Salt Stress Shifts Isatis indigotica to Prioritize Defense over Goitrin Biosynthesis

Soil salinization threatens the cultivation quality of Isatis indigotica , a medicinal plant whose root bioactivity depends on the glucosinolate-derived compound (R,S)-goitrin. Although moderate abiotic stress is widely assumed to stimulate secondary metabolite accumulation, the temporal dynamics of goitrin biosynthesis under salt stress remain poorly understood. This study quantified goitrin content across four NaCl concentrations (100 – 400 mmol/L) and four time points (2, 6, 12, and 24 h). Time-series transcriptome sequencing was performed under 100 mmol/L NaCl. Contrary to prevailing assumptions, goitrin content declined progressively from 2 to 12 h before partially recovering at 24 h, indicating that salt stress transiently suppresses goitrin accumulation rather than promoting it. Transcriptomic analysis identified 7 glucosinolate biosynthesis genes whose expression positively correlated with goitrin content (p < 0.05), and 6 salt stress-responsive genes negatively correlated with goitrin content (p < 0.05). These opposing patterns suggest that stress defense is transiently prioritized over biosynthesis, with partial metabolic recovery as plants adapt. These findings reveal a defense-biosynthesis trade-off mechanism in I. indigotica roots and provide a transcriptomic framework for understanding how abiotic stress reshapes secondary metabolism in medicinal plants.