Translating virome analyses to support biosecurity, on-farm management, and crop breeding.

Autor:	Alcalá Briseño RI; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Global Food Systems Institute, University of Florida, Gainesville, FL, United States.; Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.; Plant Pathology Department, Oregon State University, Corvallis, OR, United States., Batuman O; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States., Brawner J; Plant Pathology Department, University of Florida, Gainesville, FL, United States., Cuellar WJ; International Center for Tropical Agriculture (CIAT), Cali, Colombia., Delaquis E; International Center for Tropical Agriculture (CIAT), Vientiane, Laos., Etherton BA; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Global Food Systems Institute, University of Florida, Gainesville, FL, United States.; Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States., French-Monar RD; USDA-APHIS-PPQ-FO Plant Germplasm Quarantine Program (PGQP), Laurel, MD, United States., Kreuze JF; Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru., Navarrete I; Crop and System Sciences Division, International Potato Center (CIP), Quito, Ecuador., Ogero K; Crop and System Sciences Division, International Potato Center (CIP), Mwanza, Tanzania., Plex Sulá AI; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Global Food Systems Institute, University of Florida, Gainesville, FL, United States.; Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States., Yilmaz S; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States., Garrett KA; Plant Pathology Department, University of Florida, Gainesville, FL, United States.; Global Food Systems Institute, University of Florida, Gainesville, FL, United States.; Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2023 Mar 14; Vol. 14, pp. 1056603. Date of Electronic Publication: 2023 Mar 14 (Print Publication: 2023).
DOI:	10.3389/fpls.2023.1056603
Abstrakt:	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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Alcalá Briseño, Batuman, Brawner, Cuellar, Delaquis, Etherton, French-Monar, Kreuze, Navarrete, Ogero, Plex Sulá, Yilmaz and Garrett.)
Databáze:	MEDLINE
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