COMPARISON OF CONVENTIONAL NESTED AND REALTIME PCR FOR DETECTION OF THE CAUSAL AGENT OF RATOON STUNT IN IRAN
A. Safaie Farahani, S.M. Taghavi, K. Taher-Khani
Leifsonia (Clavibacter) xyli subsp. xyli (Lxx) is the etiological agent of ratoon stunting disease (RSD), one of the most important diseases affecting productivity of sugarcane crops. The lack of defined external symptoms in the plant is a challenge for the diagnosis of RSD. We compared sensitivity of three methods including conventional PCR, nested PCR and real- time PCR for detection of Lxx sugarcane fields of the Khuzestan province (Iran). Total genomic DNA of infected sugarcanes was extracted and various amounts of it used as template for three mentioned techniques. The results showed that conventional PCR lacks sufficient sensitivity to be used as a diagnostic tool for RSD. Nested PCR had acceptable sensitivity, however, this technique is time-consuming. Real-time PCR is the most efficient method but it is expensive and requires specialist for analyzing the data. Totally, each of these methods has its own advantages and disadvantages. Therefore, the election of these techniques for diagnosis depends on factors like disease severity, the goal and available facilities.