Detection and genetic diversity of Grapevine red blotch-associated virus isolates in table grape accessions in the National Clonal Germplasm Repository in California
Bibliographic record
Abstract
AbstractGrapevine red blotch-associated virus (GRBaV) is a recently discovered ssDNA virus that is widespread in wine grapes in California. We investigated whether GRBaV infection was present in 156 table grape accessions of Vitis vinifera that included 53 accessions exhibiting leafroll-like symptoms and 81 accessions from diverse geographic origins. Cane samples were collected during the dormant season in 2012 and analysed for GRBaV infection by PCR. A total of 73 accessions showed presence of GRBaV and these included raisin and table grape accessions with black, green and red berries. A 557 bp amplicon obtained by PCR was purified and sequenced, and the phylogenetic relationship among GRBaV isolates was examined by the maximum likelihood method. The maximum genetic variability among the isolates was only 8% and they belonged to two clades. Although it is not yet known if GRBaV is present outside of North America, 54 accessions from sources originating outside of North America tested positive for the virus.RésuméLe virus associé à la tache rouge de la vigne (VaTRV) est un virus à ADN simple brin récemment découvert et qui est très répandu chez les raisins de cuve californiens. Nous avons étudié l'infection causée par le VaTRV afin de voir si nous la trouvions dans les 156 accessions de raisins de table Vitis vinifera, qui incluaient 53 accessions affichant des symptômes semblables à l'enroulement et 81 accessions d'origines géographiques diverses. En 2012, des échantillons de tiges ont été collectés durant la saison de dormance et analysés par PCR afin d'y déceler l'infection causée par le VaTRV. En tout, 73 accessions étaient porteuses du VaTRV et celles-ci comportaient des accessions de raisins secs et de raisins de table à fruits noirs, verts et rouges. Un amplicon de 557 bp obtenu par PCR a été purifié et séquencé, et la relation phylogénétique qui existe entre les isolats de VaTRV a été examinée par la méthode de vraisemblance maximale. La variabilité génétique maximale chez les isolats n'était que de 8 % et ceux-ci appartenaient à deux variantes. Bien que nous ne sachions pas encore si le VaTRV existe ailleurs qu'en Amérique du Nord, 54 accessions de sources provenant de régions autres que nord-américaines se sont révélées positives en ce qui a trait au virus.Keywords: geminivirusgermplasm screeningPCR detectionvitus viniferaMots clés: criblage des germoplasmesdétection par PCRgéminivirusVitis vinifera AcknowledgementsThe authors acknowledge Bernard Prins, Horticulturist, NCGR, USDA-ARS, for his help in providing a list of Vitis cultivars and assistance in collecting the samples. This work was supported by USDA-ARS CRIS 5306-22000-014-00D.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".