The transcription factor CtWRKY41 acts as a hub gene enhancing low-nitrogen tolerance in Coreopsis tinctoria Nutt․

Coreopsis tinctoria Nutt. is an economically important Asteraceae species whose cultivation is often constrained by low-nitrogen (N) availability in marginal soils, leading to significant reductions in inflorescence yield and quality. However, the adaptive mechanisms of C. tinctoria to low‑N stress remain largely unexplored. To elucidate the adaptive mechanisms to N deficiency, we integrated physiological assessments with transcriptome profiling across four key flowering stages under low-N (0.5 mM) and control (5 mM) conditions. Low-N stress severely impaired inflorescence development, concomitantly triggering the accumulation of osmolytes—soluble sugars (SS) and free proline (FP)—and enhancing peroxidase (POD) activity, while suppressing soluble protein (SP) content. Weighted gene co-expression network analysis (WGCNA) identified several hub modules and genes intimately linked to these physiological traits. Further analysis revealed that the low-N response involves coordinated reprogramming of phytohormone signaling (e.g., ABA, JA and Auxin ), flavonoid biosynthesis (e.g., CHS, IFS and HCT ), starch and sucrose metabolism ( SUS6 and SUS7 ), cell wall fortification ( CAD7 and GRP ), and endocytosis ( EHD1 ). The transcription factor CtWRKY41 emerged as the highest-connectivity hub gene. Heterologous over-expression of CtWRKY41 in Arabidopsis thaliana significantly enhanced low-N tolerance, evidenced by improved growth, biomass, chlorophyll retention, and soluble protein content under N limitation. Our findings establish CtWRKY41 as a positive regulator of low-N tolerance in C. tinctoria , providing a novel molecular target for the genetic improvement of stress adaptation in nutrient-poor soils.