A quantitative real‐time <scp>PCR</scp> assay for detection of <i> <scp>C</scp> olletotrichum lindemuthianum </i> in navy bean seeds
Bibliographic record
Abstract
Bean anthracnose is a seedborne disease of common bean ( P haseolus vulgaris ) caused by the fungal pathogen C olletotrichum lindemuthianum . Using seed that did not test positive for the pathogen has been proven to be an effective strategy for bean anthracnose control. To quantify the extent of anthracnose seed infection, a real‐time PCR ‐based diagnostic assay was developed for detecting C . lindemuthianum in seeds of the commercial bean class navy bean. The ribosomal DNA ( rDNA ) region consisting of part of the18 S rDNA , 5 . 8S rDNA , internal transcribed spacers ( ITS ) 1, 2 and part of the 28 S rDNA of seven races of C . lindemuthianum , 21 isolates of C olletotrichum species and nine other bean pathogens were sequenced with the universal primer set ITS 5/ ITS 4. Based on the aligned sequence matrix, one primer set and a probe were designed for a SYBR Green dye assay and a T aq M an MGB (minor groove binder) assay. The primer set was demonstrated to be specific for C . lindemuthianum and showed a high sensitivity for the target pathogen. The detection limit of both assays was 5 fg of C . lindemuthianum genomic DNA . To explore the correlation between the lesion area and the DNA amount of C . lindemuthianum in bean seed, seeds of the navy bean cultivar N avigator with lesions of different sizes, as well as symptomless seeds, were used in both real‐time PCR assays.
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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) | 0.002 | 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 | 0.000 |
| Research integrity | 0.001 | 0.002 |
| 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".