Polymerase Chain Reaction (PCR) and Reverse Transcription (RT) PCR Based Assays for the Differentiation of Black Pepper Plants with Endogenous and Episomal Piper Yellow Mottle Virus

Piper yellow mottle virus (PYMoV), a member of the genus Badnavirus, Family Caulimoviridae, is known to infect black pepper. Besides its occurrence in episomal form, PYMoV is one among the badnaviruses which are also known to occur as endogenous viruses integrated into their host genome. In the present study, a polymerase chain reaction (PCR) and reverse transcription (RT)-PCR based approach was used to differentiate plants with endogenous and episomal forms of PYMoV. For this experiment the eight popular black pepper varieties namely, Panchami, IISR Thevam, IISR Girimunda, IISR Shakthi, IISR Malabar Excel, Subhakara, Sreekara, Pournami were initially screened by PCR followed by RT-PCR. Varieties Thekkan and Panniyur-1 with known episomal virus infection were taken as positive controls throughout the experiment. By analyzing the results of PCR and RT-PCR, tested plants were categorized as: (i) PCR (+) and RT-PCR (+) plants and (ii) PCR (+) and RT-PCR (−) plants. As only the plants with episomal virus will produce RNA, plants negative for RT-PCR can be considered to have only endogenous sequence which is integrated in the plant genome. From our study we identified plants which are positive for PCR and negative for RT-PCR suggesting that the combination of PCR and RT-PCR can be used to differentiate plants carrying endogenous and episomal virus.