Transcriptomic analysis reveals key genes and pathways involved in fruit abscission of Epimedium pubescens

Fruit abscission in Epimedium pubescens is a critical yet underexplored process affecting seed yield and agricultural efficiency. Here, we integrated transcriptomic analyses across three developmental stages (pre-abscission, abscission zone formation, and post-abscission) to unravel the molecular underpinnings of fruit shedding.

We identified 1,009 significant DEGs in the comparison between stage B and stage A, and 1,388 significant DEGs in the comparison between stage B and stage C. Enriched in lignin biosynthesis, starch-sucrose metabolism, and plant hormone signaling pathways. Key lignin-related genes (e.g., COMT, CAD) were upregulated during abscission formation, correlating with enhanced cell wall fortification. Concurrently, dynamic shifts in starch synthesis/degradation enzymes (e.g., glgC, AAM) and trehalose metabolism genes (TPS, TPP) highlighted energy reallocation and stress adaptation. Ethylene and abscisic acid signaling dominated late-stage abscission, while auxin and cytokinin pathways were active earlier. Subcellular localization revealed expansin (EXP) and lipase (GDSL) genes localized at the cell wall, implicating their roles in wall modification and detachment.

These findings delineate a regulatory network integrating hormonal cross-talk, metabolic reprogramming, and cell wall dynamics, offering targets for improving seed retention in Epimedium cultivation.