Multi-omics analysis provides preliminary insights into the mechanisms involved in dormancy and germination in asparagus (Asparagus officinalis)

Dormancy and germination are critical physiological processes in asparagus ( Asparagus officinalis ) bud development, yet their molecular regulatory networks remain poorly understood. Here, we integrated transcriptomic and metabolomic analyses to characterize gene expression and metabolic dynamics during these stages. Principal component analysis (PCA) of 12 samples revealed distinct clustering of three biological replicates for dormancy and germination. Transcriptome analysis identified 2510 common differentially expressed genes (DEGs) during dormancy release and sprouting in asparagus rhizomes. Among these, 92 transcription factors (TFs) were significantly regulated, dominated by ZF-HD (19 members), MYB (18), and WRKY (13). Gene ontology analysis (GO) enrichment highlighted microtubule-based processes, carbohydrate metabolism, and photosynthesis, while kyoto encyclopedia of genes and genomes (KEGG) analysis revealed significant pathways in phenylpropanoid biosynthesis and starch/sucrose metabolism. Metabolomic profiling detected 331 (GS vs DS) and 173 (GR vs DR) differential metabolites, with 93 shared metabolites. Integrative analysis via Procrustes (M² = 0.1828, p -value = 0.001) and O2PLS identified four key candidate genes ( AoAHG1, AoGA3ox2, AoHB13, AoPRH132 ) linking transcriptional and metabolic regulation. These findings unravel potential molecular mechanisms underlying dormancy regulation and germination activation, highlighting TF-hormone-signaling crosstalk and key metabolites in asparagus bud development. We also identified two common KEGG pathways in the transcriptome and metabolome, flavonoid biosynthesis (ko00941) and starch/sucrose metabolism (ko00500), suggesting that these two pathways play important roles in dormancy and germination. This study provides a comprehensive framework for dissecting the regulatory networks governing perennial plant dormancy and sprouting, offering targets for agricultural optimization of asparagus production.