Detection and phylogenetic analysis of four important viroids from vineyards in Zanjan province

 Viroids are classified in two families including Avsunviroid that consists of three genera (Pelamoviroid, Avsunviroid and Elaviroid) and pospiviroid including five genera (Apscaviroid, Hostuviroid, Cocaviroid, Coleviroid and Pospiviroid). Grapevine-infecting viroids belong to the three genera in the pospiviroid family. A total of 121 symptomatic and non- symptomatic leaf and green shoot samples were collected from the main vineyards in Zanjan province to detect the important viroids infecting grapevines. Total RNAs were extracted from the samples and then cDNAs were synthesized by cDNA synthesize Kit with a random hexamer primer. Specific primers used to detect Grapevine yellow speckle viroid 1(GYSVd-1), (GYSVd-2) Grapevine yellow speckle viroid 2, (HSVd) Hop stunt viroid, Australian grapevine viroid (ASGVd) in reverse transcription polymerase chain reaction (RT-PCR). The results revealed that the specific DNA fragments corresponding to each viroids were amplified in PCR. Percentage of infections were 14%, 16%, 20% and 22% for GYSVd-1, GYSVD-2, HSVd and ASGVd relative to total number of examined samples, respectively. Sequencing of seven selected PCR-amplified fragments showed that each newly sequenced segment was classified in a clade with the previously reported respective isolates from Iran. In addition, the most mixed infection related to HSVd and other viroids. This is the first assay to detect the four important viroids infecting vineyards form Zanjan province.