SHORT COMMUNICATION Differentiating tomato leaf curl viruses possessing mono/bi partite genomes using replicase gene based PCR assay: implications for developing virus specific resistance Varsha Garg & Vipin Permar & Vilas Parkhi & Elangovan Mani & Abdulrahman A. Alatar & Mohammad Faisal & Shelly Praveen Received: 15 October 2014 /Accepted: 5 January 2015 # Society for Plant Biochemistry and Biotechnology 2015 Abstract Tomato leaf curl disease (ToLCD) is associated with begomoviruses, with their generic names as Tomato leaf curl viruses (ToLCVs) and Tomato yellow leaf curl viruses (TYLCVs). ToLCVs exist both with mono/bipartite genomes, whereas TYLCVs carry monopartite genomes. For manage- ment of these viruses, three resistance loci Ty-1 to Ty-3 are being deployed, which provides different degree of resistance. These viruses encode a replication initiator protein (Rep), indispensible for virus replication. The conserved/ divergent sequences of rep gene(s) were used to develop mono/bipartite virus specific PCR assay. The implications of distinguishing viruses with mono/bipartite genomes for using virus specific resistance loci through breeding have been discussed. Keywords Monopartite . Bipartite . Ty based resistance loci Abbreviations ToLCD Tomato leaf curl disease ToLCV Tomato leaf curl virus TYLCV Tomato yellow leaf curl virus Rep/rep Replication initiator protein/gene RCR Rolling circle replication Tomato leaf curl disease causes huge loss to tomato produc- tion worldwide. This disease is caused by a group of viruses belonging to family Geminiviridae; genus Begomovirus and transmitted by a vector Bemisia tabaci. Based on the symp- toms, they have two generic names TYLCV and ToLCV. TYLCVs were first discovered in 1939 in Israel and Jordan, and it was officially named in 1964. Since then, the disease has spread to the Middle East, Mediterranean coast, East Asia, Central America, Australia, and many other countries and regions (Boulton 2003). ToLCVs were found to be predomi- nantly occurring in southern Asia with existence of various virus variants (Varma and Malathi 2003). Recent spread of ToLCVs were found to be in Iran, Peru and Spain, suggesting their global expansion (Fazeli et al. 2009; Melgarejo et al. 2013; Juarez et al. 2014) The natural source of resistance for these viruses is very scanty. Five different loci were identified from the wild culti- vars for developing resistant material. Ty-2 was originated from S.habrochaites, Ty-5 (ty-5) from S.peruvianum while Ty-1, Ty-3 and Ty-4 from different S.chilense accessions (Verlaan et al. 2013). Ty-1, 2&3 are commonly used to de- velop resistance, both for TYLCVs and ToLCVs. These resis- tances provide different level of tolerance to leaf curl/yellow leaf curl viruses. The genome of these viruses consists of ssDNA. Charac- terization of these viruses suggests the presence of different Electronic supplementary material The online version of this article (doi:10.1007/s13562-015-0299-5) contains supplementary material, which is available to authorized users. V. Garg : V. Permar : S. Praveen (*) Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India e-mail: shellypraveen@iari.res.in S. Praveen e-mail: shellypraveen@hotmail.com V. Parkhi : E. Mani Advanta Ltd., Krishnama House, Road No.7, Banjara Hills, Hyderabad 500034, India A. A. Alatar : M. Faisal Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia J. Plant Biochem. Biotechnol. DOI 10.1007/s13562-015-0299-5