Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene <i>Rvi2</i>
Bibliographic record
Abstract
Breeding elite apple cultivars with scab resistance is a key global goal, as reliance on fungicides is unsustainable. The causal fungus, Venturia inaequalis, evolves rapidly, threatening cultivars with single-gene resistance. Since the 1980s, breeding programmes have introduced novel resistance sources via backcrossing. Here, we generated a haplotype-phased genome assembly of Russian apple R12740-7A and an Oxford Nanopore assembly of the Rvi2-resistance accession TSR34T15, enabling detailed dissection of the Rvi2 resistance locus. Fine-mapping using a 'Royal Gala' × TSR34T15 segregating family delimited Rvi2 to a narrow genomic interval, within which we identified a 10 041 bp long terminal repeat retrotransposon (LTR-RT) insertion-an insert-based structural variant (SV) strongly linked with Rvi2. Notably, this LTR-RT harbours an FPPS gene, a member of the farnesyl pyrophosphate/geranylgeranyl pyrophosphate (FPP/GGPP) synthase family, located 2 kb from a key candidate defence gene. Although the FPPS gene exhibits stable expression, its integration within the retrotransposon suggests a cis-regulatory role, potentially priming adjacent defence genes for robust up-regulation upon pathogen attack. We validated the marker derived from this SV in diverse germplasms and successfully implemented it in marker-assisted selection across extensive seedling cohorts. This marker will streamline the development of scab-resistant apple varieties.
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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 | 0.001 | 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".