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Wang T, Li A, Zhao H, Wu Q, Guo J, Tian H, Wang J, Que Y, Xu L. A novel system with robust compatibility and stability for detecting Sugarcane yellow leaf virus based on CRISPR-Cas12a. Microbiol Spectr 2024:e0114924. [PMID: 39120142 DOI: 10.1128/spectrum.01149-24] [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: 05/08/2024] [Accepted: 06/30/2024] [Indexed: 08/10/2024] Open
Abstract
Sugarcane yellow leaf virus (SCYLV) can reduce sugarcane productivity. A novel detection system based on reverse transcription-multienzyme isothermal rapid amplification (RT-MIRA) combined with CRISPR-Cas12a, named RT-MIRA-CRISPR-Cas12a, was developed. This innovative approach employs crude leaf extract directly as the reaction template, streamlining the extraction process for simplicity and speed. Combining RT-MIRA and CRISPR-Cas12a in one reaction tube increases the ease of operation while reducing the risk of aerosol contamination. In addition, it exhibits sensitivity equivalent to qPCR, boasting a lower detection limit of 25 copies. Remarkably, the entire process, from sample extraction to reaction completion, requires only 52-57 minutes, just a thermostat water bath. The result can be observed and judged by the naked eye.IMPORTANCESugarcane yellow leaf disease (SCYLD) is an important viral disease that affects sugarcane yield. There is an urgent need for rapid, sensitive, and stable detection methods. The reverse transcription-multienzyme isothermal rapid amplification combined with CRISPR-Cas12a (RT-MIRA-CRISPR-Cas12a) method established in this study has good specificity and high sensitivity. In addition, the system showed good compatibility and stability with the crude leaf extract, as shown by the fact that the crude extract of the positive sample could still be stably detected after 1 week when placed at 4°C. RT-MIRA-CRISPR-Cas12a, reverse transcription polymerase chain reaction (RT-PCR), and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were used to detect SCYLV on 33 sugarcane leaf samples collected from the field, and it was found that the three methods reached consistent conclusions. This Cas12a-based detection method proves highly suitable for the rapid on-site detection of the SCYLV.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anzhen Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Helei Tian
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingwen Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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Bertasello LET, da Silva MF, Pinto LR, Nóbile PM, Carmo-Sousa M, dos Anjos IA, Perecin D, Spotti Lopes JR, Gonçalves MC. Yellow Leaf Disease Resistance and Melanaphis sacchari Preference in Commercial Sugarcane Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:3079. [PMID: 37687326 PMCID: PMC10489660 DOI: 10.3390/plants12173079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Sugarcane yellow leaf disease (YLD) caused by sugarcane yellow leaf virus (ScYLV) is a major threat for the sugarcane industry worldwide, and the aphid Melanaphis sacchari is its main vector. Breeding programs in Brazil have provided cultivars with intermediate resistance to ScYLV, whereas the incidence of ScYLV has been underestimated partly due to the complexity of YLD symptom expression and identification. Here, we evaluated YLD symptoms in a field assay using eight sugarcane genotypes comprising six well-established commercial high-sucrose cultivars, one biomass yield cultivar, and a susceptible reference under greenhouse conditions, along with estimation of virus titer through RT-qPCR from leaf samples. Additionally, a free-choice bioassay was used to determine the number of aphids feeding on the SCYLV-infected cultivars. Most of the cultivars showed some degree of resistance to YLD, while also revealing positive RT-qPCR results for ScYLV and virus titers with non-significant correlation with YLD severity. The cultivars IACSP01-5503 and IACBIO-266 were similar in terms of aphid preference and ScYLV resistance traits, whereas the least preferred cultivar by M. sacchari, IACSP96-7569, showed intermediate symptoms but similar virus titer to the susceptible reference, SP71-6163. We conclude that current genetic resistance incorporated into sugarcane commercial cultivars does not effectively prevent the spread of ScYLV by its main aphid vector.
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Affiliation(s)
- Luiz Eduardo Tilhaqui Bertasello
- School of Agricultural and Veterinary Sciences-FCAV, São Paulo State University-UNESP, Jaboticabal 17884-900, Brazil; (L.E.T.B.); (L.R.P.); (D.P.)
| | - Marcel Fernando da Silva
- Sugarcane Research Centre, Instituto Agronômico de Campinas-IAC, Ribeirão Preto 14001-970, Brazil; (M.F.d.S.); (P.M.N.); (I.A.d.A.)
| | - Luciana Rossini Pinto
- School of Agricultural and Veterinary Sciences-FCAV, São Paulo State University-UNESP, Jaboticabal 17884-900, Brazil; (L.E.T.B.); (L.R.P.); (D.P.)
- Sugarcane Research Centre, Instituto Agronômico de Campinas-IAC, Ribeirão Preto 14001-970, Brazil; (M.F.d.S.); (P.M.N.); (I.A.d.A.)
| | - Paula Macedo Nóbile
- Sugarcane Research Centre, Instituto Agronômico de Campinas-IAC, Ribeirão Preto 14001-970, Brazil; (M.F.d.S.); (P.M.N.); (I.A.d.A.)
| | - Michele Carmo-Sousa
- Department of Entomology and Acarology, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil; (M.C.-S.); (J.R.S.L.)
| | - Ivan Antônio dos Anjos
- Sugarcane Research Centre, Instituto Agronômico de Campinas-IAC, Ribeirão Preto 14001-970, Brazil; (M.F.d.S.); (P.M.N.); (I.A.d.A.)
| | - Dilermando Perecin
- School of Agricultural and Veterinary Sciences-FCAV, São Paulo State University-UNESP, Jaboticabal 17884-900, Brazil; (L.E.T.B.); (L.R.P.); (D.P.)
| | - João Roberto Spotti Lopes
- Department of Entomology and Acarology, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), University of São Paulo, Piracicaba 13418-900, Brazil; (M.C.-S.); (J.R.S.L.)
| | - Marcos Cesar Gonçalves
- School of Agricultural and Veterinary Sciences-FCAV, São Paulo State University-UNESP, Jaboticabal 17884-900, Brazil; (L.E.T.B.); (L.R.P.); (D.P.)
- Crop Protection Research Centre, Instituto Biológico-IB, São Paulo 04014-002, Brazil
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Latent potential of current plant diagnostics for detection of sugarcane diseases. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Viswanathan R. Impact of yellow leaf disease in sugarcane and its successful disease management to sustain crop production. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-021-00391-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Holkar SK, Balasubramaniam P, Kumar A, Kadirvel N, Shingote PR, Chhabra ML, Kumar S, Kumar P, Viswanathan R, Jain RK, Pathak AD. Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production. THE PLANT PATHOLOGY JOURNAL 2020; 36:536-557. [PMID: 33312090 PMCID: PMC7721539 DOI: 10.5423/ppj.rw.09.2020.0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 02/08/2023]
Abstract
Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.
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Affiliation(s)
- Somnath Kadappa Holkar
- ICAR-Indian Institute of Sugarcane Research, Biological Control Centre, Pravaranagar, Maharashtra 43 72, India
| | | | - Atul Kumar
- ICAR-Indian Institute of Sugarcane Research, Biological Control Centre, Pravaranagar, Maharashtra 43 72, India.,Amity Institute of Biotechnology, Amity University, Lucknow Campus, Lucknow 226 010, Uttar Pradesh, India
| | - Nithya Kadirvel
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore 61 007, Tamil Nadu, India
| | | | - Manohar Lal Chhabra
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Shubham Kumar
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Praveen Kumar
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Rasappa Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore 61 007, Tamil Nadu, India
| | - Rakesh Kumar Jain
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110 012, India
| | - Ashwini Dutt Pathak
- ICAR-Indian Institute of Sugarcane Research, Lucknow 226 002, Uttar Pradesh, India
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Nithya K, Parameswari B, Viswanathan R. Mixed Infection of Sugarcane Yellow Leaf Virus and Grassy Shoot Phytoplasma in Yellow Leaf Affected Indian Sugarcane Cultivars. THE PLANT PATHOLOGY JOURNAL 2020; 36:364-377. [PMID: 32788895 PMCID: PMC7403522 DOI: 10.5423/ppj.oa.06.2020.0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.
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Affiliation(s)
- Kadirvel Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore 641 007, Tamil Nadu, India
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Anandakumar L, Bagyalakshmi K, Nithya K, Parameswari B, Viswanathan R. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Rapid Diagnosis of Sugarcane yellow leaf virus in Sugarcane. SUGAR TECH 2018. [DOI: 10.1007/s12355-018-0606-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Viswanathan R. Varietal Degeneration in Sugarcane and its Management in India. SUGAR TECH 2015. [DOI: 10.1007/s12355-015-0369-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Viswanathan R, Karuppaiah R, Malathi P, Kumar VG, Chinnaraja C. Diagnosis of Sugarcane yellow leaf virus in asymptomatic sugarcane by RT-PCR. SUGAR TECH 2010. [DOI: 10.1007/s12355-009-0063-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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