Genetic Analysis of Resistance to Pythium Ultimum aMajor Component of Replant Disease in AppleRootstocks
Bibliographic record
Abstract
Apple rootstocks from the Geneva® breeding program tolerated apple replant disease in experimental and commercial plantings in North and South America, Europe and Africa. Apple replant disease (ARD) is biological in nature and composed of several fungal, oomycete and nematode actors that when combined can stunt or even kill young roots. A major contributor to the ARD syndrome is the necrotrophic soilborne oomycete Pythium ultimum, which can individually overwhelm young roots and root hairs causing them to decline. Genetic resistance to ARD and its components has been incorporated into apple rootstocks from a wild apple species Malus x robusta‘Robusta 5’. This research was aimed at increasing our understanding of the genetic complexity of the resistance to P. ultimumin progeny of ‘Robusta 5’. In a replicated experiment we phenotyped 48 individual progeny (breeding lines) belonging to a larger population derived from a cross between replant susceptible apple rootstock ‘Ottawa 3’ and resistant ‘Robusta 5’. We also leveraged existing genomic infrastructure in the form of high-density genetic maps composed of microsatellite and single nucleotide polymorphic markers segregating in the same cross. When combined with the genotypic means of the 48 progeny in Quantitative Trait Locus (QTL) analysis, candidate genomic locations were identified on chromosomes 2, 5, 13, 16 and 17 that were associated with relative susceptibility of those breeding lines to P. ultimuminfection. The allelic effects of the loci were measured using a generalized linear model and their combinatorial interactions were studied. Of the resistance allelic effects examined all but one were derived from ‘Robusta 5’. The ultimate goal of this work is to develop genetic markers that can aid in the selection of P. ultimumresistant rootstocks. However, the multi-locus nature of this resistance trait may necessitate that only loci with larger effects (on chromosome 5, 17 and 13) be targeted for further development.
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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) | 0.002 | 0.002 |
| Bibliometrics | 0.000 | 0.007 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".