Molecular characteristics of apple dimple fruit viroid isolates from different apple cultivars in Iran

Apple dimple fruit viroid (ADFVd) causes severe fruit disorder with significant economic losses in several apple cultivars. During 2020–2022, 137 leaf samples of apple trees showing round and depressed green spots, color dappling, scarring, and distortion of fruits, and others without symptoms, were collected in the west (Hamadan, Kermanshah, and Kurdistan provinces) and northwest (Ardabil, East, and West Azerbaijan provinces) of Iran. ADFVd was detected by RT-PCR in 72.3% of the tested samples, including a significant number showing no symptoms. Nine isolates were sequenced and showed minimal differences from each other and 75.9–100% nucleotide identities with ADFVd variants previously reported in GenBank. In phylogenetic analysis, Iranian isolates were placed in the cluster consisting of all ADFVd isolates originating from apples except those from Japan. The Iranian isolates were distinct from those reported in apples in China, Japan, Spain, Türkiye, and in fig in Italy, but were not differentiated from isolates in apples in Italy, showing that they probably have a common origin.