A Comprehensive Omics Study Revealed the Responses of Flax to Drought Stress and the Changes in Lignans

Flax (Linum usitatissimum L.), a crop with high lignan content, experiences significantly impaired growth under drought stress. However, the molecular mechanisms governing drought responses and lignan biosynthesis remain poorly understood. In this study, the flax cultivar LT001 was subjected to drought stress (soil moisture ≈7%) for 30 days, followed by integrated transcriptomic, metabolomic, and physiological-biochemical analyses. Results showed that drought induced leaf wilting, chlorosis, accelerated seed maturation, and significant changes in fresh weight, proline content, and antioxidant enzyme activities. Drought significantly increased the secoisolariciresinol diglucoside (SDG) and secoisolariciresinol (SECO) contents in both leaves and fruits. With a significant increase of SECO relative to SDG (particularly in fruits 600%) compared with the control. Transcriptomic and metabolomic analyses identified 10,215 and 9715 differentially expressed genes and 1252 and 1304 significantly altered metabolites in fruits and leaves, respectively. Integrated analysis revealed significantly decreased levels of adenosine 5’-diphosphate in fruits, which may limit photosynthetic efficiency. Similarly, the decreased levels of UDP-D-glucose and D-glucose-6-phosphate in leaves may modulate redox balance and metabolic flux, potentially contributing to enhanced drought tolerance in flax. This study elucidates the molecular network of drought response in flax and provides valuable insights for breeding high-resilience flax varieties.