Degenerate Primers Facilitate the Detection and Identification of Potyviruses From the Northwest Region of Iran

Background: Potyviruses are accounted for 40% of viral diseases of various crops including vegetables and legumes. Potyviruses can be transmitted through plant sap, seeds and many aphid species. Due to ease of spread of these viruses detection of such viruses are crucial as to the control of the incited diseases. Objectives: This study compared the efficiencies of two couples of primers in their detection of potyviruses infecting vegetables in North-West of Iran. Materials and Methods: To identify potyviruses infecting vegetables, total RNA preparations from leaves of diseased plants were subjected to reverse transcription (RT) with oligo d(T)15, M4T or a potyvirus-specific primer, followed by polymerase chain reactions (PCR) with two pairs of degenerate primers including Sprimer/M4 or NIb2F/NIb3R that would yield ~ 1700 or 350 bp fragments, respectively. Amplification was achieved from 7 samples when Sprimer and M4 were used, but non- specific fragments were also amplified. However, specific amplifications from 31 samples were achieved with NIb2F2 and NIb3R. PCR products resulting from the use of NIb2F/NIb3R were subjected for cloning and sequencing. Results: BLAST analysis of the sequenced data revealed that the PCR-amplified fragments belonged to Bean common mosaic virus (green bean), Bean yellow mosaic virus (broad bean), Potato virus Y (potato), Watermelon mosaic virus (squash, muskmelon or melon), Zucchini yellow mosaic virus (squash), and Soybean mosaic virus (bean). Conclusions: This study demonstrated the efficiency of NIb2F2/NIb3R in detection of potyviruses and revealed the extent of infections with diverse potyviruses species in the northwest part of Iran.