Broad range virus indexing through NGS: the safe-PGR case study

Grisoni Michel. 2014. Broad range virus indexing through NGS: the safe-PGR case study. In : International Workshop: Surveillance and control of cassava diseases in Africa, Saint-Pierre, La Réunion, 10-13 June 2014. GCP21, CIRAD, IRD. Saint-Pierre : GCP21, Résumé, 24-25. International Workshop Surveillance and Control of Cassava Diseases in Africa, Saint-Pierre, Réunion, 10 Juin 2014/13 Juin 2014.

Résumé : Biological Resources Centers (BRCs) conserve and distribute plant germplasm for research and development purposes. As such, they play a strategic role by providing breeding programs with genitors that are critical for crop adaptation to ongoing environmental and societal changes. BRCs must guarantee the sanitary status of the resources they distribute, in order to prevent the spread of diseases, particularly for vegetative propagated that do not benefit from the virus sanitation occurring through a seed cycle. The Safe-PGR project (Towards Safer Plant Genetic Resources through improved viral diagnostics) was initiated in 2012 to improve the knowledge of the viruses infecting the crops addressed by four partner's BRCs in Guadeloupe, Madeira, Azores and Reunion, and develop classical or new diagnostic techniques for the species they deal with: banana, garlic, sugarcane, sweet potato, vanilla and yam. The project is funded by the French National Agency for Research and the governing bodies of Azores, Madeira, Guadeloupe and Reunion. The research consortium involves teams from INRA (BFP, ASTRO), CIRAD (BGPI, AGAP, PVBMT), CBA Azores and ISOPLEXIS Madeira. Methods: The project aims at exploring the molecular diversity of the viral families affecting the targeted crops, optimize classical diagnostic methods taking into consideration data generated through this analysis of viral diversity and develop new multi- pathogen diagnostic methods based on metagenomics and deep-sequencing technologies (Roche 454). Eight nucleic acids extraction methods for metagenomics studies have been tested and compared. Two complementary methods based on the extraction of double-strand RNA and viral particles have been selected. Bioinformatics tools have been successfully developed for analyzing the metagenomics data. These methods are currently used for the screening of 1500 plants from the CRB germplasm collections. Virus discovery : The preliminary bioinformatics analyses of plant EST databases and of the first deep sequencing results generated, allowed the tentative identification of a total of 25 new viruses in Garlic, Sugarcane, Yam and Vanilla for which new and efficient detection assays have been developed and implemented. Further characterization of a new Allexivirus of garlic and new Potexvirus of vanilla will be presented.

Auteurs et affiliations

• Grisoni Michel, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0001-9867-9098

Source : Cirad-Agritrop (https://agritrop.cirad.fr/602574/)

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