Biological and molecular characterization of hop stunt viroid variants from pistachio trees in Iran

Abstract

Abstract Hop stunt viroid (HSVd) infects a large number of woody plants such as grapevine, citrus, plum, peach, fig, mulberry, pear, pistachio and almond. Kerman Province is the most important pistachio‐growing region in Iran. During 2015–2016, pistachio orchards were surveyed in Kerman for the detection of HSVd. A total of 106 symptomatic and asymptomatic leaf samples from pistachio trees were collected and assayed for HSVd by reverse transcription polymerase chain reaction (RT‐PCR) and dot‐blot hybridization methods. The genomes of 11 HSVd isolates were PCR amplified, cloned, sequenced and compared with those available in GenBank. The full‐length genomes of Iranian variants range from 297 to 302 nucleotides, which are comparable to those of previously known HSVd variants. Phylogenetic analyses showed that four HSVd pistachio variants from Anar region were classified together with five Tunisian HSVd pistachio variants and formed a sub‐cluster within the HSVd‐hop isolates group, whereas two variants from Shahr‐e‐Babak region were grouped with known HSVd‐citrus variants. The other remaining five variants were clustered into the recombinant isolates group (P‐H/cit3). Phylogenetically, we discuss that the presence of HSVds in pistachio trees has a long history in Iran, and Tunisian HSVd pistachio variants probably originated from Iran. The infectivity of two HSVd pistachio variants was further verified by mechanical inoculation on some Cucurbitaceae plant species. The viroid was also transmitted to three healthy pistachio rootstocks by bud grafting. This is the first report on HSVd in pistachio trees in Iran.