The millet, an important coarse grain crop, exhibits drought resistance, water conservation efficiency, and adaptability to poor soil conditions. Although

Background: 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. Results: 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 (NH ₃ ) 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. Conclusions: 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.

Foxtail millet (Setaria italica (L.) P. Beauv.) is an important traditional cereal crop in dryland ecological agriculture in China and is widely grown in India, the United States, and Nigeria. It is of significance to understand the variety–location–fertilizer (V–L–F) interaction for highly efficient production. Therefore, a two-year field experiment was conducted with six varieties in five locations, and data were analyzed by combined ANOVA analysis, redundancy analysis (RDA), and additive main multiplicative interaction (AMMI). The results showed that the mean sum of squares was significantly different among years, locations, varieties, fertilizations, and their interactions, except for Y–V and V–F interactions. The contributions of various factors to yield variation varied, location was the largest contributor (38.7%), followed by year (33.6%), and variety and fertilizer contributed 7.1% and 3.2%, respectively. JI25 was widely adapted, and its yield was stable and higher than that of others over diverse environments in two years. The RDA results showed that two principal components explained more than 66.1% of the yield variance, while more than 63.0% of the variances were clustered in the first factor. Excessive single rainfall or total rainfall and air temperature (especially minimum temperature) were significantly associated with the millet yield. The results offered an important reference for variety layout, natural resource potential mining, and formulation of efficient green cultural practices.

Introduction: To explore the mechanism underlying the effects of combined application of organic fertilizer and compound fertilizer on stem development of foxtail millet, this study used ‘ Jiza Jinmiao 3 ’ as the test material and set up three treatments: sole application of organic manure (Control1), sole application of compound fertilizer (Control2), and combined application of cattle manure-based organic fertilizer and compound fertilizer (Treatment). Methods: The effects of different fertilizer treatments were analyzed by integrating phenotypic determination, microscopic observation of stem structure, and multi-omics analyses including transcriptomics, metabolomics, and proteomics. Results: The results showed that compared with the sole application treatments, the combined application treatment significantly promoted phenotypic indicators of foxtail millet such as plant height, stem diameter, and stem fresh weight, and also significantly increased the cross-sectional area of stem vessels, the cell wall thickness of basic tissues, and the stem puncture strength. Multi-omics analyses revealed that differentially expressed genes (DEGs), differentially accumulated metabolites (DAMs), and differentially expressed proteins (DEPs) under the combined application treatment were significantly enriched in pathways related to cell wall development, such as phenylalanine metabolism and phenylpropanoid biosynthesis. Specifically, mapped to the phenylalanine pathway, the expression levels of key genes, metabolites, and proteins including Phenylalanine Ammonia - Lyase ( PAL ), Phenylalanine / Tyrosine Ammonia - Lyase ( PTAL ), and Peroxidase gene ( PRDX6 ) were significantly upregulated, and the content of phenylalanine was increased. Discussion: This study suggests that the combined application of organic fertilizer and compound fertilizer is associated with enhanced stem structural properties (including increased vascular area, cell wall thickness, and stem puncture strength) potentially linked to improved lodging resistance, with the phenylalanine pathway emerging as a candidate pathway, providing a theoretical basis and technical support for optimizing fertilization strategies and improving yield stability in the high-yield cultivation of foxtail millet.