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

Introduction Isatis indigotica is a traditional medicinal and food homology plant in China, and its cultivation is frequently limited by drought and salt stress. The GRAS transcription factor family plays a critical role in plant development and stress adaptation. However, its regulatory network in medicinal plants remains largely uncharacterized. Methods In this study, we performed a genome-wide analysis to identify IiGRAS genes in I. indigotica , followed by phylogenetic and synteny analyses, promoter cis-element analysis, and integrated transcriptomic and metabolomic analyses. Results We identified 39 IiGRAS genes in I. indigotica . Phylogenetic and synteny analyses indicated that the gene family expanded via tandem and segmental duplications, and all duplicated gene pairs were subject to strong purifying selection (Ka/Ks < 1), suggesting functional conservation. Promoter analysis identified stress-responsive cis-elements linked to abscisic acid, jasmonic acid, and drought signaling. Integrated transcriptomic and metabolomic analyses revealed that IiSCL genes are co-expressed with AP2 , bZIP , WRKY , and HLH transcription factors and are correlated with metabolites implicated in osmotic balance, membrane stability, and oxidative defense. Discussion These findings establish a molecular framework for SCL-mediated stress regulation in I. indigotica and highlight potential candidate genes for improving stress tolerance in sustainable medicinal plant cultivation.