Translating virome analyses to support biosecurity, on-farm management, and crop breeding
Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, su...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2023
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/129687 |
| _version_ | 1855528312269438976 |
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| author | Briseño, R.I.A. Batuman, O. Brawner, J. Cuéllar, Wilmer Jose Delaquis, Erik Etherton, B.A. French-Monar, R.D. Kreuze, Jan F. Navarrete, I. Ogero, K. Sulá, A.P. Yilmaz, S. Garrett, K.A. |
| author_browse | Batuman, O. Brawner, J. Briseño, R.I.A. Cuéllar, Wilmer Jose Delaquis, Erik Etherton, B.A. French-Monar, R.D. Garrett, K.A. Kreuze, Jan F. Navarrete, I. Ogero, K. Sulá, A.P. Yilmaz, S. |
| author_facet | Briseño, R.I.A. Batuman, O. Brawner, J. Cuéllar, Wilmer Jose Delaquis, Erik Etherton, B.A. French-Monar, R.D. Kreuze, Jan F. Navarrete, I. Ogero, K. Sulá, A.P. Yilmaz, S. Garrett, K.A. |
| author_sort | Briseño, R.I.A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally. |
| format | Journal Article |
| id | CGSpace129687 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1296872025-12-08T10:29:22Z Translating virome analyses to support biosecurity, on-farm management, and crop breeding Briseño, R.I.A. Batuman, O. Brawner, J. Cuéllar, Wilmer Jose Delaquis, Erik Etherton, B.A. French-Monar, R.D. Kreuze, Jan F. Navarrete, I. Ogero, K. Sulá, A.P. Yilmaz, S. Garrett, K.A. microbiomes pest management seed systems surveillance systems crops Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally. 2023-03-14 2023-03-20T16:23:52Z 2023-03-20T16:23:52Z Journal Article https://hdl.handle.net/10568/129687 en Open Access Frontiers Media Briseño, R.I.A.; Batuman, O.; Brawner, J.; Cuellar, W.J.; Delaquis, E.; Etherton, B.; French-Monar, R.D.; Kreuze, J.F.; Navarrete, I.; Ogero, K.; Sulá, A.P.; Yilmaz, S.; Garrett, K. 2023. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. Frontiers in Plant Science, 14. ISSN 1664-462X. 14 p. |
| spellingShingle | microbiomes pest management seed systems surveillance systems crops Briseño, R.I.A. Batuman, O. Brawner, J. Cuéllar, Wilmer Jose Delaquis, Erik Etherton, B.A. French-Monar, R.D. Kreuze, Jan F. Navarrete, I. Ogero, K. Sulá, A.P. Yilmaz, S. Garrett, K.A. Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title | Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title_full | Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title_fullStr | Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title_full_unstemmed | Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title_short | Translating virome analyses to support biosecurity, on-farm management, and crop breeding |
| title_sort | translating virome analyses to support biosecurity on farm management and crop breeding |
| topic | microbiomes pest management seed systems surveillance systems crops |
| url | https://hdl.handle.net/10568/129687 |
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