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Wang F, Liang Q, Lv R, Ahmad S, Bano M, Weng G, Wen R. Optimization and Validation of Reverse Transcription Recombinase-Aided Amplification (RT-RAA) for Sorghum Mosaic Virus Detection in Sugarcane. Pathogens 2023; 12:1055. [PMID: 37624015 PMCID: PMC10457762 DOI: 10.3390/pathogens12081055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Sorghum mosaic virus (SrMV) causes sugarcane mosaic disease and has significant adverse economic impacts on the cultivation of sugarcane. This study aimed to develop a rapid isotherm nucleic acid amplification method for detecting SrMV. Specific primers were designed to target the conserved region of the P3 gene of SrMV. The reverse transcription recombinase-aided amplification (RT-RAA) method was developed by screening primers and optimizing reaction conditions. Comparative analyses with RT-PCR demonstrated that the RT-RAA method exhibited superior specificity, sensitivity, and reliability for SrMV detection. Notably, using a standard plasmid diluted 10-fold continuously as a template, the sensitivity of RT-RAA was 100-fold higher than that of RT-PCR. Moreover, the RT-RAA reaction displayed flexibility in a temperature range of 24-49 °C, eliminating the need for expensive and complex temperature control equipment. Thus, this method could be utilized at ambient or even human body temperature. Within a short duration of 10 min at 39 °C, the target sequence of SrMV could be effectively amplified. Specificity analysis revealed no cross-reactivity between SrMV and other common sugarcane viruses detected via the RT-RAA. With its high sensitivity, rapid reaction time, and minimal equipment requirements, this method presents a promising diagnostic tool for the reliable and expedited detection of SrMV. Furthermore, it indicates broad applicability for successfully detecting other sugarcane viruses.
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Affiliation(s)
| | | | | | | | | | | | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Ministry and Province Co-Sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; (F.W.); (Q.L.); (R.L.); (S.A.); (M.B.); (G.W.)
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Shang H, Fang L, Qin L, Jiang H, Duan Z, Zhang H, Yang Z, Cheng G, Bao Y, Xu J, Yao W, Zhang M. Genome-wide identification of the class III peroxidase gene family of sugarcane and its expression profiles under stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1101665. [PMID: 36794222 PMCID: PMC9924293 DOI: 10.3389/fpls.2023.1101665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Plant-specific Class III peroxidases (PRXs) play a crucial role in lignification, cell elongation, seed germination, and biotic and abiotic stresses. METHODS The class III peroxidase gene family in sugarcane were identified by bioinformatics methods and realtime fluorescence quantitative PCR. RESULTS Eighty-two PRX proteins were characterized with a conserved PRX domain as members of the class III PRX gene family in R570 STP. The ShPRX family genes were divided into six groups by the phylogenetic analysis of sugarcane, Saccharum spontaneum, sorghum, rice, and Arabidopsis thaliana. The analysis of promoter cis-acting elements revealed that most ShPRX family genes contained cis-acting regulatory elements involved in ABA, MeJA, light responsiveness, anaerobic induction, and drought inducibility. An evolutionary analysis indicated that ShPRXs was formed after Poaceae and Bromeliaceae diverged, and tandem duplication events played a critical role in the expansion of ShPRX genes of sugarcane. Purifying selection maintained the function of ShPRX proteins. SsPRX genes were differentially expressed in stems and leaves at different growth stages in S. spontaneum. However, ShPRX genes were differentially expressed in the SCMV-inoculated sugarcane plants. A qRT-PCR analysis showed that SCMV, Cd, and salt could specifically induce the expression of PRX genes of sugarcane. DISCUSSION These results help elucidate the structure, evolution, and functions of the class III PRX gene family in sugarcane and provide ideas for the phytoremediation of Cd-contaminated soil and breeding new sugarcane varieties resistant to sugarcane mosaic disease, salt, and Cd stresses.
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Affiliation(s)
- Heyang Shang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Linqi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Lifang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Hongtao Jiang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Zhenzhen Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Hai Zhang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zongtao Yang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangyuan Cheng
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixue Bao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Jingsheng Xu
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- National Engineering Research Center for Sugarcane & Guangxi Key Laboratory of Sugarcane Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
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A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress. Int J Mol Sci 2022; 23:ijms23116334. [PMID: 35683012 PMCID: PMC9181594 DOI: 10.3390/ijms23116334] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022] Open
Abstract
The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.
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Lu G, Wang Z, Xu F, Pan YB, Grisham MP, Xu L. Sugarcane Mosaic Disease: Characteristics, Identification and Control. Microorganisms 2021; 9:microorganisms9091984. [PMID: 34576879 PMCID: PMC8468687 DOI: 10.3390/microorganisms9091984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/25/2023] Open
Abstract
Mosaic is one of the most important sugarcane diseases, caused by single or compound infection of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and/or Sugarcane streak mosaic virus (SCSMV). The compound infection of mosaic has become increasingly serious in the last few years. The disease directly affects the photosynthesis and growth of sugarcane, leading to a significant decrease in cane yield and sucrose content, and thus serious economic losses. This review covers four aspects of sugarcane mosaic disease management: first, the current situation of sugarcane mosaic disease and its epidemic characteristics; second, the pathogenicity and genetic diversity of the three viruses; third, the identification methods of mosaic and its pathogen species; and fourth, the prevention and control measures for sugarcane mosaic disease and potential future research focus. The review is expected to provide scientific literature and guidance for the effective prevention and control of mosaic through resistance breeding in sugarcane.
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Affiliation(s)
- Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA; (Y.-B.P.); (M.P.G.)
| | - Michael P. Grisham
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA; (Y.-B.P.); (M.P.G.)
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
- Correspondence:
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Rice JL, Hoy JW. Recovery from Mosaic Caused by Sorghum Mosaic Virus in Sugarcane and Impact on Yield. PLANT DISEASE 2020; 104:3166-3172. [PMID: 33079018 DOI: 10.1094/pdis-02-20-0376-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mosaic is a historically important viral disease of sugarcane in Louisiana caused by Sugarcane mosaic virus and, currently, by Sorghum mosaic virus (SrMV). Sugarcane clones can have variable responses to mosaic for different traits, including susceptibility to infection and yield loss. Disease incidence and rate of increase within a multiple-year crop cycle is affected by susceptibility and other epidemiological factors, possibly including recovery from symptom expression and virus infection. Recovery (defined as the emergence of asymptomatic plants from buds on planted symptomatic stalks) and the impact of mosaic on yield components were evaluated in two sugarcane cultivars, HoCP 09-804 and L 10-147. Recovery varied between the two cultivars. Across two experiments, L 10-147 had a higher frequency of recovery (range 9.4 to 19.8%) than HoCP 09-804 (range 0.9 to 2.3%). A reverse-transcription PCR assay did not detect SrMV in 96.5% of 143 L 10-147 leaf samples and 83.3% of 6 HoCP 09-804 leaf samples collected from recovered plants. When comparing symptomatic and asymptomatic plantings, mosaic reduced cane and sucrose yield in HoCP 09-804 but not L 10-147, suggesting a possible association between recovery and tolerance to virus infection.
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Affiliation(s)
- J L Rice
- Plant Pathology and Crop Physiology Department, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - J W Hoy
- Plant Pathology and Crop Physiology Department, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
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