Caractérisation de la diversité des isolats de Verticillium dahliae impliqués dans la mort prématurée de la pomme de terre (PED) dans le territoire Canadien
Bibliographic record
Abstract
La mort prématurée de la pomme de terre (PED) limite de façon majeure les rendements des agriculteurs cultivant la pomme de terre dans les provinces productrices du Canada. La maladie est principalement causée par le champignon du sol Verticillium dahliae, l’espèce la plus répandue au Canada, avec une capacité d’agressivité variable selon l’isolat. L’utilisation de marqueurs génétiques comme les polymorphismes mono-nucléotidiques (SNP) permet d’étudier la génétique des populations. Le projet visait à isoler et caractériser des souches de V. dahliae causant le PED dans 6 provinces canadiennes, en termes de diversité génétique des populations (SNP et groupes de compatibilité végétative (VCG)) et de leur agressivité. 192 isolats isogéniques purs de V. dahliae ont été obtenus à partir de cultures monosporiques. L'ADN des isolats a été séquencé par séquençage du génome complet (WGS), et ensuite alignée sur le génome de référence VdLs.17 de V. dahliae pour mettre en évidence les SNP. Deux lignées clonales prédominantes ont été trouvées dans toutes les provinces et il existe certains sous-groupes par lignée. Chaque population de V. dahliae a été comparée à des souches-types provenant de différents VCG, et semblent appartenir aux groupes 4A et 4B. La variabilité de l’agressivité des isolats non liée aux marqueurs génétiques a été évalué avec un essais avec 7 isolats. Ces analyses phylogénétiques et d’agressivité ont donc permis d’avoir un premier aperçu de la variabilité génétique et d’agressivité des populations de V. dahliae causant le PED au Canada Potato Early Dying (PED) is a common limiting factor in potato production in all of the producing provinces of Canada. The disease is mainly caused by the soil fungus Verticillium dahliae, which is the most widespread species in Canada, with a variable aggressiveness depending on the isolate. The use of genetic markers such as single nucleotide polymorphisms (SNPs) makes it possible to study the population genetics. The project aims to isolate and characterize strains of V. dahliae causing PED in 6 Canadian provinces, in terms of population genetic diversity (SNPs and compatible vegetative groups (VCG)) and their aggressiveness. 192 pure isogenic isolates of V. dahliae were obtained from monosporic cultures. The DNA of the isolates was sequenced by whole genome sequencing (WGS), and then aligned to the VdLs.17 reference genome of V. dahliae to highlight SNPs. Two predominant clonal lineages have been found in all provinces and there are some subgroups per lineage. Each population of V. dahliae has been compared to type strains from different VCGs, and appears to belong to groups 4A and 4B. The variability in the aggressiveness of isolates unrelated to genetic markers was evaluated with a trial with 7 isolates. These phylogenetic and aggressiveness analyzes therefore provided a first insight into the genetic variability of V. dahliae populations causing PED in Canada.
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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 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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 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".