Multi-tissue transcriptomic profiling of foxtail millet in response to drought and rewatering

Drought is a critical abiotic stress limiting crop productivity. However, the molecular mechanisms underlying coordinated multi-tissue responses to drought and subsequent recovery remain unclear.

In this study, leaf‑based physiological measurements, as well as transcriptomic sequencing, and molecular network analysis of four tissues (i.e., roots, stems, leaves, and grains) under prolonged drought from booting to maturity and short-term rewatering were performed to systematically dissect the dynamic regulatory programs during drought adaptation and post‑rewatering recovery in foxtail millet. The results showed that the H₂O₂, proline, and malondialdehyde contents were significantly increased under prolonged drought and decreased to near control levels after rewatering. A total of 34 584 expressed genes was detected across all four tissues, among which 4 221 and 5 844 differentially expressed genes (DEGs) correlated with drought and rewatering treatments, respectively. Gene ontology and MapMan analysis across all four tissues revealed that DEGs associated with plant hormone and photosynthesis underwent pronounced dynamic reprogramming under drought and rewatering conditions. Furthermore, we identified a conserved gene module, HPP - Golden2-like (Seita.9G137500- Seita.4G270600), that responds to both drought and rewatering. This module, identified for the first time in foxtail millet, likely coordinates drought stress signaling with rewatering‑induced repair processes.

The study reveals a multi-tissue coordination framework for drought response and post‑rewatering recovery in foxtail millet, providing new theoretical insights and genetic resources for synergistic improvement of drought tolerance and post-drought resilience in crops.