Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet

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 (<i>xm</i> 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 (<i>Accession_SiSRSN[.n]_xDy or xTy</i>) 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 <i>SiSRS</i> genes. Promoter analysis identified abundant stress-responsive <i>cis</i>-elements. Among core members, the <i>xm_SiSRS5</i> 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 <i>SiSRS5</i> as a critical target for stress tolerance engineering in foxtail millet.