Development of diagnostic tools for accurate and efficient detection of lily symptomless carlavirus by rt-pcr

To facilitate efficient and accurate detection of lily symptomless carlavirus (LSV), specific primers were designed on the basis of nucleotide sequences of LSV coat protein (CP) gene. It has been found that amongst various viruses infecting Lilium in Himachal Pradesh, LSV is the most prevalent virus infecting lilies, with an incidence as high as 95% and it causes 30% reduction in flower yield per plant. After assuring the presence of virus by serological indexing, different softwares were used for primer designing specific for CP gene of LSV viz., Exome™1.4, Web-Primer and ClustalW. Out of all these tools. primers designed by Web-Primer software were found to be the best on the basis of important parameters like length, melting temperature (Tm), GC content and secondary structures, which are necessary for proper functioning of primers. For validating the authenticity of primers, BLAST search was performed with all the virus sequences present in NCBI database. The primers were validated under laboratory conditions for characterization of LSV coat protein gene using RT-PCR. The primer pair-1, designed by Web-primer software was found to be the best one for detection of LSV infecting local lily cultivars of Himachal Pradesh.