As one of the oldest agricultural crops in China, millet (Panicum miliaceum) has powerful drought tolerance. In this study, transcriptome and metabolome analyses of ‘Hequ Red millet’ (HQ) and ‘Yanshu No.10’ (YS10) millet after 6 h of drought stress were performed. Transcriptome characteristics of drought stress in HQ and YS10 were characterized by Pacbio full-length transcriptome sequencing. The pathway analysis of the differentially expressed genes (DEGs) showed that the highly enriched categories were related to starch and sucrose metabolism, pyruvate metabolism, metabolic pathways, and the biosynthesis of secondary metabolites when the two millet varieties were subjected to drought stress. Under drought stress, 245 genes related to energy metabolism were found to show significant changes between the two strains. Further analysis showed that 219 genes related to plant hormone signal transduction also participated in the drought response. In addition, numerous genes involved in anthocyanin metabolism and photosynthesis were confirmed to be related to drought stress, and these genes showed significant differential expression and played an important role in anthocyanin metabolism and photosynthesis. Moreover, we identified 496 transcription factors related to drought stress, which came from 10 different transcription factor families, such as bHLH, C3H, MYB, and WRKY. Further analysis showed that many key genes related to energy metabolism, such as citrate synthase, isocitrate dehydrogenase, and ATP synthase, showed significant upregulation, and most of the structural genes involved in anthocyanin biosynthesis also showed significant upregulation in both strains. Most genes related to plant hormone signal transduction showed upregulated expression, while many JA and SA signaling pathway-related genes were downregulated. Metabolome analysis was performed on ‘Hequ red millet’ (HQ) and ‘Yanshu 10’ (YS10), a total of 2082 differential metabolites (DEMs) were identified. These findings indicate that energy metabolism, anthocyanins, photosynthesis, and plant hormones are closely related to the drought resistance of millet and adapt to adversity by precisely regulating the levels of various molecular pathways.

Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the TaCRY gene family was performed in wheat, identifying 12 TaCRY members localized to distinct chromosomes 2, 6, and 7. TaCRYs contain the conserved PHR and CCT domains and diverse gene structures. Collinearity relationships indicated their dynamic evolution patterns during polyploidization. Cis-acting elements of TaCRY members associated with light responsiveness, phytohormone signaling, and abiotic stress were also identified. Transcriptome analysis revealed that the differential expression patterns of TaCRY members under seed vigor process. This study expands our understanding of TaCRY diversity and provides valuable molecular information for marker-assisted selection in wheat improvement.

Pyrabactin resistance-like (PYL) proteins are core abscisic acid (ABA) receptors, but their organization and stress-responsive functions remain poorly understood in broomcorn millet (Panicum miliaceum L.). Here, we identified PmPYL genes genome-wide and characterized their phylogeny, gene structure, conserved motifs, chromosomal distribution, synteny, selection pressure, promoter cis-elements, predicted regulatory networks, tissue expression, and responses to ABA, salinity, and osmotic stress. Fifteen PmPYL genes were identified, with eight located in the A subgenome and seven in the B subgenome. Phylogenetic analysis placed 11 PmPYL proteins in Group II and four in Group III, with none in Group I. Sequence and structural analyses revealed broad conservation of receptor features associated with ABA perception and PP2C interaction. Collinearity analysis identified seven synteny-supported A/B homoeologous pairs, while the examined duplicate pairs showed low Ka/Ks ratios. Promoter analyses revealed abundant hormone- and stress-responsive elements, while predicted protein interactions supported a conserved PYL–PP2C–SnRK2 signaling module. Pairwise promoter and tissue-expression comparisons indicated regulatory variation among retained homoeologs. qRT-PCR analysis of seedling leaves further showed distinct treatment- and time-dependent expression patterns, with PmPYL10, PmPYL8, and PmPYL12 showing pronounced changes under the examined conditions. These findings reveal a conserved ABA receptor framework with substantial regulatory diversification and identify candidate PmPYL genes for functional analysis of stress adaptation in broomcorn millet.

Sucrose nonfermenting 1-related protein kinase 2 (SnRK2) proteins constitute a family of plant-specific serine/threonine kinases that play critical roles in mediating abscisic acid (ABA) signaling and responses to abiotic stresses, including drought and salinity. Nevertheless, systematic bioinformatics analysis and expression profiling of the SnRK2 gene family in broomcorn millet (Panicum miliaceum L.) have not yet been reported. A total of 16 PmSnRK2 genes were identified in the broomcorn millet genome, unevenly distributed across 12 chromosomes and phylogenetically classified into three subfamilies (I–III). Gene structure analysis revealed that the majority of PmSnRK2 genes harbor seven to eight introns. Promoter region mining uncovered abundant cis-elements responsive to hormones and abiotic stresses. Synteny analysis detected 12 PmSnRK2–PmSnRK2 paralogous pairs, with duplication events dated between ~ 1.28 and 219.36 million years ago; all Ka/Ks ratios were below 1, consistent with strong purifying selection. Multiple sequence alignment confirmed the presence of the conserved serine/threonine kinase active-site motif, the ATP-binding signature, and two characteristic C-terminal domains (I and II) across all family members. Structural superimposition of four representative PmSnRK2 proteins (PmSnRK2.6.2, PmSnRK2.11.1, PmSnRK2.13.1, PmSnRK2.15.1) onto Arabidopsis AtSnRK2.3 (PDB: 3UC3) yielded RMSD values of 0.922–1.134 Å within the kinase domain, underscoring three-dimensional conservation. Expression profiling using public RNA-seq datasets demonstrated that all 16 genes are transcribed in at least one of eight tissues, with individual members peaking in shoots, leaf blades, stems, inflorescences, roots, or seeds. Under exogenous ABA (50–100 µM), salt (100 mM NaCl), and PEG (20%) treatments, PmSnRK2 genes exhibited distinct induction and repression dynamics, revealing functional divergence in stress-response pathways. Our study provides comprehensive insights into the genomic characteristics, evolutionary patterns, and potential functional roles of the PmSnRK2 gene family in broomcorn millet. These results enhance the current understanding of how PmSnRK2 genes may contribute to abiotic stress tolerance, offering a valuable foundation for further functional validation and targeted improvement in broomcorn millet breeding programs.

Heterotrimeric GTP-binding proteins, commonly known as G proteins, act as core molecular switches in plant signal transduction, governing multiple biological processes including plant growth, development, phytohormone signaling, and abiotic stress adaptation. In this study, a total of 12 G-protein-related genes were identified in foxtail millet, consisting of six Gα subunit-encoding genes, one Gβ subunit-encoding gene, and five Gγ subunit-encoding genes. Gene structure and conserved motif analyses showed that members classified into the same subunit clade possessed highly conserved exon–intron organization and motif distribution, indicating evolutionary structural conservation within each G-protein subfamily. Promoter Cis-acting element analysis revealed that all G-protein family genes harbored light-responsive elements, as well as multiple regulatory elements associated with phytohormone signaling and abiotic stress responses. Transcriptome analysis showed that different G-protein genes exhibited distinct expression patterns under salt stress. Notably, SiαXLG2 exhibited drastically induced expression upon salt stress, which serves as a pivotal candidate gene for salt-stress response in foxtail millet. Collectively, this study provides a systematic characterization of the G-protein gene family and offers candidate gene resources for further elucidating G-protein-mediated salt-stress regulatory mechanisms in foxtail millet.