Primers Evaluation for Detection of Potyviruses Using RT-PCR Technique

Abstract

Detection and identification using polymerase chain reaction (PCR) is an initial step to diagnose viruses as the causal agents of plant disease. Early diagnosis is important to prevent and reduce yield losses in economically valuable crops. Primers are crucial components that determine the success of PCR detection. This study compares the sensitivity and specificity of species-specific and genus-universal primers in detecting several potyviruses using the reverse transcription (RT)-PCR technique. The test samples consisted of various plants exhibiting symptoms such as mosaic, leaf malformation, and vein banding or vein clearing. Detection was performed using one-step RT-PCR with specific primer pairs PRSV-326/PRSV-800, P-RT3/P-RT4, OG-RT1/OG-RT2, ChiVMV F Ind/ChiVMV R Ind, and PVY-cpF/PVY-cpR for the respective target viruses Papaya ringspot virus (PRSV), Leek yellow stripe virus (LYSV), Onion yellow dwarf virus (OYDV), Chilli veinal mottle virus (ChiVMV), and Potato virus Y (PVY). The universal potyvirus primers used were U341/Poty1 and MJ1/MJ2. There were differences in amplification results when using specific and universal primers for samples infected with PRSV, LYSV, and OYDV. Each specific primer of PRSV, LYSV, and OYDV successfully detected the target virus in more samples compared to detection using universal primers. Meanwhile, detection of ChiVMV and PVY using specific primers yielded the same results as detection using universal primers. Additionally, the universal primers U341/Poty1 and MJ1/MJ2 provided good results for detecting potyviruses from the field samples, specifically Celery mosaic virus (CeMV) and Yambean mosaic virus (YBMV).