Zhou Wei, Qiao Yue, Li Rui, Dai Chunyang, Cui Xiuyan, Chen Ling, Wang Haigang, Wang Junjie
Shanxi Institute for Functional Food, Shanxi Agricultural University, Taiyuan, 030031, China.
HouJi Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, 030031, China.
BMC Genomics. 2025 Sep 2;26(1):797. doi: 10.1186/s12864-025-11992-1.
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.
蔗糖非发酵1相关蛋白激酶2（SnRK2）蛋白构成了植物特有的丝氨酸/苏氨酸激酶家族，在介导脱落酸（ABA）信号传导以及对包括干旱和盐度在内的非生物胁迫的响应中发挥关键作用。然而，尚未见关于黍稷（Panicum miliaceum L.）中SnRK2基因家族的系统生物信息学分析和表达谱研究报道。
在黍稷基因组中总共鉴定出16个PmSnRK2基因，它们不均匀地分布在12条染色体上，系统发育上分为三个亚家族（I - III）。基因结构分析表明，大多数PmSnRK2基因含有7至8个内含子。启动子区域挖掘发现了大量响应激素和非生物胁迫的顺式元件。共线性分析检测到12对PmSnRK2 - PmSnRK2旁系同源基因对，复制事件发生在约1280万至2.1936亿年前；所有的Ka/Ks比值均低于1，这与强烈的纯化选择一致。多序列比对证实所有家族成员均存在保守的丝氨酸/苏氨酸激酶活性位点基序、ATP结合特征以及两个特征性的C末端结构域（I和II）。将四个代表性的PmSnRK2蛋白（PmSnRK2.6.2、PmSnRK2.11.1、PmSnRK2.13.1、PmSnRK2.15.1）与拟南芥AtSnRK2.3（PDB：3UC3）进行结构叠加，在激酶结构域内的RMSD值为0.922 - 1.134 Å，突出了三维结构的保守性。使用公共RNA-seq数据集进行的表达谱分析表明，所有16个基因在八个组织中的至少一个中被转录，个别成员在茎尖、叶片、茎、花序、根或种子中表达量达到峰值。在外源ABA（50 - 100 μM）、盐（100 mM NaCl）和PEG（20%）处理下，PmSnRK2基因表现出不同的诱导和抑制动态，揭示了胁迫响应途径中的功能差异。
我们的研究全面深入地了解了黍稷中PmSnRK2基因家族的基因组特征、进化模式和潜在功能作用。这些结果加深了我们对PmSnRK2基因如何有助于非生物胁迫耐受性的当前理解，为黍稷育种计划中的进一步功能验证和定向改良提供了有价值的基础。
