Journal Article

Comprehensive analysis of the sucrose nonfermenting 1-related protein kinase 2 gene family in broomcorn millet (Panicum miliaceum L.) under abiotic stress conditions

Dai, Chunyang, Wang, Haigang, Li, Rui, Qiao, Yue, Zhou, Wei, Cui, Xiuyan, Chen, Ling, Wang, Junjie

2025

Overview

Background 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. Results 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. Conclusion 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Abscisic acid / Amino acids / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Chromosomes / Comment / Conserved sequence / Drought / Ecosystem components / Environmental aspects / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Plant / Genes / Genetic aspects / Genetic research / Genomes / Homeostasis / Hormones / Introns / Kinases / Life Sciences / Localization / Metabolism / Microarrays / Microbial Genetics and Genomics / Millet / Multigene Family / Nucleotide sequence / Panicum - enzymology / Panicum - genetics / Panicum miliaceum / Phosphatase / Phylogeny / Physicochemical properties / Physiological aspects / Physiology / Plant genetics / Plant Genetics and Genomics / Plant growth / Plant Proteins - chemistry / Plant Proteins - genetics / Plant Proteins - metabolism / Productivity / Promoter Regions, Genetic / Protein kinases / Protein Serine-Threonine Kinases - chemistry / Protein Serine-Threonine Kinases - genetics / Protein Serine-Threonine Kinases - metabolism / Protein-serine/threonine kinase / Proteins / Proteomics / Roles / Salinity / Seeds / Signal transduction / Sodium chloride / Stress (Physiology) / Stress, Physiological - genetics / Stresses / Structural analysis / Sucrose / Synteny / Transcription factors