Integrating <scp>ATAC</scp> ‐Seq and Pan‐Genomics Identifies Stress‐Memory <i>AP2/ERF</i> Hubs in Foxtail Millet
Bibliographic record
Abstract
ABSTRACT Foxtail millet ( Setaria italica ), a key cereal crop, has developed robust mechanisms to adapt to drought conditions. Investigating genes associated with drought memory is crucial for improving the plant's resilience against recurring drought events. Our study leveraged ATAC‐seq and RNA‐seq to reveal significant changes in chromatin accessibility and gene expression in response to secondary drought stress. The AP2/ERF transcription factor motifs were the most enriched within different chromatin regions in both leaf and root tissues. Transcriptome analysis identified 80 significantly upregulated AP2/ERF genes in foxtail millet. Pan‐genome analysis of 111 accessions revealed 16,778 AP2/ERF genes, categorized into 17 groups, highlighting gene number variations across populations. Codon usage analysis showed biased preferences across groups and populations. Natural selection studies indicated that most AP2/ERF genes are under strong purifying selection (Ka/Ks < 1), while dispensable genes exhibit greater evolutionary flexibility. Collinearity analysis has validated the conservation of 107 AP2/ERF genes across four Poaceae species, underscoring their ancient and critical functions in drought response. Of particular interest, 57 of these conserved genes were significantly upregulated in the leaves or roots under secondary drought stress, with SiERF‐51 showing the highest expression levels in both tissues, a finding verified by qRT‐PCR analysis. This study not only demonstrated the pivotal role of the AP2/ERF superfamily in drought memory but also provides a wealth of genetic resources for further investigations into the molecular mechanisms of drought adaptation in foxtail millet.
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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 | 0.001 | 0.001 |
| 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 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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".