A comparative analysis of root system characteristics, endogenous hormones, and transcriptome responses in tissue cultured ginger

Ginger holds significant culinary and medicinal value. This study investigates the variations in field performance and the mechanisms by root characteristics influence plant morphology and yield in different generations of ginger. The results indicate that certified seed (CS) ginger outperforms per-basic seed (PBS) and basic seed (BS) gingers above ground. However, anatomical analysis reveals that CS ginger has smaller fibrous roots diameter and a lower cortex-to-stele ratio in fleshy roots compared to BS and PBS gingers. Transcriptomic analysis further highlights the relationship between root development and metabolic regulation. Compared to BS root (BSR), CS root (CSR) exhibit significantly higher expression levels of differentially expressed genes (DEGs) associated with starch and sucrose metabolism, along with increased activity of starch-degrading enzymes, influencing starch and sucrose accumulation and conversion. Meanwhile, the expression of DEGs related to flavonoid biosynthesis and key enzymes activity in CSR, leading to a significant reduction in flavonoid content. Additionally, levels of Abscisic acid (ABA), trans-Zeatin riboside (TZR) and Salicylic acid (SA) were lower in CSR, whereas the concentrations of Indole-3-acetic acid (IAA), Jasmonic acid (JA) and Gibberellin A3 (GA3) were significantly higher. In conclusion, CS ginger exhibits weaker root biomass likely due to the dynamic regulations of starch and sucrose metabolism, flavonoid biosynthesis and phytohormone levels. These findings provide valuable theoretical insights and practical recommendations for optimizing the field cultivation of tissue-cultured ginger.