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: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1056603/full |
| _version_ | 1797871355636482048 |
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| author | Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ozgur Batuman Ozgur Batuman Jeremy Brawner Wilmer J. Cuellar Erik Delaquis Berea A. Etherton Berea A. Etherton Berea A. Etherton Ronald D. French-Monar Jan F. Kreuze Israel Navarrete Kwame Ogero Aaron I. Plex Sulá Aaron I. Plex Sulá Aaron I. Plex Sulá Salih Yilmaz Salih Yilmaz Karen A. Garrett Karen A. Garrett Karen A. Garrett |
| author_facet | Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ozgur Batuman Ozgur Batuman Jeremy Brawner Wilmer J. Cuellar Erik Delaquis Berea A. Etherton Berea A. Etherton Berea A. Etherton Ronald D. French-Monar Jan F. Kreuze Israel Navarrete Kwame Ogero Aaron I. Plex Sulá Aaron I. Plex Sulá Aaron I. Plex Sulá Salih Yilmaz Salih Yilmaz Karen A. Garrett Karen A. Garrett Karen A. Garrett |
| author_sort | Ricardo I. Alcalá Briseño |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-10T00:41:31Z |
| format | Article |
| id | doaj.art-2de8768f75ef474eafb65bb046b333d7 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T00:41:31Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-2de8768f75ef474eafb65bb046b333d72023-03-14T05:34:26ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.10566031056603Translating virome analyses to support biosecurity, on-farm management, and crop breedingRicardo I. Alcalá Briseño0Ricardo I. Alcalá Briseño1Ricardo I. Alcalá Briseño2Ricardo I. Alcalá Briseño3Ozgur Batuman4Ozgur Batuman5Jeremy Brawner6Wilmer J. Cuellar7Erik Delaquis8Berea A. Etherton9Berea A. Etherton10Berea A. Etherton11Ronald D. French-Monar12Jan F. Kreuze13Israel Navarrete14Kwame Ogero15Aaron I. Plex Sulá16Aaron I. Plex Sulá17Aaron I. Plex Sulá18Salih Yilmaz19Salih Yilmaz20Karen A. Garrett21Karen A. Garrett22Karen A. Garrett23Plant Pathology Department, University of Florida, Gainesville, FL, United StatesGlobal Food Systems Institute, University of Florida, Gainesville, FL, United StatesEmerging Pathogens Institute, University of Florida, Gainesville, FL, United StatesPlant Pathology Department, Oregon State University, Corvallis, OR, United StatesPlant Pathology Department, University of Florida, Gainesville, FL, United StatesSouthwest Florida Research and Education Center (SWFREC), Immokalee, FL, United StatesPlant Pathology Department, University of Florida, Gainesville, FL, United StatesInternational Center for Tropical Agriculture (CIAT), Cali, ColombiaInternational Center for Tropical Agriculture (CIAT), Vientiane, LaosPlant Pathology Department, University of Florida, Gainesville, FL, United StatesGlobal Food Systems Institute, University of Florida, Gainesville, FL, United StatesEmerging Pathogens Institute, University of Florida, Gainesville, FL, United StatesUSDA-APHIS-PPQ-FO Plant Germplasm Quarantine Program (PGQP), Laurel, MD, United StatesCrop and System Sciences Division, International Potato Center (CIP), Lima, Peru0Crop and System Sciences Division, International Potato Center (CIP), Quito, Ecuador1Crop and System Sciences Division, International Potato Center (CIP), Mwanza, TanzaniaPlant Pathology Department, University of Florida, Gainesville, FL, United StatesGlobal Food Systems Institute, University of Florida, Gainesville, FL, United StatesEmerging Pathogens Institute, University of Florida, Gainesville, FL, United StatesPlant Pathology Department, University of Florida, Gainesville, FL, United StatesSouthwest Florida Research and Education Center (SWFREC), Immokalee, FL, United StatesPlant Pathology Department, University of Florida, Gainesville, FL, United StatesGlobal Food Systems Institute, University of Florida, Gainesville, FL, United StatesEmerging Pathogens Institute, University of Florida, Gainesville, FL, United StatesVirome 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1056603/fullcrop breedingmicrobiomespest managementphytosanitary standardsseed systemssurveillance |
| spellingShingle | Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ricardo I. Alcalá Briseño Ozgur Batuman Ozgur Batuman Jeremy Brawner Wilmer J. Cuellar Erik Delaquis Berea A. Etherton Berea A. Etherton Berea A. Etherton Ronald D. French-Monar Jan F. Kreuze Israel Navarrete Kwame Ogero Aaron I. Plex Sulá Aaron I. Plex Sulá Aaron I. Plex Sulá Salih Yilmaz Salih Yilmaz Karen A. Garrett Karen A. Garrett Karen A. Garrett Translating virome analyses to support biosecurity, on-farm management, and crop breeding Frontiers in Plant Science crop breeding microbiomes pest management phytosanitary standards seed systems surveillance |
| 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 | crop breeding microbiomes pest management phytosanitary standards seed systems surveillance |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1056603/full |
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