Objective To identify members of the WRKY transcription factor family in Codonopsis pilosula at the genome-wide level and analyze their characteristics, and explore their potential roles in response to salt stress, thereby laying a foundation for functional studies of C. pilosula WRKY transcription factors. Methods Potential gene family members were screened across the entire genome based on conserved protein domains using the Hidden Markov model (HMM). Protein sequence alignment, conserved domain analysis, phylogenetic tree construction, gene synteny analysis, and cis-acting element analysis in the promoter region were performed using software and online tools including MAFFT, IQ-TREE, MEME, Plant CARE and TBtools. Expression patterns of WRKY genes were analyzed based on transcriptome data from different tissues (roots, stems, leaves, and flowers) and qRT-PCR was used to determine their relative expression levels. In addition, the transcriptome data of C. pilosula treated with 0, 60, and 120 mmol/L NaCl were analyzed to examine the expression changes of WRKY genes under salt stress. Results A total of 50 WRKY transcription factor members were identified in C. pilosula. Motif analysis showed that all members contained the typical WRKY domain with the conserved sequence WRKYGQK. Phylogenetic analysis with WRKY transcription factors from Arabidopsis thaliana and Oryza sativa classified the 50 C. pilosula WRKY transcription factors into three groups, with group II further divided into five subgroups. The amino acid lengths of the identified WRKY proteins ranged from 103 to 986 residues, with isoelectric points (pI) of 4.87−9.99 and molecular weights (MW) of 12 435.14−107 946.28. Gene expression analysis revealed significant differences in the expression levels of CpWRKY26, CpWRKY48, CpWRKY2, and CpWRKY49 among roots, stems, leaves, and flowers of C. pilosula. The results of salt stress treatment indicated that most CpWRKY genes showed differential expression trends under different concentrations of NaCl, and some members cluster phylogenetically with previously reported salt-tolerant WRKY genes, suggesting that they may be involved in the regulation of C. pilosula salt stress responses. Conclusion This study represents the first systematic identification and bioinformatics analysis of the WRKY gene family in C. pilosula at the genome-wide level. By combining tissue expression and salt stress response analyses, the study reveales that the WRKY genes in C. pilosula may be involved in physiological processes such as growth and development, secondary metabolite biosynthesis, and stress responses. This lays a theoretical foundation for further research on the functions of WRKY genes and their roles in regulating medicinal components, and provides gene resources and scientific evidence for molecular-assisted breeding of C. pilosula.

Codonopsis pilosula(Franch.) Nannf.  /  WRKY transcription factor  /  genome-wide identification  /  salt stress  /  functional analysis