Abstract
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 BaMMV. 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.
Highlights
The barley yellow mosaic disease has unexpectedly increased in prevalence in France over the past few years and is an important concern in winter barley crops
Pathotyping of Barley yellow mosaic virus (BaYMV) isolates was performed by Sanger sequencing or dCAPS. 101 of the 151 collected samples were tested by PCR for other frequent barley-infecting viruses: WDV, BSMV, BYDV-MAV, BYDV-PAV and CYDV-RPV
Using two sampling protocols from 2013 to 2016, classical detection and characterization techniques (RT-PCR, Sanger sequencing, dCAPS) and NGS-based approaches, this study provides a description of the viruses responsible for mosaic symptoms on winter barley in the main French malting barley production areas
Summary
The barley yellow mosaic disease has unexpectedly increased in prevalence in France over the past few years and is an important concern in winter barley crops. In Europe and Asia, two potyviruses belonging to the genus Bymovirus, Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), are responsible for this disease. These two soil-borne viruses have the typical bipartite genome of members of this genus [1, 2] and are transmitted by Polymyxa graminis [3, 4]. As for many other recessive resistance genes against Potyviridae members [7], the rym4/rym alleles encode mutated versions of the host translation initiation factor eIF4E which are unable to support the virus cycle [8, 9]
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