Detection of Rosellinia pepo and Rosellinia bunodes associated with root rots by real time PCR (qPCR). Detección de Rosellinia pepo y Rosellinia bunodes asociadas a llagas radicales, mediante PCR en tiempo real (qPCR).

Root rot caused by the soil-borne fungus Rosellinia spp. is a terminal disease in coffee (Coffea spp.) because plants do not recover from the infection and the area of untreated foci grows with time. Due to the difficulty of controlling the outbreaks that occur in plantation lots, an integrated management to face the problems caused by these pathogens in the Colombian coffee zones is recommended. This study aimed to develop specific and sensitive PCR-based methods to detect remaining inoculum levels in order to verify soil suitability for new  plantations  or  to  check  the  recovery  of  previously  affected  sites  for  replanting  purposes.  Primer  pairs  for quantitative PCR (qPCR) were designed based on sequences obtained a priori from polymorphic AFLP markers. Four combinations of primers that allowed the individual and simultaneous discrimination between the R. pepo and R. bunodes species were validated by conventional PCR and real-time PCR. This is the first report of a diagnosis with PCR tool to identify species of Rosellinia associated with coffee in Colombia and it is the initial step for the development of soil inoculum diagnostic tools for the management of the disease.