Genetic variation of Saffron latent virus (SaLV) based on CP and P1 genomic regions in Iran

Saffron (Crocus sativus L., Iridaceae) is one of the most important industrial and export products in Iran. In this study, genetic diversity of new potyvirus Saffron latent virus (SaLV) was investigated based on CP and P1 genomic regions. Following random sampling of saffron plants from Razavi and South Khorasan, Isfahan, Tehran and Fars provinces, SaLV-infected samples were determined by ELISA. Reverse transcription- polymerase chain reaction (RT-PCR) was performed by specific primer pairs corresponding to CP and P1 genomic regions and amplified fragments of fifteen isolates were cloned and subsequently sequenced. Multiple alignments of CP and P1 nucleotide sequences were performed by MEGA 7 and genetic diversity and population structure parameters were assessed by DnaSP v.5. Based on the results, genetic diversity among the isolates in CP region (0.021 ± 0.003) was less than that of P1 region (0.049 ± 0.004). dN/dS values in CP and P1 regions were less than one, indicating that negative selection was imposed on the CP and P1 regions to maintain conservation of protein sequences. dN/dS value of P1 (0.182) was more than that of CP (0.0139), indicating the less conservation and natural selection pressure on the P1 region than the CP region. FST values of both genomic regions among geographical subpopulations were < 0.33, as an evidence of ongoing gene flow between subpopulations. These results are consistent with vegetative propagation of saffron through corms from the main origin of saffron corms (Razavi Khorasan and South Khorasan) to other regions of Iran.

Keywords:

Genetic variation , Potyvirus , Saffron