Multi-omics dissects long seed dormancy dynamics during wheat maturation

Seed dormancy is a critical adaptive trait conferring resistance to pre-harvest sprouting (PHS) in wheat, yet the molecular mechanisms underlying long dormancy remain elusive. This study integrated metabolomic and transcriptomic analyses of developing seeds from the long-dormant Yunnan hulled wheat variety YT34 and the non-dormant variety ‘Huapei 5’ at 10, 20, 30, and 40 days after anthesis (DPA), with three biological replicates per time point. Germination assays confirmed that YT34 exhibited significantly deeper dormancy than Huapei 5, with final germination percentages of 15.3% ± 2.1% versus 96.7% ± 1.5% (P<0.001). Genotype was the primary driver of differences of omics differences, with developmental stage playing a secondary role. We identified 156 core differentially accumulated metabolites in YT34, primarily organic oxygen compounds, fatty acyls, and carboxylic acid derivatives. Exogenous application of these metabolites at multiple concentrations, individually or in combination, did not significantly reduce germination (P>0.05), indicating that single metabolites are insufficient to induce deep dormancy. Transcriptome analysis revealed 1,798 shared differentially expressed genes as a core regulator, with downregulated genes outnumbering upregulated genes at 40 DPA, reflecting a transcriptional suppression during dormancy establishment. GO and KEGG enrichment analyses showed a temporal functional transition: from photosynthetic carbon metabolism (early stages) to energy metabolism and stress responses (middle stages), and finally to chromatin remodeling (late maturation). Key pathways, including ABC transporters, plant hormone signal transduction, glycolysis and TCA cycle, were identified as potential co-regulators. Quantitative integrative analyses (WGCNA, O2PLS, and correlation networks) revealed that 65% of the covariance between transcriptomic and metabolomic datasets was attributable to genotypic differences, identifying 12 hub genes and 8 hub metabolites as central nodes in the dormancy-associated regulatory network. Collectively, these findings suggest that plant hormone signaling, carbohydrate metabolism, amino acid metabolism, secondary metabolism, and energy metabolism pathways may collectively contribute to seed dormancy depth. This study provides a foundation for understanding long dormancy in wheat and offers candidate targets for breeding PHS-resistant varieties, though functional validation is needed to establish causality.