Abstract:

Objective Salt-tolerance-specific gene modules were explored by investigating RNA-seq, which elucidated the molecular mechanisms underlying salt adaptation in Karelinia caspia. Method Leaves of K. caspia subjected to different NaCl concentrations (200, 300, and 400 mmol/L) were analyzed using RNA-seq and weighted gene co-expression network analysis (WGCNA). Key salt-responsive modules and genes were identified by functional annotation and network topology. Result RNA-seq generated 103.66 GB of data, yielding 66 823 unigenes, of which 45.15% (30 171) were annotated across six public protein databases. A total of 10 243 differentially expressed genes (DEGs) were identified, with 10 co-expression modules extracted via WGCNA. Notably, the brown, pink, and yellow modules demonstrated strong positive correlations with the 400, 300, and 200 mmol/L NaCl treatments, respectively. KEGG enrichment analysis revealed that genes within these modules were significantly involved in secondary metabolite biosynthesis, plant hormone signal transduction, and MAPK signaling pathways. Hub genes, such as PILS6, REM4.1, DOF21, MAPKKK18, GATA8-like, SAUR76, ABH, CIPK6, DIR22, and 4CL2, were screened based on connectivity and functional annotation. These suggested that they might play a pivotal role in adaptation of K. caspia to salt. Conclusion This study identified key salt-tolerance-specific gene modules and hub genes in K. caspia via integrated transcriptome and WGCNA analyses, thereby providing a theoretical foundation for exploration and utilization of salt-tolerant genetic resources in K. caspia.

Key words: Karelinia caspia, tolerance to salt, RNA-Seq, weighted gene co-expression network analysis, hub gene