DOG1-Mediated Priming Followed by Environmentally Tunable Plasticity: A Two-Phase Model for Dormancy Establishment in Xanthium strumarium

Background: Seed dormancy is crucial for plant survival and agricultural productivity, yet its molecular mechanisms, particularly the role of maternal effects, remain poorly understood. Methods: In this study, we applied a SWATH-based, label-free, quantitative shotgun proteomic mass spectrometry approach to investigate the temporal dynamics of dormancy establishment in Xanthium strumarium, a wild plant with two seeds in one burr that, despite sharing the same genetic and environmental conditions, exhibit distinct dormancy states. Results: Our data show that dormant seeds undergo coordinated metabolic suppression, marked by a decrease in energy metabolism, cell cycle arrest, and auxin signaling, explaining their smaller size. Simultaneously, dormant seeds exhibit metabolic re-prioritization towards fatty acid desaturation, cell wall modification, and an active epigenetic program stabilized by dormancy-promoting factors alongside a transcriptionally quiescent state in early–mid development. However, in the late developmental stage, molecular signaling pathways showed a recalibration distinguished by changes in seed metabolism (such as carbon–nitrogen reallocation, sulfur assimilation, and GABA production), hormonal fluctuations, and epigenetic regulation. Notably, previously reported high DOG1 transcript abundance, together with the absence of detectable DOG1 protein in the proteomic dataset, suggests that post-transcriptional mechanisms may contribute to DOG1 regulation. Conclusions: Based on these findings and the available literature, we propose a framework whereby dormancy establishment occurs in two phases: an early DOG1-mediated priming phase followed by a temperature-sensitive plasticity phase during seed maturation.