The Metabolic Awakening of Barley Seedlings: A Time-Resolved View of How Germination and Light Shape Tissue-Specific...

Integration of internal metabolism with environmental cues is essential for successful establishment and survival of seedlings, with light an important mediator of the transition from skotomorphogenesis to photomorphogenesis. However, detailed knowledge of the metabolic events associated with this critical transition in developing tissues of barley germlings/seedlings is currently lacking. We systematically mapped the temporal and tissue-resolved metabolic reprogramming in seedlings grown under light/dark photoperiod and complete darkness, using nontargeted high-resolution LC-MS metabolomics to characterize seeds, shoots, and roots at 3-9 days postimbibition. Dark-grown seedlings displayed allocation of resources to length rather than density. Multivariate analyses revealed distinct, light-induced metabolic reprogramming in each tissue type. Among 192 annotated metabolites, seed metabolism was dominated by mobilization and pre-emptive defense priming, with roots developing energy-centered networks. In darkness, shoots directed metabolism toward rapid elongation and synthesis of defensive hordatine isoforms A and B, alongside linolenic acid and tryptophan derivatives. Light triggered metabolic switches where shoots allocated resources toward photoprotective flavonoids and antifungal hordatine C. This work provides the first spatiotemporal metabolic atlas of metabolic awakening in germinating barley seeds and seedling establishment based on data-driven insights into metabolic pathways. It redefines skotomorphogenesis as an active escape-and-defense strategy and offers insight into photomorphogenesis in support of tissue-specific metabolomic differentiation.