Polymerase chain reaction detection of disease is based on principal of thermal cycling in which PCR instrument allow to run generally 60-65 thermal cycle, during PCR operation it allow different stages of cycle at different temperatures for different period of time i.e. initiation (940C), denaturation (940C), primer annealing (600C), extension/elongation step (720C), final elongation (720C) and holding temperature (40C). After all completion of procedure and cost effective analysis of different DNA extension and isolation method. Final following conclusions are drawn 1) PCR based diagnosis system is developed for detection of greening bacteria 2) The comparative cost of detection by various combination of reagent and sampling time was determined and cost effective technology was standardized and validated.