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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.
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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
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Nithya K, Parameswari B, Kumar S, Annadurai A, Nithyanantham R, Mahadevaswamy HK, Viswanathan R. Prospecting true ScYLV resistance in Saccharum hybrid parental population in India by symptom phenotyping and viral titre quantification. 3 Biotech 2023; 13:125. [PMID: 37041801 PMCID: PMC10082694 DOI: 10.1007/s13205-023-03541-y] [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: 10/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
In sugarcane (Saccharum spp. hybrids) cultivation, viral diseases pose a great challenge across the globe. Yellow leaf (YL) disease is one of the important viral diseases caused by Sugarcane yellow leaf virus (ScYLV), a positive-sense ssRNA virus, genus Polerovirus, family Solemoviridae. The disease symptoms appear in later stages of crop growth during grand growth to maturity phase with intense midrib yellowing in the abaxial leaf surface. At present, this disease is managed through tissue (meristem) culture and healthy seed nurseries in India. However, the virus-free plants are infected quickly by secondary inoculum from aphid vectors in the field, which necessitates the importance of developing YL-resistant varieties. We screened about 600-625 sugarcane parental clones to identify true YL resistance based on 0-5 disease rating scale since 2015 and categorised them as resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible. Leaf samples were collected from all these categories of plants during 2018-20 for the viral titre estimation through absolute quantification method (qRT-PCR assay). The viral load was invariably high in all categories of susceptible samples that ranged from 4.40 × 102 to 8.429 × 106, whereas in YL-free asymptomatic clones, the viral load ranged from 82.35 ± 5.90 to 5.121 × 104. The results clearly indicated that highest viral titre of 105-107 copies was present in all the susceptible clones irrespective of their disease severity grades. Our results clearly established that about 22.85% of apparently resistant sugarcane clones remained free from YL symptoms with significantly low ScYLV titre although we could not find a significant correlation between virus titre and symptom expression. The identified resistant parents will serve as sources of YL resistance to develop virus resistant sugarcane varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03541-y.
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Affiliation(s)
- K. Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - B. Parameswari
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Hyderabad, 500030 India
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - Subham Kumar
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - A. Annadurai
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | | | | | - R. Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
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Viswanathan R, Ramasubramanian T, Chinnaraja C, Selvakumar R, Pathy TL, Manivannan K, Nithyanantham R. Population dynamics of Melanaphis sacchari (Zehntner), the aphid vector of sugarcane yellow leaf virus under tropical conditions in India. TROPICAL PLANT PATHOLOGY 2022. [DOI: 10.1007/s40858-021-00483-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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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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Parameswari B, Nithya K, Kumar S, Holkar SK, Chabbra ML, Kumar P, Viswanathan R. Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-021-00323-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations. Sci Rep 2021; 11:7149. [PMID: 33785787 PMCID: PMC8009895 DOI: 10.1038/s41598-021-86472-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/15/2021] [Indexed: 11/08/2022] Open
Abstract
Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775-5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1-G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0-24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.
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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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Boukari W, Kaye C, Wei C, Hincapie M, LaBorde C, Irey M, Rott P. Field Infection of Virus-Free Sugarcane by Sugarcane Yellow Leaf Virus and Effect of Yellow Leaf on Sugarcane Grown on Organic and on Mineral Soils in Florida. PLANT DISEASE 2019; 103:2367-2373. [PMID: 31318645 DOI: 10.1094/pdis-01-19-0199-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, is widespread in Florida. Two field trials were set up, one on organic soil and one on mineral soil, to investigate the rate and timing of sugarcane infection by SCYLV under field conditions and the effect of the virus on yield. Each trial consisted of plots planted with healthy or SCYLV-infected seed cane of two commercial cultivars. Virus prevalence varied from 83 to 100% in plots planted with infected seed cane regardless of cultivar, location, and crop season. On organic soil, plants of virus-free plots became progressively infected in plant cane and first ratoon crops. On mineral soil, healthy sugarcane became initially infected in the first ratoon crop. After three crop seasons, the highest SCYLV prevalence rates were 33 and 7% on organic and mineral soils, respectively. No significant negative effect of SCYLV on yield was found in plant cane crop regardless of cultivar and soil type. However, yield reductions in ratoon crops varied from nonsignificant to 27% depending on cultivar and soil type. Low virus prevalence observed after three crop seasons suggested that planting virus-free seed cane should limit the impact of SCYLV on sugarcane production in Florida.
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Affiliation(s)
- Wardatou Boukari
- Plant Pathology Department, Everglades Research and Education Center, University of Florida, Belle Glade 33430, FL, U.S.A
| | - Claudia Kaye
- U.S. Sugar Corporation, Clewiston 33440, FL, U.S.A
| | - Chunyan Wei
- Plant Pathology Department, Everglades Research and Education Center, University of Florida, Belle Glade 33430, FL, U.S.A
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Martha Hincapie
- Plant Pathology Department, Everglades Research and Education Center, University of Florida, Belle Glade 33430, FL, U.S.A
| | | | - Michael Irey
- U.S. Sugar Corporation, Clewiston 33440, FL, U.S.A
| | - Philippe Rott
- Plant Pathology Department, Everglades Research and Education Center, University of Florida, Belle Glade 33430, FL, U.S.A
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Filloux D, Fernandez E, Comstock JC, Mollov D, Roumagnac P, Rott P. Viral Metagenomic-Based Screening of Sugarcane from Florida Reveals Occurrence of Six Sugarcane-Infecting Viruses and High Prevalence of Sugarcane yellow leaf virus. PLANT DISEASE 2018; 102:2317-2323. [PMID: 30207899 DOI: 10.1094/pdis-04-18-0581-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013 to 2014 to analyze occurrence of known and potentially new viruses. In total, 214 sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses present within the collected leaf samples. VANA sequence reads were obtained for 204 leaf samples and all four previously reported sugarcane viruses occurring in Florida were detected: Sugarcane yellow leaf virus (SCYLV, 150 infected samples out of 204), Sugarcane mosaic virus (1 of 204), Sugarcane mild mosaic virus (13 of 204), and Sugarcane bacilliform virus (54 of 204). High prevalence of SCYLV in Florida commercial fields and germplasm collections was confirmed by reverse-transcription polymerase chain reaction. Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus. This viral metagenomics approach also resulted in the detection of a new sugarcane-infecting mastrevirus (recently described and named Sugarcane striate virus), and two potential new viruses in the genera Chrysovirus and Umbravirus.
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Affiliation(s)
- D Filloux
- CIRAD, BGPI, Montpellier, France, and BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - E Fernandez
- CIRAD, BGPI, Montpellier, France, and BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - J C Comstock
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Canal Point, FL 33438
| | - D Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705
| | | | - P Rott
- University of Florida, Department of Plant Pathology, Everglades Research & Education Center, Belle Glade 33430
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Khalil F, Yueyu X, Naiyan X, Di L, Tayyab M, Hengbo W, Islam W, Rauf S, Pinghua C. Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding. Microb Pathog 2018; 120:187-197. [PMID: 29730517 DOI: 10.1016/j.micpath.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 12/28/2022]
Abstract
Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV.
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Affiliation(s)
- Farghama Khalil
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xu Yueyu
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiao Naiyan
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Liu Di
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Muhammad Tayyab
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wang Hengbo
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Saeed Rauf
- University College of Agriculture, University of Sargodha, Pakistan
| | - Chen Pinghua
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; GMOs LAB of Quality Supervision Inspection &Testing Center for Sugarcane and Derived Products, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Amata RL, Fernandez E, Filloux D, Martin DP, Rott P, Roumagnac P. Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method. PLANT DISEASE 2016; 100:260-268. [PMID: 30694143 DOI: 10.1094/pdis-05-15-0602-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.
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Affiliation(s)
- Ruth L Amata
- Kenya Agricultural and Livestock Research Organization, Nairobi, 00200 Kenya
| | - Emmanuel Fernandez
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, UCT Faculty of Health Sciences, Observatory 7925, South Africa
| | - Philippe Rott
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet; and Plant Pathology Department, Everglades Research and Education Center, University of Florida, IFAS, Belle Glade, 33430
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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Chinnaraja C, Viswanathan R. Quantification of sugarcane yellow leaf virus in sugarcane following transmission through aphid vector, Melanaphis sacchari. Virusdisease 2015; 26:237-42. [PMID: 26645033 PMCID: PMC4663716 DOI: 10.1007/s13337-015-0267-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 02/05/2023] Open
Abstract
Yellow leaf caused by Sugarcane yellow leaf virus (SCYLV) is a serious constraint to sugarcane production in India and currently the disease epidemics occur on many of the susceptible varieties under field conditions. Studies were conducted on the virus transmission by sugarcane aphid Melanaphis sacchari in sugarcane by inoculating virus-free meristem derived from micro- propagated plants of sugarcane cv Co 86032 with viruliferous aphids. Virus transmission was confirmed through RT-PCR assays and subsequently SCYLV population was established through RT-qPCR. A maximum of 22.3 × 10(3), 3.16 × 10(6) and 4.78 × 10(6) copies of SCYLV-RNA targets were recorded in the plants after 7, 180 and 300 days, respectively. This study showed that the aphid species M. sacchari acts as an effective vector of SCYLV. The relative standard curve method in RT-qPCR efficiently detected the increment in SCYLV copy numbers in sugarcane following transmission through M. sacchari.
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Affiliation(s)
- C. Chinnaraja
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007 India
| | - R. Viswanathan
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007 India
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ElSayed AI, Komor E, Boulila M, Viswanathan R, Odero DC. Biology and management of sugarcane yellow leaf virus: an historical overview. Arch Virol 2015; 160:2921-34. [PMID: 26424197 DOI: 10.1007/s00705-015-2618-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 09/17/2015] [Indexed: 02/05/2023]
Abstract
Sugarcane yellow leaf virus (SCYLV) is one of the most widespread viruses causing disease in sugarcane worldwide. The virus has been responsible for drastic economic losses in most sugarcane-growing regions and remains a major concern for sugarcane breeders. Infection with SCYLV results in intense yellowing of the midrib, which extends to the leaf blade, followed by tissue necrosis from the leaf tip towards the leaf base. Such symptomatic leaves are usually characterized by increased respiration, reduced photosynthesis, a change in the ratio of hexose to sucrose, and an increase in starch content. SCYLV infection affects carbon assimilation and metabolism in sugarcane, resulting in stunted plants in severe cases. SCYLV is mainly propagated by planting cuttings from infected stalks. Phylogenetic analysis has confirmed the worldwide distribution of at least eight SCYLV genotypes (BRA, CHN1, CHN3, CUB, HAW, IND, PER, and REU). Evidence of recombination has been found in the SCYLV genome, which contains potential recombination signals in ORF1/2 and ORF5. This shows that recombination plays an important role in the evolution of SCYLV.
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Affiliation(s)
- Abdelaleim Ismail ElSayed
- Biochemistry Department, Faculty of Agriculture, Zagazig University, 44519, Zagazig, Egypt. .,Everglades Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 3200 East Palm Beach Road, Belle Glade, FL, 33430-4702, USA.
| | - Ewald Komor
- Plant Physiology, University Bayreuth, 95440, Bayreuth, Germany
| | - Moncef Boulila
- Institut de l'Olivier, B.P. 14, 4061, Sousse Ibn-khaldoun, Tunisia
| | - Rasappa Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007, India
| | - Dennis C Odero
- Everglades Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 3200 East Palm Beach Road, Belle Glade, FL, 33430-4702, USA
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Bertani RP, Perera MF, Arias ME, Luque C, Funes C, González V, Cuenya MI, Ploper LD, Welin B, Castagnaro AP. A Study of the Sugarcane Yellow Leaf Disease in Argentina. PLANT DISEASE 2014; 98:1036-1042. [PMID: 30708784 DOI: 10.1094/pdis-12-13-1251-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Yellow leaf disease, caused by Sugarcane yellow leaf virus (SCYLV), is widespread around the world but very little information is available on this viral disease in Argentina. Therefore, the aims of the study were to assess the presence of SCYLV, analyze its distribution in the main sugarcane production areas of Argentina, characterize the virus, and determine histological alterations caused by its presence. For this purpose, 148 sugarcane samples with and without symptoms were collected in 2011 and 2012 from the province of Tucumán. One additional sample was collected in Salta, a different geographical, agroecological, and producing region. Results showed that SCYLV is widely distributed in commercial varieties of sugarcane throughout Tucumán in both symptomatic and asymptomatic leaves. A low but statistically significant positive correlation with virus detection and disease symptoms was found. BRA-PER was the only genotype detected by reverse-transcription polymerase chain reaction and sequence analysis of the SCYLV capsid protein gene. SCYLV-positive samples showed high starch levels in bundle sheath cells, whereas the asymptomatic ones, probably in an early stage of infection, were found to contain more chloroplasts. Symptomatic noninfected samples presented crystal formation probably associated with phytoplasma infection.
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Affiliation(s)
- R P Bertani
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), C.P. T4101XAC, Las Talitas, Tucumán, R. Argentina
| | - M F Perera
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), C.P. T4101XAC, Las Talitas, Tucumán, R. Argentina
| | - M E Arias
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán (UNT), Miguel Lillo 205, C.P. 4000 San Miguel de Tucumán, Tucumán, Argentina; and Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca (UNCa), Belgrano 300, C.P. 4700, San Fernando del Valle de Catamarca, Catamarca, Argentina
| | - C Luque
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, UNT
| | | | | | | | | | - B Welin
- EEAOC-CONICET, ITANOA, Argentina
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Molecular evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor-coding genes. J Mol Evol 2014; 78:349-65. [PMID: 24952671 DOI: 10.1007/s00239-014-9630-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
RNA-dependent RNA polymerase (RdRp) encoded by ORF2 and putative aphid transmission factor (PATF) encoded by ORF5 of Sugarcane yellow leaf virus (SCYLV) were detected in six sugarcane cultivars affected by yellow leaf using RT-PCR and real-time RT-PCR assays. Expression of both genes varied among infected plants, but overall expression of RdRp was higher than expression of PATF. Cultivar H87-4094 from Hawaii yielded the highest transcript levels of RdRp, whereas cultivar C1051-73 from Cuba exhibited the lowest levels. Sequence comparisons among 25 SCYLV isolates from various geographical locations revealed an amino acid similarity of 72.1-99.4 and 84.7-99.8 % for the RdRp and PATF genes, respectively. The 25 SCYLV isolates were separated into three (RdRp) and two (PATF) phylogenetic groups using the MEGA6 program that does not account for genetic recombination. However, the SCYLV genome contained potential recombination signals in the RdRp and PATF coding genes based on the GARD genetic algorithm. Use of this later program resulted in the reconstruction of phylogenies on the left as well as on the right sides of the putative recombination breaking points, and the 25 SCYLV isolates were distributed into three distinct phylogenetic groups based on either RdRp or PATF sequences. As a result, recombination reshuffled the affiliation of the accessions to the different clusters. Analysis of selection pressures exerted on RdRp and PATF encoded proteins revealed that ORF 2 and ORF 5 underwent predominantly purifying selection. However, a few sites were also under positive selection as assessed by various models such as FEL, IFEL, REL, FUBAR, MEME, GA-Branch, and PRIME.
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Impact of Sugarcane yellow leaf virus (ScYLV) infection on physiological efficiency and growth parameters of sugarcane under tropical climatic conditions in India. ACTA PHYSIOLOGIAE PLANTARUM 2014. [DOI: 10.1007/s11738-014-1554-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Lin YH, Gao SJ, Damaj MB, Fu HY, Chen RK, Mirkov TE. Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype. Arch Virol 2014; 159:1421-9. [DOI: 10.1007/s00705-013-1957-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
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19
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Sailaja B, Anjum N, Patil YK, Agarwal S, Malathi P, Krishnaveni D, Balachandran SM, Viraktamath BC, Mangrauthia SK. The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates. Virus Genes 2013; 47:515-23. [PMID: 23925555 DOI: 10.1007/s11262-013-0964-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/24/2013] [Indexed: 11/25/2022]
Abstract
In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.
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Affiliation(s)
- B Sailaja
- Biotechnology Section, Directorate of Rice Research, Hyderabad, 500030, India
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