White seed color in common bean (<i>Phaseolus vulgaris</i>) results from convergent evolution in the <i>P</i> (<i>pigment</i>) gene
Bibliographic record
Abstract
The presence of seed color in common bean (Phaseolus vulgaris) requires the dominant-acting P (pigment) gene, and white seed is a recessive phenotype in all domesticated races of the species. P was classically associated with seed size, thus describing it as the first genetic marker for a quantitative trait. The molecular structure of P was characterized to understand the selection of white seeds during bean diversification and the relationship of P to seed weight. P was identified by homology searches, a genome-wide association study (GWAS) and gene remodeling, and confirmed by gene silencing. Allelic variation was assessed by a combination of resequencing and marker development, and the relationship between P and seed weight was assessed by a GWAS study. P is a member of clade B of subclass IIIf of plant basic helix-loop-helix (bHLH) proteins. Ten race-specific P alleles conditioned the white seed phenotype, and each causative mutation affected at least one bHLH domain required for color expression. GWAS analysis confirmed the classic association of P with seed weight. In common bean, white seeds are the result of convergent evolution and, among plant species, orthologous convergence on a single transcription factor gene was observed.
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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 | 0.000 |
| 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) | 0.000 | 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 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".