski, Growth curve, and modified Poisson models. The parameters of each model are described, and their application or performance in the context of the tobacco mosaic virus is explored. This overview highlights the enduring value of the infectivity dilution curve in tobamovirus quantification, providing valuable insights for researchers or practitioners of bioassays and theoreticians of modeling.
Collapse
Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität in Berlin, Lentzeallee 55–57, 14197 Berlin, Germany; (S.N.); (J.E.); (M.B.); (C.B.)
| | - Mehran Monavari
- Section eScience, Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany;
| | - Amin Nourinejhad Zarghani
- School of Mechanical Engineering, Hamburg University of Technology, Eissendorfer Str. 38, 21073 Hamburg, Germany;
| | - Sahar Nouri
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität in Berlin, Lentzeallee 55–57, 14197 Berlin, Germany; (S.N.); (J.E.); (M.B.); (C.B.)
| | - Jens Ehlers
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität in Berlin, Lentzeallee 55–57, 14197 Berlin, Germany; (S.N.); (J.E.); (M.B.); (C.B.)
- Menno Chemie Vertrieb GmbH, Langer Kamp 104, 22850 Norderstedt, Germany
| | - Joachim Hamacher
- Institute of Crop Science and Resource Conservation (INRES)—Plant Pathology, Universität Bonn, Nussallee 9, 53115 Bonn, Germany;
| | - Martina Bandte
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität in Berlin, Lentzeallee 55–57, 14197 Berlin, Germany; (S.N.); (J.E.); (M.B.); (C.B.)
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität in Berlin, Lentzeallee 55–57, 14197 Berlin, Germany; (S.N.); (J.E.); (M.B.); (C.B.)
| |
Collapse
|
24
|
Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
Collapse
Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
| |
Collapse
|
25
|
Zvereva AS, Klingenbrunner M, Teige M. Calcium signaling: an emerging player in plant antiviral defense. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1265-1273. [PMID: 37940194 PMCID: PMC10901205 DOI: 10.1093/jxb/erad442] [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: 12/20/2022] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
Calcium is a universal messenger in different kingdoms of living organisms and regulates most physiological processes, including defense against pathogens. The threat of viral infections in humans has become very clear in recent years, and this has triggered detailed research into all aspects of host-virus interactions, including the suppression of calcium signaling in infected cells. At the same time, however, the threat of plant viral infections is underestimated in society, and research in the field of calcium signaling during plant viral infections is scarce. Here we highlight an emerging role of calcium signaling for antiviral protection in plants, in parallel with the known evidence from studies of animal cells. Obtaining more knowledge in this domain might open up new perspectives for future crop protection and the improvement of food security.
Collapse
Affiliation(s)
- Anna S Zvereva
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Michael Klingenbrunner
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Markus Teige
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| |
Collapse
|
26
|
Fang Y, Wang C, Wang Y, Hu J, Lai M, Liu P, Zhang H. Naked-eye detection of plant viral disease using polymerase chain reaction amplification and DNAzyme. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1003-1011. [PMID: 38269430 DOI: 10.1039/d3ay01367g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Plant viral diseases can seriously affect the yield and quality of crops. In this work, a convenient and highly sensitive biosensor for the visual detection of plant viral disease is proposed by the PCR-induced generation of DNAzyme. In the absence of nucleic acid for a target plant virus, the primers prohibited the production of G-quadruplex by forming a hairpin structure. However, PCR amplification occurred and generated a number of specific PCR products with free G-quadruplex sequences at both ends in the presence of the target cDNA. A catalytically active G-quadruplex DNAzyme was formed with the help of K+ and hemin, resulting in the formation of colored products visible to the naked eye and a strong absorbance by the addition of ABTS2- and H2O2. The absorbance and the logarithm of target cDNA concentrations showed a good linear relationship in the range of 10 fM-1.0 nM, with a linear regression equation of A = 0.1402 lg c + 0.3761 (c: fM) and a detection limit of 0.19 fM. This method was successfully applied to the analysis of emerging tobacco mosaic virus (TMV) infections in tobacco leaf samples collected in the field due to its flexibility and convenience, indicating a potential application for the early detection of plant viral disease.
Collapse
Affiliation(s)
- Yongwei Fang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Chuang Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Yuli Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Jiandong Hu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou, Henan 450002, China
| | - Miao Lai
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Pengfei Liu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| |
Collapse
|
27
|
Hamim I, Sipes B, Wang Y. Editorial: Detection, characterization, and management of plant pathogens. FRONTIERS IN PLANT SCIENCE 2024; 15:1354042. [PMID: 38414641 PMCID: PMC10897511 DOI: 10.3389/fpls.2024.1354042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Affiliation(s)
- Islam Hamim
- Department of Plant Pathology, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Brent Sipes
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yanan Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| |
Collapse
|
28
|
Smith KC, Blanchong JA. Detection of lymphoproliferative disease virus in Iowa Wild Turkeys (Meleagris gallopavo): Comparison of two sections of the proviral genome. PLoS One 2024; 19:e0296856. [PMID: 38346036 PMCID: PMC10861079 DOI: 10.1371/journal.pone.0296856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/20/2023] [Indexed: 02/15/2024] Open
Abstract
An accurate diagnostic test is an essential aspect of successfully monitoring and managing wildlife diseases. Lymphoproliferative Disease Virus (LPDV) is an avian retrovirus that was first identified in domestic turkeys in Europe and was first reported in a Wild Turkey (Meleagris gallopavo) in the United States in 2009. It has since been found to be widely distributed throughout North America. The majority of studies have utilized bone marrow and PCR primers targeting a 413-nucleotide sequence of the gag gene of the provirus to detect infection. While prior studies have evaluated the viability of other tissues for LPDV detection (whole blood, spleen, liver, cloacal swabs) none to date have studied differences in detection rates when utilizing different genomic regions of the provirus. This study examined the effectiveness of another section of the provirus, a 335-nucleotide sequence starting in the U3 region of the LTR (Long Terminal Repeat) and extending into the Matrix of the gag region (henceforth LTR), for detecting LPDV. Bone marrow samples from hunter-harvested Wild Turkeys (n = 925) were tested for LPDV with the gag gene and a subset (n = 417) including both those testing positive and those where LPDV was not detected was re-tested with LTR. The positive percent agreement (PPA) was 97.1% (68 of 70 gag positive samples tested positive with LTR) while the negative percent agreement (NPA) was only 68.0% (236 of 347 gag negative samples tested negative with LTR). Cohen's Kappa (κ = 0.402, Z = 10.26, p<0.0001) and the McNemar test (OR = 55.5, p<0.0001) indicated weak agreement between the two gene regions. We found that in Iowa Wild Turkeys use of the LTR region identified LPDV in many samples in which we failed to detect LPDV using the gag region and that LTR may be more appropriate for LPDV surveillance and monitoring. However, neither region of the provirus resulted in perfect detection and additional work is necessary to determine if LTR is more reliable in other geographic regions where LPDV occurs.
Collapse
Affiliation(s)
- Kelsey C. Smith
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, United States of Ameria
| | - Julie A. Blanchong
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, United States of Ameria
| |
Collapse
|
29
|
Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
Collapse
Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| |
Collapse
|
30
|
Metwally RA, Taha MA, El-Moaty NMA, Abdelhameed RE. Attenuation of Zucchini mosaic virus disease in cucumber plants by mycorrhizal symbiosis. PLANT CELL REPORTS 2024; 43:54. [PMID: 38315215 PMCID: PMC10844420 DOI: 10.1007/s00299-023-03138-y] [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: 10/12/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024]
Abstract
KEY MESSAGE Arbuscular mycorrhizal fungi generated systemic acquired resistance in cucumber to Zucchini yellow mosaic virus, indicating their prospective application in the soil as a sustainable, environmentally friendly approach to inhibit the spread of pathogens. The wide spread of plant pathogens affects the whole world, causing several plant diseases and threatening national food security as it disrupts the quantity and quality of economically important crops. Recently, environmentally acceptable mitigating practices have been required for sustainable agriculture, restricting the use of chemical fertilizers in agricultural areas. Herein, the biological control of Zucchini yellow mosaic virus (ZYMV) in cucumber (Cucumis sativus L.) plants using arbuscular mycorrhizal (AM) fungi was investigated. Compared to control plants, ZYMV-infected plants displayed high disease incidence (DI) and severity (DS) with various symptoms, including severe yellow mosaic, mottling and green blisters of leaves. However, AM fungal inoculation exhibited 50% inhibition for these symptoms and limited DS to 26% as compared to non-colonized ones. The detection of ZYMV by the Enzyme-Linked Immunosorbent Assay technique exhibited a significant reduction in AM-inoculated plants (5.23-fold) compared with non-colonized ones. Besides, mycorrhizal root colonization (F%) was slightly reduced by ZYMV infection. ZYMV infection decreased all growth parameters and pigment fractions and increased the malondialdehyde (MDA) content, however, these parameters were significantly enhanced and the MDA content was decreased by AM fungal colonization. Also, the protein, proline and antioxidant enzymes (POX and CAT) were increased with ZYMV infection with more enhancements due to AM root colonization. Remarkably, defence pathogenesis-related (PR) genes such as PR-a, PR-b, and PR-10 were quickly expressed in response to AM treatment. Our findings demonstrated the beneficial function of AM fungi in triggering the plant defence against ZYMV as they caused systemic acquired resistance in cucumber plants and supported their potential use in the soil as an environment-friendly method of hindering the spread of pathogenic microorganisms sustainably.
Collapse
Affiliation(s)
- Rabab A Metwally
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Mohamed A Taha
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Nada M Abd El-Moaty
- Microbiology Department, Soil, Water and Environment Research Institute (SWERI), Agricultural Research Center, Giza, Egypt
| | - Reda E Abdelhameed
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| |
Collapse
|
31
|
Alfaro-Fernández A, Taengua R, Font-San-Ambrosio I, Sanahuja-Edo E, Peiró R, Galipienso L, Rubio L. Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain. PLANTS (BASEL, SWITZERLAND) 2024; 13:250. [PMID: 38256804 PMCID: PMC10818716 DOI: 10.3390/plants13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate from Australia and the other two containing isolates from Iran and Europe, as well as four subclades. EMDV isolates from Spain were genetically very similar and grouped in a subclade together with one isolate from Germany and one from the UK. No new recombination events were detected in addition to one recombination previously reported, suggesting that recombination is rare for EMDV. The comparison of synonymous and non-synonymous rates showed that negative selection played an important role, and only two codons were under positive selection. Genetic differentiation (Fst test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations with high gene flow between both.
Collapse
Affiliation(s)
- Ana Alfaro-Fernández
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rafael Taengua
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Isabel Font-San-Ambrosio
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Esmeralda Sanahuja-Edo
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain; (A.A.-F.); (I.F.-S.-A.); (E.S.-E.)
| | - Rosa Peiró
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), 46022 Valencia, Valencia, Spain;
| | - Luis Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain; (R.T.); (L.G.)
| |
Collapse
|
32
|
Kim DY, Patel SKS, Rasool K, Lone N, Bhatia SK, Seth CS, Ghodake GS. Bioinspired silver nanoparticle-based nanocomposites for effective control of plant pathogens: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168318. [PMID: 37956842 DOI: 10.1016/j.scitotenv.2023.168318] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Plant pathogens, including bacteria, fungi, and viruses, pose significant challenges to the farming community due to their extensive diversity, the rapidly evolving phenomenon of multi-drug resistance (MDR), and the limited availability of effective control measures. Amid mounting global pressure, particularly from the World Health Organization, to limit the use of antibiotics in agriculture and livestock management, there is increasing consideration of engineered nanomaterials (ENMs) as promising alternatives for antimicrobial applications. Studies focusing on the application of ENMs in the fight against MDR pathogens are receiving increasing attention, driven by significant losses in agriculture and critical knowledge gaps in this crucial field. In this review, we explore the potential contributions of silver nanoparticles (AgNPs) and their nanocomposites in combating plant diseases, within the emerging interdisciplinary arena of nano-phytopathology. AgNPs and their nanocomposites are increasingly acknowledged as promising countermeasures against plant pathogens, owing to their unique physicochemical characteristics and inherent antimicrobial properties. This review explores recent advancements in engineered nanocomposites, highlights their diverse mechanisms for pathogen control, and draws attention to their potential in antibacterial, antifungal, and antiviral applications. In the discussion, we briefly address three crucial dimensions of combating plant pathogens: green synthesis approaches, toxicity-environmental concerns, and factors influencing antimicrobial efficacy. Finally, we outline recent advancements, existing challenges, and prospects in scholarly research to facilitate the integration of nanotechnology across interdisciplinary fields for more effective treatment and prevention of plant diseases.
Collapse
Affiliation(s)
- Dae-Young Kim
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea
| | | | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nasreena Lone
- School of Allied Healthcare and Sciences, JAIN Deemed University, Whitefield, Bangalore 560066, India
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | | | - Gajanan Sampatrao Ghodake
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea.
| |
Collapse
|
33
|
Zhao X, Wu J, Ma Z, Shi Y, Fang Z, Wu J, Yang X, Zhou X. Development and application of monoclonal antibody-based dot-ELISA and colloidal gold immunochromatographic strip for rapid, specific, and sensitive detection of tomato brown rugose fruit virus. J Virol Methods 2024; 323:114841. [PMID: 37939857 DOI: 10.1016/j.jviromet.2023.114841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) is an emerging tobamovirus that has become a great concern to tomato production industry. Due to the lack of resistant cultivars, precise detection of ToBRFV is essential to prevent the spread of ToBRFV. In this study, we produced highly sensitive and specific monoclonal antibodies against ToBRFV and established dot-enzyme-linked immunosorbent assay (dot-ELISA) and colloidal gold immunochromatographic strip (CGICS)-based methods for ToBRFV detection. These two methods could specifically detect ToBRFV without cross-reaction with seven tested tobamoviruses and three frequently occurring tomato-infecting viruses. Sensitivity analysis showed that the limit of detection of the established dot-ELISA and CGICS methods reached up to 1:6400 and 1:10,000 (w/v, g/mL) dilution of ToBRFV-infected tomato tissue, respectively. Further analyses using field-collected tomato foliar and fruit samples showed that the results obtained by dot-ELISA and CGICS were consistent with those obtained by reverse transcription polymerase chain reaction. The established methods here allow for specific, sensitive, and robust detection of ToBRFV, and will be helpful for precise monitoring and early warning of ToBRFV.
Collapse
Affiliation(s)
- Xinru Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiayu Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ziyue Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yujie Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhu Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
34
|
Dutta P, Mäkinen K. Absolute and Relative Quantification of Single-Stranded Positive-Sense RNA Viruses from Plant Tissue. Methods Mol Biol 2024; 2724:81-91. [PMID: 37987900 DOI: 10.1007/978-1-0716-3485-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Reverse transcription quantitative PCR (RT-qPCR) allows sensitive and specific measurement of mRNA transcripts from a given sample in a short period of time. Relative and absolute RT-qPCR are two strategies that could be used to quantify mRNA transcripts, based on the goal of the experiment. Here, we describe the protocol for the quantification of plant viral RNA transcripts from an infected sample using both strategies.
Collapse
Affiliation(s)
- Pinky Dutta
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
35
|
Sidharthan VK, Ashajyothi M. Neolamarckia cadamba hosts a putative novel deltapartitivirus: a revelation by transcriptome data-mining. Virusdisease 2023; 34:550-553. [PMID: 38046061 PMCID: PMC10686936 DOI: 10.1007/s13337-023-00845-8] [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: 06/18/2023] [Accepted: 08/28/2023] [Indexed: 12/05/2023] Open
Abstract
Neolamarckia cadamba (Roxb.) Bosser is a medicinally important, fast-growing, timber-yielding tree species. In the present study, the virome of N. cadamba was explored using the publicly available N. cadamba transcriptome datasets and a putative novel virus, tentatively named as cadamba cryptic virus 1 (CdbCV1), was identified. CdbCV1 contained two genome segments, each coding for a single protein. CdbCV1 RNA1 (1564 nt) encoded for an RNA dependent RNA polymerase (RdRp) protein while CdbCV1 RNA2 (1492 nt) encoded for a coat protein (CP). Phylogenetic and sequence similarity analyses revealed the relatedness of CdbCV1 to pepper cryptic virus 1 and pittosporum cryptic virus 1. Based on the species demarcation criteria, genome organization and phylogeny, CdbCV1 can be regarded a new member of the genus Deltapartitivirus. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00845-8.
Collapse
Affiliation(s)
| | - Mushineni Ashajyothi
- Plant Protection Lab, ICAR–Central Agroforestry Research Institute, Jhansi, 284003 India
| |
Collapse
|
36
|
Grunwald DJ, Stroschein SM, Grinstead S, Mollov D, Rioux RA, Rakotondrafara AM. Targeting the Highly Conserved 3' Untranslated Region of Iris Severe Mosaic Virus for Sensitive Monitoring of the Disease Prevalence in Iris Production. PLANT DISEASE 2023; 107:3763-3772. [PMID: 37386702 DOI: 10.1094/pdis-04-23-0631-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: 07/01/2023]
Abstract
Iris severe mosaic virus (ISMV, Potyviridae) can threaten the sustainability of iris production and the marketability of the plants. Effective intervention and control strategies require rapid and early detection of viral infections. The wide range of viral symptoms, from asymptomatic to severe chlorosis of the leaves, renders diagnosis solely based on visual indicators ineffective. A nested PCR-based diagnostic assay was developed for the reliable detection of ISMV in iris leaves and in rhizomes. Considering the genetic variability of ISMV, two primer pairs were designed to detect the highly conserved 3' untranslated region (UTR) of the viral genomic RNA. The specificity of the primer pairs was confirmed against four other potyviruses. The sensitivity of detection was enhanced by one order of magnitude using diluted cDNA and a nested approach. Nested PCR facilitated detecting ISMV on field-grown samples beyond the capabilities of a currently available immunological test and in iris rhizome, which would facilitate ensuring clean stock is planted. This approach dramatically improves the detection threshold of ISMV on potentially low virus titer samples. The study provides a practical, accurate, and sensitive tool for the early detection of a deleterious virus that infects a popular ornamental and landscape plant.
Collapse
Affiliation(s)
- Derrick J Grunwald
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
| | | | - Sam Grinstead
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD 20705
| | - Dimitre Mollov
- Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330
| | - Renée A Rioux
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53705
| | | |
Collapse
|
37
|
Ramathani I, Sserumaga JP, Nanyiti S, Mukasa SB, Alicai T. Molecular Diversity of Rice Yellow Mottle Virus in Uganda and Relationships with Other Strains from Africa. PLANT DISEASE 2023; 107:3475-3486. [PMID: 37133339 DOI: 10.1094/pdis-08-22-1989-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: 05/04/2023]
Abstract
Rice yellow mottle virus disease, caused by Rice yellow mottle virus (RYMV), is the most important disease of lowland rice in Uganda. However, little is known about its genetic diversity in Uganda and relationships with other strains elsewhere across Africa. A new degenerate primer pair that targets amplification of the entire RYMV coat protein gene (circa 738 bp) was designed to aid virus variability analysis using RT-PCR and Sanger sequencing. A total of 112 rice leaf samples from plants with RYMV mottling symptoms were collected during the year 2022 in 35 lowland rice fields within Uganda. The RYMV RT-PCR results were 100% positive, and all 112 PCR products were sequenced. BLASTn analysis revealed that all isolates were closely related (93 to 98%) to those previously studied originating from Kenya, Tanzania, and Madagascar. Despite high purifying selection pressure, diversity analysis on 81 out of 112 RYMV CP sequences revealed a very low diversity index of 3 and 1.0% at the nucleotide and amino acid levels, respectively. Except for glutamine, amino acid profile analysis revealed that all 81 Ugandan isolates shared the primary 19 amino acids based on the RYMV coat protein region examined. Except for one isolate (UG68) from eastern Uganda that clustered alone, phylogeny analysis revealed two major clades. The Ugandan RYMV isolates were phylogenetically related to those from the Democratic Republic of Congo, Madagascar, and Malawi but not to RYMV isolates in West Africa. Thus, the RYMV isolates in this study are related to serotype 4, a strain common in eastern and southern Africa. RYMV serotype 4 originated in Tanzania, where evolutionary forces of mutation have resulted in the emergence and spread of new variants. Furthermore, mutations are evident within the coat protein gene of the Ugandan isolates, which may be attributed to changing RYMV pathosystems as a result of rice production intensification in Uganda. Overall, the diversity of RYMV was limited and most noticeably in eastern Uganda.
Collapse
Affiliation(s)
- Idd Ramathani
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Julius P Sserumaga
- National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Sarah Nanyiti
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
| | - Settumba B Mukasa
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), National Agricultural Research Organisation, Kampala, Uganda
| |
Collapse
|
38
|
Rott P, Grinstead S, Dallot S, Foster ZSL, Daugrois JH, Fernandez E, Kaye CJ, Hendrickson L, Hu X, Adhikari B, Malapi M, Grünwald NJ, Roumagnac P, Mollov D. Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations Worldwide. PLANT DISEASE 2023; 107:3437-3447. [PMID: 37079008 DOI: 10.1094/pdis-10-22-2405-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: 05/03/2023]
Abstract
Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, has been reported in an increasing number of sugarcane-growing locations since its first report in the 1990s in Brazil, Florida, and Hawaii. In this study, the genetic diversity of SCYLV was investigated using the genome coding sequence (5,561 to 5,612 nt) of 109 virus isolates from 19 geographical locations, including 65 new isolates from 16 geographical regions worldwide. These isolates were distributed in three major phylogenetic lineages (BRA, CUB, and REU), except for one isolate from Guatemala. Twenty-two recombination events were identified among the 109 isolates of SCYLV, thus confirming that recombination was a significant driving force in the genetic diversity and evolution of this virus. No temporal signal was found in the genomic sequence dataset, most likely because of the short temporal window of the 109 SCYLV isolates (1998 to 2020). Among 27 primers reported in the literature for the detection of the virus by RT-PCR, none matched 100% with all 109 SCYLV sequences, suggesting that the use of some primer pairs may not result in the detection of all virus isolates. Primers YLS111/YLS462, which were the first primer pair used by numerous research organizations to detect the virus by RT-PCR, failed to detect isolates belonging to the CUB lineage. In contrast, primer pair ScYLVf1/ScYLVr1 efficiently detected isolates of all three lineages. Continuous pursuit of knowledge of SCYLV genetic variability is therefore critical for effective diagnosis of yellow leaf, especially in virus-infected and mainly asymptomatic sugarcane plants.
Collapse
Affiliation(s)
- Philippe Rott
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sam Grinstead
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Sylvie Dallot
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Zachary S L Foster
- Horticultural Crops Disease and Pest Management Research Unit, USDA-ARS, Corvallis, OR 97330, U.S.A
| | - Jean H Daugrois
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Xiaojun Hu
- Plant Germplasm Quarantine Program, USDA-APHIS, Beltsville, MD 20705, U.S.A
| | - Bishwo Adhikari
- Plant Germplasm Quarantine Program, USDA-APHIS, Beltsville, MD 20705, U.S.A
| | - Martha Malapi
- Plant Germplasm Quarantine Program, USDA-APHIS, Beltsville, MD 20705, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA-ARS, Corvallis, OR 97330, U.S.A
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34398 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Dimitre Mollov
- Horticultural Crops Disease and Pest Management Research Unit, USDA-ARS, Corvallis, OR 97330, U.S.A
| |
Collapse
|
39
|
Zhao Y, Yang S, Jiang L, Yang Q, Luo L, Jiang J, Malichan S, Zhao J, Xie X. Pitaya Virus X Coat Protein Acts as an RNA Silencing Suppressor and Can Be Used as a Specific Target for Detection Using RT-LAMP. PLANT DISEASE 2023; 107:3378-3382. [PMID: 37079007 DOI: 10.1094/pdis-11-22-2570-sc] [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: 05/03/2023]
Abstract
Selenicereus undatus (Haworth) D.R. Hunt (pitaya) is a tropical fruit that has been commonly cultivated in Guizhou Province, China, in recent years due to its good taste and high nutritional value. This planting area currently ranks third in China. Viral diseases have increasingly emerged in pitaya cultivation because of the expansion of the pitaya planting area and the characteristics of asexual propagation. The spread of pitaya virus X (PiVX; a Potexvirus) is among the most severe viruses threatening the quality and yield of pitaya fruit. To investigate the occurrence of PiVX in pitaya cultivations in Guizhou Province, we developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method that can detect PiVX with high sensitivity and specificity at a low cost and produce a visualized result. Our best RT-LAMP system was significantly more sensitive than RT-PCR and was highly specific to PiVX. Furthermore, PiVX coat protein (CP) can form a homodimer, and PiVX may use its CP as a plant RNA silencing suppressor to enhance infection. To the best of our knowledge, this is the first report of fast detection of PiVX and functional exploration of CP in a Potexvirus. These findings will provide an opportunity for early diagnosis and prevention of viruses in pitaya.
Collapse
Affiliation(s)
- Yue Zhao
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Shutong Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Ling Jiang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Qian Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Liting Luo
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P.R. China
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Jin Zhao
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| |
Collapse
|
40
|
Oh C, Zhou A, O'Brien K, Schmidt AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Appl Environ Microbiol 2023; 89:e0033123. [PMID: 37791775 PMCID: PMC10654041 DOI: 10.1128/aem.00331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023] Open
Abstract
Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.
Collapse
Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua Geltz
- Division of Laboratories, Illinois Department of Public Health, Springfield, Illinois, USA
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
41
|
Shoaib M, Shah B, Sayed N, Ali F, Ullah R, Hussain I. Deep learning for plant bioinformatics: an explainable gradient-based approach for disease detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1283235. [PMID: 37900739 PMCID: PMC10612337 DOI: 10.3389/fpls.2023.1283235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023]
Abstract
Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a combination of these omics data to learn crucial plant disease detection characteristics. We trained our model with multiple hyperparameters, such as the learning rate, number of hidden layers, and dropout rate, and attained a test set accuracy of 95.5%. We also conducted a sensitivity analysis to determine the model's resistance to hyperparameter variations. Our analysis revealed that our model exhibited a notable degree of resilience in the face of these variations, resulting in only marginal changes in performance. Furthermore, we conducted a comparative examination of the time efficiency of our EG-CNN model in relation to baseline models, including SVM, Random Forest, and Logistic Regression. Although our model necessitates additional time for training and validation due to its intricate architecture, it demonstrates a faster testing time per sample, offering potential advantages in real-world scenarios where speed is paramount. To gain insights into the internal representations of our EG-CNN model, we employed saliency maps for a qualitative analysis. This visualization approach allowed us to ascertain that our model effectively captures crucial aspects of plant disease, encompassing alterations in gene expression, metabolite levels, and spectral discrepancies within plant tissues. Leveraging omics data and hyperspectral images, this study underscores the potential of deep learning methods in the realm of plant disease detection. The proposed EG-CNN model exhibited impressive accuracy and displayed a remarkable degree of insensitivity to hyperparameter variations, which holds promise for future plant bioinformatics applications.
Collapse
Affiliation(s)
- Muhammad Shoaib
- Department of Computer Science, CECOS University of IT and Emerging Sciences, Peshawar, Pakistan
| | - Babar Shah
- College of Technological Innovation, Zayed University, Dubai, United Arab Emirates
| | - Nasir Sayed
- Department of Computer Science, Islamia College Peshawar, Peshawar, Pakistan
| | - Farman Ali
- Department of Computer Science and Engineering, School of Convergence, College of Computing and Informatics, Sungkyunkwan University, Seoul, Republic of Korea
| | - Rafi Ullah
- Department of Medical Laboratory Technology, Riphah International University, Islamabad, Pakistan
| | - Irfan Hussain
- Centre for Autonomous Robotic Systems, Khalifa University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
42
|
Manzoor S, Nabi SU, Baranwal VK, Verma MK, Parveen S, Rather TR, Raja WH, Shafi M. Overview on century progress in research on mosaic disease of apple (Malus domestica Borkh) incited by apple mosaic virus/apple necrotic mosaic virus. Virology 2023; 587:109846. [PMID: 37586234 DOI: 10.1016/j.virol.2023.109846] [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: 04/25/2023] [Revised: 07/04/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Apple mosaic is widely distributed disease throughout the apple growing regions leading to the major adverse effects both qualitatively and quantitatively. Earlier the apple mosaic virus-ApMV was regarded as the only causal agent of the disease, but recently a novel virus apple necrotic mosaic virus-ApNMV have been reported as the causal pathogen from various apple growing countries. Accurate diagnosis of disease and detection of ApMV and ApNMV are of utmost importance, because without this ability we can neither understand nor control this disease. Both the viruses are mostly controlled through quarantine, isolation, sanitation and certification programs depending on sensitive and specific detection methods available. Here we review the 100-year progress in research on apple mosaic disease, which includes history, yield losses, causal agents, their genome organization, replication, traditional to recent detection methods, transmission, distribution and host range of associated viruses and management of the disease.
Collapse
Affiliation(s)
- Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201, India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India.
| | | | - Mahendra K Verma
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Shugufta Parveen
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Tariq Rasool Rather
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025, India
| | - Wasim H Raja
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132, India
| | - Mansoor Shafi
- Department of Plant Resources and Environment, Jeju National University, Jeju-si, 63243, Republic of Korea
| |
Collapse
|
43
|
Mäkinen K, Aspelin W, Pollari M, Wang L. How do they do it? The infection biology of potyviruses. Adv Virus Res 2023; 117:1-79. [PMID: 37832990 DOI: 10.1016/bs.aivir.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Affiliation(s)
- Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - William Aspelin
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Maija Pollari
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Linping Wang
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| |
Collapse
|
44
|
Rabadán MP, Juárez M, Gómez P. Long-Term Monitoring of Aphid-Transmitted Viruses in Melon and Zucchini Crops: Genetic Diversity and Population Structure of Cucurbit Aphid-Borne Yellows Virus and Watermelon Mosaic Virus. PHYTOPATHOLOGY 2023; 113:1761-1772. [PMID: 37014099 DOI: 10.1094/phyto-10-22-0394-v] [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: 06/19/2023]
Abstract
Understanding the emergence and prevalence of viral diseases in crops requires the systematic epidemiological monitoring of viruses, as well as the analysis of how ecological and evolutionary processes combine to shape viral population dynamics. Here, we extensively monitored the occurrence of six aphid-transmitted viruses in melon and zucchini crops in Spain for 10 consecutive cropping seasons between 2011 and 2020. The most prevalent viruses were cucurbit aphid-borne yellows virus (CABYV) and watermelon mosaic virus (WMV), found in 31 and 26% of samples with yellowing and mosaic symptoms. Other viruses, such as zucchini yellow mosaic virus, cucumber mosaic virus, Moroccan watermelon mosaic virus, and papaya ring spot virus, were detected less frequently (<3%) and mostly in mixed infections. Notably, our statistical analysis showed a significant association between CABYV and WMV in melon and zucchini hosts, suggesting that mixed infections might be influencing the evolutionary epidemiology of these viral diseases. We then carried out a comprehensive genetic characterization of the full-length genome sequences from CABYV and WMV isolates by using the Pacific Biosciences single-molecule real-time (PacBio) high-throughput technology to assess the genetic variation and structure of their populations. Our results showed that the CABYV population displayed seven codons under positive selection, and although most isolates clustered in the Mediterranean clade, a subsequent analysis of molecular variance revealed a significant, fine-scale temporal structure, which was in part explained by the level of the variance between isolates from single and mixed infections. In contrast, the WMV population genetic analysis showed that most of the isolates grouped into the Emergent clade, with no genetic differentiation and under purifying selection. These results underlie the epidemiological relevance of mixed infections for CABYV and provide a link between genetic diversity and CABYV dynamics at the whole-genome level.
Collapse
Affiliation(s)
- M P Rabadán
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100, Murcia, Spain
| | - M Juárez
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO), Universidad Miguel Hernández de Elche, Ctra de Beniel km 3,2 03312 Orihuela, Alicante, Spain
| | - P Gómez
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100, Murcia, Spain
| |
Collapse
|
45
|
Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
Collapse
Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | | |
Collapse
|
46
|
Jiang T, Zhou T. Unraveling the Mechanisms of Virus-Induced Symptom Development in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2830. [PMID: 37570983 PMCID: PMC10421249 DOI: 10.3390/plants12152830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Plant viruses, as obligate intracellular parasites, induce significant changes in the cellular physiology of host cells to facilitate their multiplication. These alterations often lead to the development of symptoms that interfere with normal growth and development, causing USD 60 billion worth of losses per year, worldwide, in both agricultural and horticultural crops. However, existing literature often lacks a clear and concise presentation of the key information regarding the mechanisms underlying plant virus-induced symptoms. To address this, we conducted a comprehensive review to highlight the crucial interactions between plant viruses and host factors, discussing key genes that increase viral virulence and their roles in influencing cellular processes such as dysfunction of chloroplast proteins, hormone manipulation, reactive oxidative species accumulation, and cell cycle control, which are critical for symptom development. Moreover, we explore the alterations in host metabolism and gene expression that are associated with virus-induced symptoms. In addition, the influence of environmental factors on virus-induced symptom development is discussed. By integrating these various aspects, this review provides valuable insights into the complex mechanisms underlying virus-induced symptoms in plants, and emphasizes the urgency of addressing viral diseases to ensure sustainable agriculture and food production.
Collapse
Affiliation(s)
| | - Tao Zhou
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
47
|
Samaniego-Gámez BY, Valle-Gough RE, Garruña-Hernández R, Reyes-Ramírez A, Latournerie-Moreno L, Tun-Suárez JM, Villanueva-Alonzo HDJ, Nuñez-Ramírez F, Diaz LC, Samaniego-Gámez SU, Minero-García Y, Hernandez-Zepeda C, Moreno-Valenzuela OA. Induced Systemic Resistance in the Bacillus spp.- Capsicum chinense Jacq.-PepGMV Interaction, Elicited by Defense-Related Gene Expression. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112069. [PMID: 37299048 DOI: 10.3390/plants12112069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
Induced systemic resistance (ISR) is a mechanism involved in the plant defense response against pathogens. Certain members of the Bacillus genus are able to promote the ISR by maintaining a healthy photosynthetic apparatus, which prepares the plant for future stress situations. The goal of the present study was to analyze the effect of the inoculation of Bacillus on the expression of genes involved in plant responses to pathogens, as a part of the ISR, during the interaction of Capsicum chinense infected with PepGMV. The effects of the inoculation of the Bacillus strains in pepper plants infected with PepGMV were evaluated by observing the accumulation of viral DNA and the visible symptoms of pepper plants during a time-course experiment in greenhouse and in in vitro experiments. The relative expression of the defense genes CcNPR1, CcPR10, and CcCOI1 were also evaluated. The results showed that the plants inoculated with Bacillus subtilis K47, Bacillus cereus K46, and Bacillus sp. M9 had a reduction in the PepGMV viral titer, and the symptoms in these plants were less severe compared to the plants infected with PepGMV and non-inoculated with Bacillus. Additionally, an increase in the transcript levels of CcNPR1, CcPR10, and CcCOI1 was observed in plants inoculated with Bacillus strains. Our results suggest that the inoculation of Bacillus strains interferes with the viral replication, through the increase in the transcription of pathogenesis-related genes, which is reflected in a lowered plant symptomatology and an improved yield in the greenhouse, regardless of PepGMV infection status.
Collapse
Affiliation(s)
- Blancka Yesenia Samaniego-Gámez
- Institute of Agricultural Sciences, Autonomous University of Baja California, Delta Highway s/n Ejido Nuevo León, Mexicali P.O. Box 21705, Baja California, Mexico
| | - Raúl Enrique Valle-Gough
- Institute of Agricultural Sciences, Autonomous University of Baja California, Delta Highway s/n Ejido Nuevo León, Mexicali P.O. Box 21705, Baja California, Mexico
| | - René Garruña-Hernández
- CONACYT-National Technological Institute of Mexico, Technological Institute of Conkal, CONACYT, Tecnológico Ave. s/n, Conkal P.O. Box 97345, Yucatán, Mexico
| | - Arturo Reyes-Ramírez
- National Technological Institute of Mexico, Conkal Institute of Technology, Division of Graduate Studies and Research, Av. Tecnológico s/n, Conkal P.O. Box 97345, Yucatán, Mexico
| | - Luis Latournerie-Moreno
- National Technological Institute of Mexico, Conkal Institute of Technology, Division of Graduate Studies and Research, Av. Tecnológico s/n, Conkal P.O. Box 97345, Yucatán, Mexico
| | - José María Tun-Suárez
- National Technological Institute of Mexico, Conkal Institute of Technology, Division of Graduate Studies and Research, Av. Tecnológico s/n, Conkal P.O. Box 97345, Yucatán, Mexico
| | - Hernán de Jesús Villanueva-Alonzo
- Regional Research Center "Dr. Hideyo Noguchi", Cell Biology Laboratory, Autonomous University of Yucatan, Av. Itzáez, Nmbr. 490 by 59 St. Centro, Merida P.O. Box 97000, Yucatán, Mexico
| | - Fidel Nuñez-Ramírez
- Institute of Agricultural Sciences, Autonomous University of Baja California, Delta Highway s/n Ejido Nuevo León, Mexicali P.O. Box 21705, Baja California, Mexico
| | - Lourdes Cervantes Diaz
- Institute of Agricultural Sciences, Autonomous University of Baja California, Delta Highway s/n Ejido Nuevo León, Mexicali P.O. Box 21705, Baja California, Mexico
| | - Samuel Uriel Samaniego-Gámez
- Institute of Agricultural Sciences, Autonomous University of Baja California, Delta Highway s/n Ejido Nuevo León, Mexicali P.O. Box 21705, Baja California, Mexico
| | - Yereni Minero-García
- Yucatan Center of Scientific Research, Plant Biochemistry and Molecular Biology Unit, 43 St., Nmbr. 130, Chuburna de Hidalgo, Merida P.O. Box 97200, Yucatán, Mexico
| | - Cecilia Hernandez-Zepeda
- Yucatan Center of Scientific Research, Water Sciences Unit, 8 St., Nmbr. 39, SM 64, Mz. 29, Cancun P.O. Box 77500, Quintana Roo, Mexico
| | - Oscar A Moreno-Valenzuela
- Yucatan Center of Scientific Research, Plant Biochemistry and Molecular Biology Unit, 43 St., Nmbr. 130, Chuburna de Hidalgo, Merida P.O. Box 97200, Yucatán, Mexico
| |
Collapse
|
48
|
Li J, Wu X, Liu H, Wang X, Yi S, Zhong X, Wang Y, Wang Z. Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China. Viruses 2023; 15:v15041029. [PMID: 37113009 PMCID: PMC10141686 DOI: 10.3390/v15041029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5'-untranslated region (UTR) and a 76-nt 3'-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1.
Collapse
Affiliation(s)
- Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hui Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaomei Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| |
Collapse
|
49
|
Dossou L, Pinel-Galzi A, Aribi J, Poulicard N, Albar L, Fatogoma S, Ndjiondjop MN, Koné D, Hébrard E. Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates. Viruses 2023; 15:v15040959. [PMID: 37112939 PMCID: PMC10144094 DOI: 10.3390/v15040959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.
Collapse
Affiliation(s)
- Laurence Dossou
- AfricaRice Center, M'bé Research Station, Bouaké 01 BP 2551, Côte d'Ivoire
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Jamel Aribi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Laurence Albar
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Sorho Fatogoma
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | | | - Daouda Koné
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| |
Collapse
|
50
|
Martin AP, Martínez MF, Chiesa MA, Garcia L, Gerhardt N, Uviedo F, Torres PS, Marano MR. Priming crop plants with rosemary (Salvia rosmarinus Spenn, syn Rosmarinus officinalis L.) extract triggers protective defense response against pathogens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107644. [PMID: 36996636 DOI: 10.1016/j.plaphy.2023.107644] [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: 01/05/2023] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Plant bioactive compounds provide novel straightforward approaches to control plant diseases. Rosemary (Salvia rosmarinus)-derived extracts carry many prominent pharmacological activities, including antimicrobial and antioxidant, mainly due to its phenolic compounds, rosmarinic acid (RA), carnosic acid and carnosol. However, the effects of these extracts on plant diseases are still unknown, which constrains its potential application as bioprotectant in the agricultural production. In this study we demonstrate the antiviral effect of the aqueous rosemary extract (ARE) against tobacco necrosis virus strain A (TNVA) in ARE-treated tobacco (Nicotiana tabacum) plants. Our results show that ARE-treatment enhances plant defense response, contributing to reduce virus replication and systemic movement in tobacco plants. RA, the main phenolic compound detected in this extract, is one of the main inducers of TNVA control. The ARE-induced protection in TNVA-infected plants was characterized by the expression of H2O2 scavengers and defense-related genes, involving salicylic acid- and jasmonic acid-regulated pathways. Furthermore, treatment with ARE in lemon (Citrus limon) and soybean (Glycine max) leaves protects the plants against Xanthomonas citri subsp. citri and Diaporthe phaseolorum var. meridionalis, respectively. Additionally, ARE treatment also promotes growth and development, suggesting a biostimulant activity in soybean. These results open the way for the potential use of ARE as a bioprotective agent in disease management.
Collapse
Affiliation(s)
- Ana Paula Martin
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina
| | - María Florencia Martínez
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina
| | - María Amalia Chiesa
- Laboratorio de Eco-Fisiología Vegetal (LEFIVE), Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-UNR/CONICET, Parque Villarino S/N, 2125, Zavalla, Santa Fe, Argentina
| | - Lucila Garcia
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina
| | - Nadia Gerhardt
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina
| | - Facundo Uviedo
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina
| | - Pablo S Torres
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina
| | - María Rosa Marano
- Instituto de Biología Molecular y Celular de Rosario (IBR)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Ocampo y Esmeralda S/N, S2002 FHN, Rosario, Argentina; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 590, S2002LRK, Rosario, Argentina.
| |
Collapse
|