Li Ruimiao, Lei Cuiyun, Zhang Qiang, Guo Xiaomeng, Cui Xiting, Wang Xingchun, Li Xukai, Gao Jianhua
Shanxi Hou Ji Laboratory, College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China.
Plants (Basel). 2025 Apr 21;14(8):1257. doi: 10.3390/plants14081257.
The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes ( and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature () was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on genes. Promoter analysis identified abundant stress-responsive -elements. Among core members, the gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes as a critical target for stress tolerance engineering in foxtail millet.
短节间相关序列（SRS）家族是一类对多种生物学过程至关重要的植物特异性转录因子，本研究利用来自110份核心种质资源的泛基因组数据以及两个高质量基因组（ 和豫谷1）对谷子进行了系统研究。我们鉴定了SRS成员，并分析了它们的种内分布模式，包括拷贝数变异（CNV）和染色体间易位。提出了一种新颖的标准化命名法（ ）以统一基因家族命名，从而能够直接可视化种质间成员数量的变异，并识别核心/可变成员，同时突出染色体易位。聚焦于两个均含有6个核心SRS成员的高质量基因组，我们与拟南芥、水稻、玉米、大豆和青狗尾草进行了全基因组共线性分析。共线基因对的Ka/Ks分析表明纯化选择作用于 基因。启动子分析鉴定出丰富的胁迫响应 -元件。在核心成员中， 基因在营养生长期间表达最高，但在干旱和盐胁迫下显著下调，表明其在非生物胁迫响应中作为关键负调控因子的作用。本研究证明了泛基因组学在解析基因家族动态方面的实用性，并将 确立为谷子耐逆性工程的关键靶点。
