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Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France

Affiliation
Groupe d'Etude et de controà le des VarieÂteÂs Et des Semences, Beaucouze , France
Rolland, Mathieu;
Affiliation
Groupe d'Etude et de controà le des VarieÂteÂs Et des Semences, Beaucouze , France
Villemot, Julie;
Affiliation
Unite Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Universite de Bordeaux, Villenave d'Ornon, France
Marais, Armelle;
Affiliation
Unite Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Universite de Bordeaux, Villenave d'Ornon, France
Theil, Sebastien;
Affiliation
Unite Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Universite de Bordeaux, Villenave d'Ornon, France
Faure, Chantal;
Affiliation
Groupe d'Etude et de controà le des VarieÂteÂs Et des Semences, Beaucouze , France
Cadot, Valerie;
Affiliation
ARVALIS±Institut du veÂge tal, Thiverval-Grignon, France
Valade, Romain;
Affiliation
ARVALIS±Institut du veÂge tal, Thiverval-Grignon, France
Vitry, Cindy;
GND
1058968432
Affiliation
Julius Kühn-Institut, Quedlinburg, Germany
Rabenstein, Frank;
Affiliation
Unite Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Universite de Bordeaux, Villenave d'Ornon, France
Candresse, Thierry

Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease. A collection of 241 symptomatic leaf samples from susceptible, rym4 and rym5 varieties was gathered from 117 sites. The viruses present in all samples were identified by specific RT-PCR assays and, for selected samples, by double-stranded RNA next-generation sequencing (NGS). The results show that BaYMV-2 is responsible for the symptoms observed in varieties carrying the resistance gene rym4. In susceptible varieties, both BaYMV-1 and BaYMV-2 were detected, together with BMMV. Phylogenetic analyses indicate that the rym4 resistance-breaking ability independently evolved in multiple genetic backgrounds. Parallel analyses revealed a similar scenario of multiple independent emergence events in BaMMV for rym5 resistance-breaking, likely involving multiple amino acid positions in the viral-linked genome protein. NGS analyses and classical techniques provided highly convergent results, highlighting and validating the power of NGS approaches for diagnostics and viral population characterization.

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