Application of a SYBR green qPCR assay for <i>Ilyonectria radicicola</i> (Cabral) in ginseng garden soil
Bibliographic record
Abstract
American ginseng (Panax quinquefolius 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 Ilyonectria mors-panacis (A.A. Hildebr.) A. Cabral & 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. mors-panacis 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 Ilyonectria radicicola (Cabral) clade and did not cross-react with other common soil-borne fungi or fungus-like organisms of genera Fusarium, Verticillium, Pythium and Phytophthora. To validate the assay, the qPCR was used over three years to monitor Ilyonectria 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 Ilyonectria species and can be used to make risk assessments of replant disease affecting commercial ginseng production.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".