A quantitative PCR method to detect the tomato corky root rot pathogens, Pseudopyrenochaeta lycopersici and Pseudopyrenochaeta terrestris

Authors: Testen, Anna; Shaw, Robert - Scott; ROTONDO, FRANCESCA - The Ohio State University; Moodispaw, Margaret; MILLER, SALLY - The Ohio State University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2023
Publication Date: 2/12/2023
Citation: Testen, A.L., Shaw, R.S., Rotondo, F., Moodispaw, M., Miller, S.A. 2023. A quantitative PCR method to detect the tomato corky root rot pathogens, Pseudopyrenochaeta lycopersici and Pseudopyrenochaeta terrestris. Plant Disease. https://doi.org/10.1094/PDIS-08-22-2009-RE.
DOI: https://doi.org/10.1094/PDIS-08-22-2009-RE

Interpretive Summary: Tomato production is hampered by corky root rot, a soilborne disease that reduces yield and can prevent farmers from growing tomatoes in high tunnels (hoop houses). The corky root rot pathogens are difficult to detect and quantify in soils, which limits how we can study this disease. We developed a quantitative polymerase chain reaction (qPCR) assay, a diagnostic assay, for the two species of fungi that cause tomato corky root rot. This qPCR assay allows us to rapidly detect the corky root rot pathogens in soils and tomato roots. This diagnostic assay speeds diagnosis of tomato corky root rot. We can now better study the biology and management of the corky root rot pathogens to improve tomato yields.

Technical Abstract: Corky root rot is an important disease in tomato production systems and is caused by Pseudopyrenochaeta terrestris and Pseudopyrenochaeta lycopersici (formerly Pyrenochaeta lycopersici Types 1 and 2, respectively). The corky root rot pathogens are slow growing, and difficult to isolate and quantify in soil and plant tissue. A multiplex hydrolysis probe-based qPCR assay was designed to allow for simultaneous detection and quantification of P. lycopersici and P. terrestris with a competitive internal control to indicate if qPCR inhibitors are present. Single species and multiplexed assays for Pseudopyrenochaeta spp. detected DNA levels above 0.15 pg DNA per reaction. These highly specific assays had no non-target amplification of other fungal and oomycete pathogens or rhizosphere-associated fungi of tomatoes that were tested. This assay can be used to quantify Pseudopyrenochaeta populations in roots and soils to better determine the impacts of disease management strategies on Pseudopyrenochaeta spp. and provides a tool to study the biology of Pseudopyrenochaeta spp.