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Integrating ATAC-Seq and Pan-Genomics Identifies Stress-Memory AP2/ERF Hubs in Foxtail Millet
Tingting Li1, Wenhui Liao2, Hao Wang2
1College of Bioengineering Shaanxi A&F Technology University Yangling Shaanxi China.
Food Science & Nutrition
|December 1, 2025
Summary
Foxtail millet utilizes AP2/ERF genes for drought memory, enhancing resilience to recurring stress. This study identifies key genes, like SiERF-51, crucial for adaptation and provides valuable genetic resources.
Area of Science:
- Plant Biology
- Genomics
- Molecular Biology
Background:
- Foxtail millet (Setaria italica) possesses drought adaptation mechanisms.
- Understanding drought memory genes is vital for improving crop resilience against recurrent drought.
Purpose of the Study:
- To investigate the role of AP2/ERF genes in foxtail millet's drought memory.
- To identify key genes and genetic resources for drought adaptation.
Main Methods:
- ATAC-seq and RNA-seq were used to analyze chromatin accessibility and gene expression under secondary drought stress.
- Pan-genome analysis, codon usage analysis, natural selection studies, and collinearity analysis were performed on AP2/ERF genes.
Main Results:
- AP2/ERF transcription factor motifs were highly enriched in chromatin regions responsive to drought.
- 80 AP2/ERF genes were upregulated, and 16,778 AP2/ERF genes were identified across 111 accessions.
- 57 conserved AP2/ERF genes showed significant upregulation under drought, with SiERF-51 exhibiting the highest expression.
Conclusions:
- The AP2/ERF superfamily plays a pivotal role in foxtail millet's drought memory.
- This research provides essential genetic resources for future studies on drought adaptation mechanisms.
