Integrating ATAC-Seq and Pan-Genomics Identifies Stress-Memory AP2/ERF Hubs in Foxtail Millet

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.