Apple ( Malus domestica Borkh), a member of the rose family (Rosaceae), is one of the important fruits of cold and temperate regions in Iran. Apple stem grooving virus (ASGV, genus Capillovirus ) and Apple stem pitting virus (ASPV, genus Foveavirus ), the members of Betaflexiviridae family and Tymovirales order, are the most important viruses of apple trees among the viruses affecting pome fruits around the world. These viruses are symptomless in most commercial apple varieties. For detection and determination of certain molecular properties of ASPV and ASGV, during a survey in 2011 and 2012, symptomatic and symptomless apple leaves and blossoms were collected from the main apple growing provinces of Iran (Isfahan, Western Azarbaijan and Alborz). The dsRNA was extracted from the leaves and blossoms and used as template in reverse transcription polymerase chain reaction (RT-PCR) with ASPV and ASGV specific primers. The amplified PCR products of 273 bp and 404 bp with ASGV specific primer pairs (ASGV-F/ASGV-R and ASGV-Pf/ASGV-Pr) and 264 bp and 370 bp with ASPV specific primer pairs (ASP-C/ASP-A and ASPV-F/ASPV-R) confirmed infection of samples with ASGV and ASPV, respectively. ASPV and ASGV were also detected in some samples as mixed infection. The primers were designed for the amplification of full length of ASPV and ASGV coat protein genes based on available sequences at GenBank. The PCR products of 713 bp and 1434 bp with designed ASGV and ASPV specific primers were amplified in some samples. The RT-PCR products were sent for sequencing. The BLAST comparisons showed high homology between nucleotide sequences of Iranian isolates of ASPV and ASGV and those of other ASPV and ASGV isolates available at GenBank. Multiple alignment of 713 bp segment of ASGV coat protein gene with those of other ASPV and ASGV isolates available at GenBank revealed Iranian isolate of ASGV had highest (99.1%) and lowest (98.5%) identity with South Korean (JN792477) and Indian isolates (FJ952160), respectively. Phylogenetic analysis of nucleotide sequence of ASGV coat protein gene revealed closer relationship between ASGV Iranian and Korean isolates (JN792477) than other ASGV isolates available at GenBank. The Nucleotide sequence of 370 bp of ASPV showed highest (86.6%) and lowest (82.8%) identity with Japan (AB045371) and Czech Republic (AJ968944) isolates. To our knowledge, this is the first report of ASGV and ASPV on apple trees in Iran. Key words : Apple stem pitting virus, Apple stem grooving virus, RT-PCR, Alignment, Phylogenetic tree.
