Whole-genome analysis of recombinant inbred rice lines reveals a quantitative trait locus on chromosome 3 with genotype-by-environment interaction effects
Bibliographic record
Abstract
Elucidating genotype-by-environment interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. Genotype-by-environment interactions are of practical importance, as they determine the performance of cultivars grown in different environments, prompting the need for an efficient approach for evaluating genotype-by-environment interactions. Here, we describe a method for genotype-by-environment detection that involves comparing linear mixed models. This method successfully detected genotype-by-environment interactions in rice (Oryza sativa) recombinant inbred lines grown at 3 locations. We identified a quantitative trait locus (QTL) on chromosome 3 that was associated with heading date, grain number, and leaf length. The effect of this QTL on plant growth-related traits varied with environmental conditions, indicating the presence of genotype-by-environment interactions. Therefore, our method enables a powerful genotype-by-environment detection pipeline that should facilitate the production of high-yielding crops in a given environment.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| 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 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".