Detection and molecular characterization of viruses infecting tomatoes grown in greenhouses in Western Central Anatolia

Tomato, is very important place in agricultural economy and one of the important sources of income for farmers in Turkey. In recent years, tomato productions in greenhouses in highland conditions has started in order to ensure the continuity of production. The highland greenhouse production eliminates the gap in tomato production due to the excessive heat in the summer in the coastal regions of Turkey where intensive greenhouse tomato produced. In this study, surveys were conducted in the highland tomato greenhouses in Afyonkarahisar, Burdur, Denizli, Isparta, Kütahya ve Uşak, provinces and 282 samples were collected from plants showing virus-like symptoms. The samples were tested separately for 18 different viruses infecting tomato by SYBR Green-based two step RT-qPCR method, and 224 of the samples tested were infected at least with one virus. In addition, mixed infections of more then one viruses were detected in 98 samples. Burdur, was the region with the most virus infected samples and TSWV, ToBRFV, ToMV, TMV, PVY and PepMV were the most common viruses in the survey area. Up to 4 isolates representing each most commonly detected viruses and different areas were selected and the coat protein (CP) genes of the selected TSWV and ToBRFV isolates were amplified by RT-PCR. The amplified CP genes were purified and cloned and their sequences were determined. The CP gene sequences of virus isolates from different regions were compared with that of virus isolates from different production regions of the world obtained from the GenBank database. The similarity and phylogenetic relationships of virus isolates determined. In addition, TaqMan probe-based RT-qPCR method was developed for the multiplex detection of TSWV, ToMV, ToBRFV and PVY viruses in a sensitive, reliable and rapid manner in the same reaction in one tube.