Identification of a Novel Haplotype Associated with Roan Coat Color in American Quarter Horses
Bibliographic record
Abstract
Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the KIT region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, RN1 and RN2, in the KIT region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a third novel haplotype, RN3, found in American Quarter Horses, that accounts for an additional 30% of American Quarter Horses negative for RN1 and RN2 that display the roan phenotype. Within this haplotype, we observe a variant chr3:79656505 (G > A), which we believe is a founder allele for the RN3 haplotype. In our sample set of horses, these three haplotypes account for more than 95% of the American Quarter Horse population studied and about 50–60% of roan horses in other breeds. Using whole genome sequencing of distantly related animals with a particular phenotype, together with a larger number of control horses, improves the odds of finding linked and/or causative variants.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| 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 | 0.000 |
| 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".