A TaqMan real-time polymerase chain reaction assay for accurate detection and quantification of Fusarium solani in strawberry plants and soil

Abstract

Abstract A new TaqMan real-time polymerase chain reaction (qPCR) was developed to accurately detect and quantify the soil-borne fungus Fusarium solani, pathogen to strawberry, in plant and soil samples. The assay was designed using sequences from the translation elongation factor 1 alpha (EF-1α) gene. The assay is highly specific: it specifically detected F. solani isolates when tested against 95 fungal isolates from 27 different species. The detection limit of the assay was 50 fg for F. solani genomic DNA and 102 conidia/g soil. A significant correlation (P = 0.0002) was observed between the amount of genomic DNA of F. solani detected by qPCR and the number of fungal propagules present in artificially inoculated soils. The effectiveness of the assay was validated by comparing it to traditional methods for the detection of F. solani in diseased strawberry plants and pre-planting soils from strawberry fields. A substantial and moderate correlation was found between the qPCR-based and traditional detection methods in diseased plants and soils. The amount of F. solani DNA estimated in roots and crowns of symptomatic strawberry plants ranged from 16 to 190 pg/mg fresh tissue. Inoculum densities in pre-planting soils varied between 3.1 × 102 and 1.3 × 105 colony-forming units per gram (CFU/g) of soil. Effectiveness was also evaluated by assessing the ability of the assay to detect decreasing levels of F. solani populations during biosolarization treatment. Taken together, this novel qPCR assay represents a useful tool for rapid assessment of pre-planting soils and nursery plants to prevent F. solani infection and production losses.