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Bettoni JC, Wang MR, Li JW, Fan X, Fazio G, Hurtado-Gonzales OP, Volk GM, Wang QC. Application of Biotechniques for In Vitro Virus and Viroid Elimination in Pome Fruit Crops. PHYTOPATHOLOGY 2024; 114:930-954. [PMID: 38408117 DOI: 10.1094/phyto-07-23-0232-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: 02/28/2024]
Abstract
Sustainable production of pome fruit crops is dependent upon having virus-free planting materials. The production and distribution of plants derived from virus- and viroid-negative sources is necessary not only to control pome fruit viral diseases but also for sustainable breeding activities, as well as the safe movement of plant materials across borders. With variable success rates, different in vitro-based techniques, including shoot tip culture, micrografting, thermotherapy, chemotherapy, and shoot tip cryotherapy, have been employed to eliminate viruses from pome fruits. Higher pathogen eradication efficiencies have been achieved by combining two or more of these techniques. An accurate diagnosis that confirms complete viral elimination is crucial for developing effective management strategies. In recent years, considerable efforts have resulted in new reliable and efficient virus detection methods. This comprehensive review documents the development and recent advances in biotechnological methods that produce healthy pome fruit plants. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jean Carlos Bettoni
- Independent Researcher, 35 Brasil Correia Street, Videira, SC 89560510, Brazil
| | - Min-Rui Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Jing-Wei Li
- Institute of Vegetable Industry Technology Research, Guizhou University, Guiyang 550025, China
| | - Xudong Fan
- National Center for Eliminating Viruses from Deciduous Fruit Trees, Institute of Pomology of CAAS, Xingcheng 125100, China
| | - Gennaro Fazio
- U.S. Department of Agriculture-Agricultural Research Service Plant Genetic Resources Unit, Geneva, NY 14456, U.S.A
| | - Oscar P Hurtado-Gonzales
- U.S. Department of Agriculture-APHIS Plant Germplasm Quarantine Program, BARC-East, Beltsville, MD 20705, U.S.A
| | - Gayle M Volk
- U.S. Department of Agriculture-Agricultural Research Service National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, U.S.A
| | - Qiao-Chun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China
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Bettoni JC, Fazio G, Carvalho Costa L, Hurtado-Gonzales OP, Rwahnih MA, Nedrow A, Volk GM. Thermotherapy Followed by Shoot Tip Cryotherapy Eradicates Latent Viruses and Apple Hammerhead Viroid from In Vitro Apple Rootstocks. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050582. [PMID: 35270052 PMCID: PMC8912313 DOI: 10.3390/plants11050582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 05/06/2023]
Abstract
Virus and viroid-free apple rootstocks are necessary for large-scale nursery propagation of apple (Malus domestica) trees. Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV) are among the most serious apple viruses that are prevalent in most apple growing regions. In addition to these viruses, a new infectious agent named Apple hammerhead viroid (AHVd) has been identified. We investigated whether thermotherapy or cryotherapy alone or a combination of both could effectively eradicate ACLSV, ASGV, and AHVd from in vitro cultures of four apple rootstocks developed in the Cornell-Geneva apple rootstock breeding program (CG 2034, CG 4213, CG 5257, and CG 6006). For thermotherapy treatments, in vitro plants were treated for four weeks at 36 °C (day) and 32 °C (night). Plant vitrification solution 2 (PVS2) and cryotherapy treatments included a shoot tip preculture in 2 M glycerol + 0.8 M sucrose for one day followed by exposure to PVS2 for 60 or 75 min at 22 °C, either without or with liquid nitrogen (LN, cryotherapy) exposure. Combinations of thermotherapy and PVS2/cryotherapy treatments were also performed. Following treatments, shoot tips were warmed, recovered on growth medium, transferred to the greenhouse, grown, placed in dormancy inducing conditions, and then grown again prior to sampling leaves for the presence of viruses and viroids. Overall, thermotherapy combined with cryotherapy treatment resulted in the highest percentage of virus- and viroid-free plants, suggesting great potential for producing virus- and viroid-free planting materials for the apple industry. Furthermore, it could also be a valuable tool to support the global exchange of apple germplasm.
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Affiliation(s)
- Jean Carlos Bettoni
- The New Zealand Institute for Plant and Food Research Limited, Batchelar Road, Palmerston North 4410, New Zealand
- Correspondence:
| | - Gennaro Fazio
- USDA-ARS Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY 14456, USA; (G.F.); (A.N.)
| | - Larissa Carvalho Costa
- USDA-APHIS Plant Germplasm Quarantine Program, 9901 Powder Mill Road, Bldg 580, BARC-East, Beltsville, MD 20705, USA; (L.C.C.); (O.P.H.-G.)
| | - Oscar P. Hurtado-Gonzales
- USDA-APHIS Plant Germplasm Quarantine Program, 9901 Powder Mill Road, Bldg 580, BARC-East, Beltsville, MD 20705, USA; (L.C.C.); (O.P.H.-G.)
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
| | - Abby Nedrow
- USDA-ARS Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY 14456, USA; (G.F.); (A.N.)
| | - Gayle M. Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 S. Mason Street, Fort Collins, CO 80521, USA;
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Rodríguez-Verástegui LL, Ramírez-Zavaleta CY, Capilla-Hernández MF, Gregorio-Jorge J. Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:203. [PMID: 35050091 PMCID: PMC8778216 DOI: 10.3390/plants11020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 05/12/2023]
Abstract
Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.
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Affiliation(s)
| | - Candy Yuriria Ramírez-Zavaleta
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - María Fernanda Capilla-Hernández
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Ciudad de Mexico 03940, Mexico
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Nabi SU, Madhu GS, Rao GP, Baranwal VK. Development of multiplex RT‐PCR assay for simultaneous detection of four viruses infecting apple (
Malus domestica
). Lett Appl Microbiol 2021; 74:586-592. [DOI: 10.1111/lam.13643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Sajad Un Nabi
- ICAR‐Central Institute of Temperate Horticulture Old Air Field Rangreth Srinagar
| | - GS Madhu
- ICAR‐Central Institute of Temperate Horticulture Old Air Field Rangreth Srinagar
| | - Govind P Rao
- Advanced Center of Plant Virology Division of Plant Pathology ICAR‐IARI New Delhi India
| | - Virendra K Baranwal
- Advanced Center of Plant Virology Division of Plant Pathology ICAR‐IARI New Delhi India
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Lee HJ, Han YS, Cho IS, Jeong RD. Development and application of reverse transcription droplet digital PCR assay for sensitive detection of apple scar skin viroid during in vitro propagation of apple plantlets. Mol Cell Probes 2021; 61:101789. [PMID: 34965481 DOI: 10.1016/j.mcp.2021.101789] [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: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/28/2022]
Abstract
Apple scar skin viroid (ASSVd), of the genus Apscaviroid, causes serious pome fruit diseases, such as apple scar skin, dapple apple, pear rusty skin, pear fruit crinkle, and pear dimple fruit. This study aimed at establishing a sensitive and accurate method for quantification of ASSVd in apple leaves and plantlets using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The specificity was analyzed using other apple viruses, and the negative amplification of the cross-reaction assay demonstrated the high specificity of RT-ddPCR. The detection limit of ASSVd by RT-ddPCR was 1.75 × 102 copies/μL (0.14 concentration), and the sensitivity was ten-fold higher than that of RT-qPCR. Similarly, positive detection in apple plantlet samples by RT-ddPCR was higher than that by RT-qPCR. The RT-ddPCR assay represents a promising alternative for accurate quantitative detection and diagnosis of ASSVd infection in ASSVd-free certification programs.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - Yeon Soo Han
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, South Korea
| | - Rae-Dong Jeong
- Department of Applied Biology and Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea.
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Nabi SU, Baranwal VK, Yadav MK, Rao GP. Association of Apple necrotic mosaic virus (ApNMV) with mosaic disease in commercially grown cultivars of apple ( Malus domestica Borkh) in India. 3 Biotech 2020; 10:122. [PMID: 32123646 DOI: 10.1007/s13205-020-2117-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/02/2020] [Indexed: 10/25/2022] Open
Abstract
During the course of survey, an incidence of 7.14-90% of apple mosaic disease (AMD) was recorded in apple orchards in Jammu and Kashmir among various commercially grown cultivars. The maximum incidence of mosaic disease was observed in cultivar Golden Delicious. In addition to mosaic, symptoms of chlorosis, necrosis and ring spots were also observed. In the present study association of Apple necrotic mosaic virus (ApNMV) was confirmed by RT-PCR and sequencing of whole coat protein gene in samples tested negative for Apple mosaic virus (ApMV) in DAS-ELISA. Out of 18 samples tested in RT-PCR, ten were found positive for ApNMV. Out of ten ApNMV positive samples, amplicon of 680 bp of samples representing five cultivars were sequenced and sequence analysis showed 89-91% sequence identity with ApNMV. The phylogenetic analysis grouped Indian isolates into two sub-clusters under one major cluster (ApNMV group). The sub-cluster-I, included ApNMV isolates from cultivars, Oregon Spur, Red Delicious and Fuji Aztec along with Chinese and Korean isolates. Sub-cluster-II included ApNMV isolates associated with Golden Delicious and Royal Delicious. The comparison of coat protein gene-based sequence identity matrix showed maximum and minimum similarity of 89-99% with ApNMV isolates from China. It also showed maximum identity with PNRSV (61.6%) and ApMV (52.8%) under subgroup 3 of genus Illarvirus. Our study indicates that the ApNMV is commonly associated with AMD in India and may be a major cause of the mosaic disease in apple cultivars. To the best of our knowledge, this is the first report of the association of ApNMV with apple mosaic disease from India.
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Bettoni JC, Costa MD, Souza JA, Volk GM, Nickel O, da Silva FN, Kretzschmar AA. Cryotherapy by encapsulation-dehydration is effective for in vitro eradication of latent viruses from 'Marubakaido' apple rootstock. J Biotechnol 2018; 269:1-7. [PMID: 29408198 DOI: 10.1016/j.jbiotec.2018.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/15/2018] [Accepted: 01/21/2018] [Indexed: 10/18/2022]
Abstract
Apple stem pitting virus (ASPV), Apple chlorotic leaf spot virus (ACLSV) and Apple stem grooving virus (ASGV) are several major viral pathogens of apple trees, responsible for substantial damage to the world's apple industry. This study aimed to evaluate the effectiveness of the encapsulation-dehydration cryopreservation technique to eradicate these viral pathogens from in vitro shoot tips excised from 'Marubakaido' apple rootstock cultures. Axillary shoot tips were excised from in vitro cultures, encapsulated in alginate beads, precultured in MS salts, dehydrated in a laminar flow hood, immersed in liquid nitrogen, then warmed and recovered on medium. After LN exposure, in vitro rooting and acclimatization, recovered 'Marubakaido' plants exhibited 52% survival and 35% regrowth without callus formation. After 8 months of regrowth, PCR analyses revealed that all the plants were free of ACLSV and ASPV, but 2 out of 20 recovered plants were still infected with ASGV. This is the first report in Brazil of the application of cryotherapy to eradicate viral complexes in Malus. Cryotherapy can facilitate the production of virus-free plants by producing high quality plant material.
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Affiliation(s)
- Jean Carlos Bettoni
- Santa Catarina State University (UDESC), Lages, Santa Catarina, 88520000, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília - DF, Zip Code 70.040-02, Brazil.
| | | | | | - Gayle M Volk
- USDA- ARS National Laboratory for Genetic Resources Preservation, Fort Collins, CO, 80521, USA
| | - Osmar Nickel
- Embrapa Grape & Wine, Bento Gonçalves, Rio Grande do Sul, 95700000, Brazil
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Malandraki I, Beris D, Isaioglou I, Olmos A, Varveri C, Vassilakos N. Simultaneous detection of three pome fruit tree viruses by one-step multiplex quantitative RT-PCR. PLoS One 2017; 12:e0180877. [PMID: 28749955 PMCID: PMC5547701 DOI: 10.1371/journal.pone.0180877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/22/2017] [Indexed: 12/26/2022] Open
Abstract
A one-step multiplex real-time reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan probes was developed for the simultaneous detection of Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in total RNA of pome trees extracted with a CTAB method. The sensitivity of the method was established using in vitro synthesized viral transcripts serially diluted in RNA from healthy, virus-tested (negative) pome trees. The three viruses were simultaneously detected up to a 10-4 dilution of total RNA from a naturally triple-infected apple tree prepared in total RNA of healthy apple tissue. The newly developed RT-qPCR assay was at least one hundred times more sensitive than conventional single RT-PCRs. The assay was validated with 36 field samples for which nine triple and 11 double infections were detected. All viruses were detected simultaneously in composite samples at least up to the ratio of 1:150 triple-infected to healthy pear tissue, suggesting the assay has the capacity to examine rapidly a large number of samples in pome tree certification programs and surveys for virus presence.
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Affiliation(s)
- Ioanna Malandraki
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Despoina Beris
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Ioannis Isaioglou
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Antonio Olmos
- Plant Protection and Biotechnology Centre, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Christina Varveri
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Nikon Vassilakos
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
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Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 2016; 17:579. [PMID: 27507588 PMCID: PMC4977635 DOI: 10.1186/s12864-016-2994-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Background Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. Results We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Conclusions Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
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