Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza
Bibliographic record
Abstract
Abstract Heading date determines rice’s adaptation to its area and cropping season. We analyzed the molecular evolution of the Hd6 quantitative trait locus for photoperiod sensitivity in a total of 20 cultivated varieties and wild rice species and found 74 polymorphic sites within its coding region (1,002 bp), of which five were nonsynonymous substitutions. Thus, natural mutations and modifications of the coding region of Hd6 within the genus Oryza have been suppressed during its evolution; this is supported by low Ka (≤0.003) and Ka/Ks (≤0.576) values between species, indicating purifying selection for a protein-coding gene. A nonsynonymous substitution detected in the japonica variety “Nipponbare” (a premature stop codon and nonfunctional allele) was found within only some local Japanese japonica varieties, which suggests that this point mutation happened recently, probably after the introduction of Chinese rice to Japan, and is likely involved in rice adaptation to high latitudes. Phylogenetic analysis and genome divergence using the entire Hd6 genomic region confirmed the current taxonomic sections of Oryza and supported the hypothesis of independent domestication of indica and japonica rice.
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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".