# Integrated transcriptome and metabolome analysis reveals the molecular mechanisms of drought response in Setaria italica during the booting stage

## TL;DR

This study explores how foxtail millet responds to drought during a critical growth stage, identifying key genes and metabolic pathways involved in its drought tolerance.

## Contribution

The study identifies novel drought-responsive genes and metabolic pathways in foxtail millet during the booting stage using integrated transcriptomic and metabolomic analysis.

## Key findings

- Drought at the booting stage caused the highest yield reduction (34.94%) and the most differentially expressed genes (566 DEGs).
- Three core pathways were identified: phenylpropanoid biosynthesis, photosynthetic carbon fixation, and glyoxylate metabolism.
- Key genes like gcvT and metabolites like sinapyl alcohol showed significant changes under drought stress.

## Abstract

Drought is one of the most severe and prevalent abiotic stresses affecting crop production. Foxtail millet (Setaria italica), an important cereal crop in the Poaceae family, is considered an ideal crop for future sustainable agriculture due to its remarkable drought tolerance, water-use efficiency (WUE), and strong adaptability to poor soils. The booting stage is widely acknowledged as a pivotal developmental phase in foxtail millet, and this consensus has been well established in existing research. However, the molecular mechanisms underlying the drought response of foxtail millet during this critical stage remain poorly elucidated. In the present study, we employed an integrated approach combining transcriptomic and metabolomic sequencing to identify the core regulatory mechanisms and key genes governing the drought stress response in foxtail millet at the booting stage.

In this study, phenotypic variations, gene expression profiles, and metabolite accumulation patterns in foxtail millet were determined following drought treatments at different growth stages. Among these stages, drought stress imposed at the booting stage resulted in the most severe yield reduction of 34.94%, accompanied by the identification of 566 differentially expressed genes (DEGs) — the highest number across all tested stages. These findings indicated that the booting stage was the most vulnerable period to drought stress during foxtail millet growth. Furthermore, analyses of photosynthetic parameters and yield-related traits revealed that drought stress at the booting stage significantly inhibited photosynthetic capacity, which may represent a critical factor contributing to the yield decline observed in foxtail millet subjected to drought stress during the booting stage. Multi-omics integration analysis identified three core responsive pathways: phenylpropanoid biosynthesis, photosynthetic carbon fixation, and glyoxylate and dicarboxylate metabolism. Based on these findings, we constructed a drought resistance regulatory network model for the booting stage, revealing significant expression changes GAPA, ALDO, tktA, glpx, PRK, RPE, rbcS, maeB, GLUL, and gcvT. At the metabolic level, we observed significant accumulation of metabolites such as sinapyl alcohol, aconitic acid, citric acid, isocitric acid, and mesaconic acid, while the contents of methyl isoeugenol, eugenol, p-coumaric acid, chlorogenic acid, sedoheptulose, aspartic acid, and malic acid were markedly reduced. Most notably, this study revealed that downregulation of gcvT expression may restrict ammonia (NH3) supply, thereby activating the methanesulfonate synthesis pathway as an alternative nitrogen (N) source. This discovery provided novel insights into N metabolic remodeling under drought stress in plants.

This study laid the foundation for preliminary exploration of the molecular mechanisms underlying drought stress response during the booting stage in foxtail millet. Furthermore, these findings had identified valuable key candidate genes that may contribute to the breeding of high-yield and drought-resistant foxtail millet varieties.

The online version contains supplementary material available at 10.1186/s12870-026-08353-9.