A real time PCR assay to detect and quantify root-knot nematodes from soil extracts

Root-knot nematodes cause forking and stubbing of the growing carrot root tip, decreasing market value and reducing yield by up to 45%. Since crop damage by these nematodes depends on their initial population densities at planting, pre-plant detection of potentially low nematode numbers is critical for predicting future yield loss. The aim of this study was to overcome some of the drawbacks of the labor and time-intensive process of root-knot nematode identification and quantification by developing and field testing a real time PCR (qPCR) assay. Primers were designed targeting the root-knot nematode Meloidogyne incognita species complex, which includes M. incognita as well as the closely related Meloidogyne javanica and Meloidogyne arenaria. The qPCR assay successfully detected each species and showed little amplification for non-target nematode groups except for the sister group Meloidogyne enterolobii, which is not known to occur in California. Predicted nematode densities related well with microscopic counts of nematodes from prepared solutions, as well as from solutions extracted from field soil. In a greenhouse experiment, the qPCR assay distinguished between low, medium and high levels of M. incognita infection and qPCR predicted densities at planting were negatively related in linear models with final carrot fresh weight, length and diameter. These results suggest that qPCR assays could be a valuable diagnostic tool to predict nematode infections and prevent crop losses.