Molecular detection and identification of Hop stunt viroid isolates infecting grapevines in some regions of Iran

ObjectiveThe Hop stunt viroid has the widest host range among viroids and is prevalent worldwide. This research aims to detect and characterize HSVd variants in the vineyards of Kerman province and some other parts of Iran and analyze the variants' phylogenetic status.Materials and methodsSeventy-four leaf samples were collected from grapevines in Kerman, East Azerbaijan (Tabriz), and Fars (Beyza) provinces during the summers of 2018–2020. The samples were processed and subjected to RT-PCR to detect HSVd using specific primers. Then, complete genomes of seven HSVd variants were sequenced and blasted into GenBank. In the MEGA 7.0 program, the neighbor-joining statistical method was used to construct a phylogenetic tree to consider relationships between the detected HSVd variants and those obtainable in GenBank. Furthermore, the homology of the grapevine-related variants was analyzed by SDT v1.2 software. Finally, eight plant species and varieties were experimentally inoculated by two HSVd variants to study symptom expression and determine host range.ResultsThroughout the world, HSVd variants have been grouped into five phylogenetic groups: Citrus, Hop, Plum, Plum-Hop/cit3, and Plum-Citrus. Accordingly, the identified seven HSVd variants in this study and several previously reported variants from grapevines in Iran and Germany were classified under the main group, Hop. The HSVd variants from grapevine had genome lengths ranging from 297 to 300 nucleotides, with 93.3–98.7% nucleotide sequence similarity. Three of the seven HSVd isolates identified in Kerman province vineyards and four isolates previously reported from grapevines in Iran and Germany formed a subgroup within the Hop cluster. In addition, the Hop group included four Iranian pistachio HSVd isolates from the Kerman province and some Tunisian pistachios HSVd isolates with Iranian provenance.ConclusionsGiven that HSVd infection of grapevines has been documented in Iran before pistachio infection, pistachios were most likely infected via HSVd inocula transferred from affected grapevines. Therefore, based on molecular studies and available evidence, grapevines can be assumed to be the source of infection for pistachio trees.