Latent-Space Modeling Reveals Transcriptional Strategy Divergence in Flax Root Drought Response

Drought stress severely constrains flax (Linum usitatissimum L.) production, yet the transcriptional logic underlying genotypic variation in root drought tolerance remains unclear. We subjected 20 flax cultivars to drought at peak flowering, constructed a continuous Drought Tolerance Index (DTI) based on biomass maintenance, and generated 120 root transcriptome profiles. Integrative analyses combining PCA/UMAP, β–variational autoencoder (β–VAE) latent space modeling, gene co-expression-network analysis (WGCNA), Random Forest–SHAP (SHapley Additive exPlanations), and virtual knockout were performed. We found that drought-tolerant and drought-sensitive cultivars underwent transcriptional remodeling of similar magnitude, but diverged in direction along a latent strategy axis, corresponding to “water-conserving” and “growth-maintenance” strategies, respectively. The water-conserving strategy was characterized by upregulation of genes involved in stress protection, protein folding, and ABA signaling, whereas the growth-maintenance strategy showed elevated expression of oxidative and cell wall-related genes. Drought strengthened co-expression coordination within a core regulatory module—enriched for transcription factors and hormone signaling—despite its overall expression decline. A small set of leverage genes were identified that accurately predicted DTI; these genes were not network hubs, yet their virtual knockout induced substantial drift in the latent strategy space, confirming their non-redundant predictive information. This framework uncovers transcriptional strategy divergence underlying flax root drought tolerance and offers candidate targets for molecular breeding.