Integrated multi-omics preliminarily reveals sex-biased gene networks controlling dormancy release in Asparagus...

Understanding dormancy regulation in Asparagus (Asparagus officinalis L.), a globally valued dioecious vegetable, is critical for optimizing uniform spear emergence and yield. This study integrates transcriptomic, proteomic, and endogenous hormone analyses across key dormancy and sprouting stages in male and female plants to elucidate the underlying molecular mechanisms. We identified 12,211 differentially expressed genes (DEGs) and 3610 differentially expressed proteins (DEPs), revealing significant sex-specific and stage-specific dynamics, particularly during the female pre-sprouting phase (F2). Co-expression analysis of 1256 concordant mRNA-protein pairs pinpointed a core regulatory module centered on jasmonic acid (JA) signaling. Hormone profiling demonstrated declining abscisic acid (ABA) and contrasting JA trends between sexes during dormancy release, alongside distinct gibberellin (GA) and auxin (IAA) patterns. Weighted gene co-expression network analysis (WGCNA) of integrated data pinpointed three hub genes-LOC109832576 (gibberellin-regulated protein), LOC109840481 (MAP kinase kinase 4), and LOC109824138 (transcription factor VIP1)-centrally coordinating dormancy exit, validated functionally via homolog roles in ABA/GA signaling and germination in model plants. These findings provide the first multi-omics framework for asparagus dormancy transition, identifying key regulatory nodes and hormone cross-talk. The study provides valuable genetic targets for molecular breeding of early-germinating asparagus varieties via marker-assisted selection, enhancing emergence uniformity and adaptability to diverse environments. Moreover, the identified conserved regulatory modules offer cross-species insights for dormancy research in perennial plants, facilitating breakthroughs in crop improvement and stress resilience.