Molecular Detection and Phylogenetic Determinant of Strawberry crinkle virus in Strawberry Fields of Kurdistan Province Based on the Partial Polymerase- Gene Sequences

Leaf crinkle symptoms in some strawberry plants were observed in field, and therefore 55 leaf samples (symptomatic and asymptomatic) were collected from Kurdistan province and tested for infection with Strawberry crinkle virus (SCV) by RT-PCR. Total RNA was extracted by silica-capture method and subjected to cDNA synthesize with random hexamer primers. RT-PCR was done by specific SCV-primers and PCR products were observed on 1.2% agarose gels. RT-PCR results were showed that 51.9% of the samples were infected by SCV. Based on the geographical origin, cultivar and symptom, seven isolates were selected, sequenced and analyzed for molecular characterization and phylogenetic studies on SCV L-gene. Phylogenetic analysis showed that all the seven isolates from Kurdistan were placed in a distinct subgroup, phylogenetic group II. The average genetic distance between the isolates from Iran was 0.031 ± 0.005 but between these isolates and the other isolates, available in GenBank, was 0.069 ± 0.014. Pairwise comparisons of the sequences showed that isolate SAr6 had the highest nucleotide similarity (95.1%) to isolate 4MM of Argentina whereas isolate SS26 had the lowest nucleotide identity with isolate HB-A1 of Netherlands. This is the first report on occurrence of SCV on strawberry in Kurdistan province and also the first report of molecular detection of SCV in Iran.