Development of a Translation Elongation Factor 1-Alpha (TEF)–Based TaqMan qPCR Assay for <i>Diaporthe humulicola</i> , the Causal Agent of Halo Blight of Hop
Bibliographic record
Abstract
Halo blight of hop, caused by Diaporthe humulicola, was first described in 2018 and is a major concern for growers in the eastern United States and Canada. This pathogen can cause quality and yield losses by desiccating hop cones, leading to shatter. However, traditional disease diagnosis is time-consuming, with morphological features taking up to 30 days to develop in culture. To address this issue, a quantitative PCR (qPCR) assay based on the translation elongation factor 1-alpha (TEF) gene was developed. We assessed capabilities and limitations of this assay for detection of D. humulicola in plant tissue and investigated aspects of the disease through (i) testing of hop rhizomes for the presence of fungal pathogens, (ii) determining the time required to detect D. humulicola in detached hop leaves, and (iii) comparing plating methods with the qPCR assay to monitor D. humulicola in a hop yard. The limit of detection for the assay was 100 fg/μl of DNA. The assay showed no cross-reactivity with other hop pathogens, endophytes, or other Diaporthe species tested. Detection of D. humulicola occurred 1 day after inoculation. The assay detected D. humulicola in both asymptomatic and symptomatic rhizome tissue, but further investigation is required to determine the cause of the observed symptoms. The assay successfully detected the pathogen in individual hop cones and inflorescences throughout the season, with higher positive identification rates than culture-based assays. This assay will provide time-limited diagnosticians with a tool for the detection of D. humulicola.
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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 | 0.002 | 0.003 |
| 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 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".