Detection and genetic diversity of Hop stunt viroid infecting Pistachio (Pistacia vera L.) trees in Turkey

Hop stunt viroid (HSVd) infects a large number of woody plants such as grapevine, citrus, plum, peach, fig, mulberry, pear, pistachio, and almond. Pistachio ( Pistacia vera L.) is an important crop in Turkey and very few reports described the presence of viruses or viroids affecting that crop. The viroid was recently detected in one P. vera tree out of a limited number of samples in Kahramanmaras which is one of the most important pistachio-growing areas. Therefore, an extensive research was carried out to investigate the prevalence and genetic diversity of HSVd in Kahramanmaras and two additional major pistachio growing areas. During 2016–2017, a total of 70 leaf samples from pistachio trees were collected and assayed for HSVd by reverse transcription polymerase chain reaction (RT-PCR). The prevalence incidence of HSVd infection was relatively low in the tested plant materials. Comparative analysis of the three Turkish HSVd-pistachio variants was performed with viroidal genome sequences from the NCBI database. Phylogenetic analysis showed that one HSVd-pistachio variant was classified with the reference HSVd isolate from Japan and formed a sub-cluster within the HSVd-hop isolates group, whereas the remaining two variants were clustered into the plum-hop/cit3 group with four Tunisian HSVd-pistachio variants. Further studies are required to verify its infectivity in healthy pistachio trees.