Identification of new QTLs for resistance to Plasmodiophora brassicae in Brassica napus using genome wide association mapping
Bibliographic record
Abstract
Abstract Background Clubroot of canola ( Brassica napus ), caused by the obligate pathogen Plasmodiophora brassicae Woronin, is a major disease worldwide. Genetic resistance remains the best strategy to manage this disease. The objective of the study was to identify and map new sources of resistance to clubroot in B. napus using genome-wide association mapping. The reaction of a collection of 177 accessions to four highly virulent pathotypes of P. brassicae was assessed. These pathotypes were selected because they were most recently identified and showed different virulence patterns on the Canadian clubroot differential (CCD) lines. The collection was then genotyped using genotyping by sequencing (GBS) method. Multi-locus mixed linear model (MMLM) was used to perform the association analysis. Results The majority of accessions were highly susceptible (70 –100 DSI), while few individual accessions showed strong resistance (0–20 DSI) to 5X (2 accessions), 2B (7 accessions), 3A (8 accessions) and 3D (15 accessions). In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to two major populations. SNPs were associated with resistance to each pathotype using MLMM. In total, 23 significant SNP loci were identified, with 14 SNPs mapped to the A-genome and 9 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (4 SNPs), 2B (9), 3A (5) and 3D (5). A blast search of 2 Mb upstream and downstream identified 61 disease resistance genes, of which 24 belonged to TIR-NBS-LRR proteins and 20 belonged to CC-NBS-LRR proteins. The distance between a SNP locus and the nearest resistance genes ranged from 0.11–1.66 Mb. This indicated that NBS-LRR gene family might have an important role in clubroot resistance in B. napus . Conclusion The resistant B. napus lines and the SNP markers identified in this study can be used for breeding for resistance to clubroot and contribute to understanding the genetic mechanism of resistance to clubroot.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| 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) | 0.002 | 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".