Genome-wide identification of the GRAS transcription factor family and regulation of metabolites under drought and salt stress in Isatis indigotica

Background The GRAS transcription factor family plays essential roles in plant development and adaptation to environmental stress. However, its genomic organization and regulatory mechanisms remain largely unknown in medicinal plants. Result Through genome-wide analysis, 39 IiGRAS genes were identified in I. indigotica . Phylogenetic, structural, and synteny analyses indicated that family expansion was driven by tandem and segmental duplications under strong purifying selection. Promoter analysis revealed stress-responsive cis-elements related to abscisic acid, jasmonic acid, and drought signaling. Integrated transcriptomic and metabolomic analyses further showed that IiSCL genes are co-expressed with transcription factors such as AP2, bZIP, WRKY, and HLH, and correlate with metabolites including trehalose-6-phosphate, lysophosphatidylcholine (LPC 18:1), and N-lactoyl-phenylalanine. These associations suggest IiSCL genes participate in coordinated transcriptional and metabolic regulation, contributing to osmotic balance, membrane stability, and oxidative defense under stress. Conclusion This study establishes a molecular framework for understanding SCL-mediated regulatory networks in I. indigotica and identifies potential genetic targets for improving stress tolerance, thereby supporting the sustainable cultivation of medicinal plants.