Discrimination between tobamoviruses and their pathotypes for L-gene-mediated resistance in green pepper (Capsicum annuum L.) by reverse transcription-polymerase chain reaction

A new method to discriminate between tobamoviruses and their pathotypes that infect green pepper (Capsicum annuum L.) was developed using reverse transcription-polymerase chain reaction (RT-PCR). The P₀ pathotype (Tobacco mosaic virus, Tomato mosaic virus, and Tobacco mild green mosaic virus) and the P₁ pathotype (Paprika mild mottle virus) were distinguished by RT-PCR using primers specific to each pathotype. However, the P_1,2 and P_1,2,3 pathotypes of Pepper mild mottle virus (PMMoV) could not be distinguished from each other using this procedure. The P_1,2 and P_1,2,3 pathotypes were differentiated by RT-nested PCR, in which a DNA fragment was first produced by RT-PCR using primers containing conserved sequences of PMMoV. The product was then used as the DNA template in a second PCR using primers specific to each pathotype. An immunocapture (IC) RT-PCR method was developed based on results from this study, which facilitated detection of tobamoviruses in pepper plants, seeds, and field soils and allowed the identification of their pathotypes.