A dCAPS assay detects and characterizes BaYMV according to its ability to overcome rym4-mediated resistance

Winter barley is subjected to severe yield losses due to the yellow mosaic virus disease. Two soil borne bymoviruses, BaYMV (Barley yellow mosaic virus) and BaMMV (Barley mild mosaic virus) are responsible for this disease in Europe. As breeding resistant cultivars is the only control method against the disease, barley varieties carrying the recessive resistance rym4 were introduced. However, a new pathotype BaYMV-2 overcoming rym4 resistance appeared in the late 1980s. In France, little is known about BaYMV-2 and the common BaYMV (BaYMV-1) distribution, but the increase of the disease occurrence is becoming a concern. There is currently no valid molecular tool for BaYMV-1 and BaYMV-2 differentiation; thus the development of a dCAPS (derived Cleaved Amplified Polymorphic Sequences) tool was investigated. BaYMV-1 and BaYMV-2 diversity was first estimated by Sanger sequencing. The Single Nucleotide Polymorphism (SNP) previously described as providing the ability to overcome rym4-mediated resistance was targeted. A dCAPS tool was developed to digest specifically BaYMV-1. This assay was successfully tested with seventy naturally infected samples. This new tool will be useful to investigate BaYMV-1 and 2 distributions.