Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.

Hydroponics is emerging as a vital method for producing resilient leafy greens in controlled environments. To systematically capture how hydroponically grown crops respond to stress, we subjected three species-cai xin, lettuce, and spinach-to 24 environmental and nutrient treatments. Growth measurements showed that extreme temperatures, reduced photoperiods, and severe macronutrient (N, P, K) deficiencies significantly limit fresh weight. Transcriptomic profiling (276 RNA-seq libraries) highlighted strong, shared downregulation of photosynthesis-related genes and upregulation of stress response and signaling genes across all three species. Leveraging a novel pipeline that merges regression-based gene network inference with orthology, we identified highly conserved gene regulatory networks (GRNs) spanning all three species-marking the first cross-species analysis of stress-responsive GRNs in economically important hydroponic leafy vegetables. These networks are anchored by well-known transcription factor families (e.g., WRKY, AP2/ERF, GARP), yet show lineage-specific differences compared to Arabidopsis, suggesting partial divergence in key regulatory components. Lastly, we introduce StressCoNekT (https://stress.plant.tools/), an interactive, publicly available database that hosts our transcriptomic data and offers comparative tools to accelerate the discovery of robust stress-responsive genes and cross-species analysis. This study not only deepens our understanding of abiotic stress adaptation in hydroponic systems but also provides a critical foundation for breeding stress-resilient crops and developing smart agriculture solutions.