Application of a SYBR green qPCR assay for <i>Ilyonectria radicicola</i> (Cabral) in ginseng garden soil

American ginseng (<i>Panax quinquefolius</i> L.) is an economically valuable medicinal crop that is native to North America. Commercial cultivation of ginseng is under pressure because of replant disease involving the fungus <i>Ilyonectria mors-panacis</i> (A.A. Hildebr.) A. Cabral &amp; Crous. An SYBR green qPCR assay was developed with a primer set to amplify a portion of the internal transcribed 5.8S region of the <i>I. mors-panacis</i> nuclear ribosomal sequence to quantify the pathogen. The assay was sensitive and detected 2.5 fg µL⁻¹ total DNA extracted from pure pathogen cultures. In soil, the qPCR had a minimal detection limit of 87 DNA copies per microlitre from total DNA extracted from 10 g of soil. The assay was genus-specific to members of the <i>Ilyonectria radicicola</i> (Cabral) clade and did not cross-react with other common soil-borne fungi or fungus-like organisms of genera <i>Fusarium, Verticillium, Pythium</i> and <i>Phytophthora</i>. To validate the assay, the qPCR was used over three years to monitor <i>Ilyonectria</i> species in a field trial prone to ginseng replant disease. The qPCR could discriminate between pre-seeding soil treatments that reduced pathogen levels compared to the nontreated check. The density of American ginseng plants decreased from 996 to 367 by the second year following treatment and there was an inverse correlation with pathogen DNA copy number. This study provides a sensitive and reliable SYBR green PCR method for the detection of <i>Ilyonectria</i> species and can be used to make risk assessments of replant disease affecting commercial ginseng production.