Integrated Analysis of Hormone Metabolomics and Transcriptomics Reveals the Differential Mechanism of Ginger (Zingiber officinale Roscoe) Rhizome Bulking

As a product and reproductive organ of ginger (Zingiber officinale Roscoe), the degree of rhizome bulking is a key factor in determining the yield and economic value of ginger. There are few studies on the regulatory mechanism of rhizome bulking in ginger. This study aims to identify the key hormone that regulates ginger rhizome bulking and to screen for critical hormone-associated genes. As research subjects, two ginger accessions—large (L) with a thickened rhizome and small (S) with a slender rhizome—were derived from the same parent plant. The ploidy differences between the two determine variations in gene dosage as well as differential expression patterns. The levels of eight hormones in the rhizome of L and S during different growth stages were analyzed. Differentially expressed genes (DEGs) were identified by combining third-generation transcriptome sequencing technology (PacBio SMART) with quantitative real time PCR (qRT-PCR). Through screening methods such as Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), auxin, cytokinin, and salicylic acid were identified as the key differential hormones across various growth periods. Among these, changes in IAA level showed a positive correlation with rhizome bulking. Among them, change in IAA levels was positively correlated with the degree of rhizome bulking. Transcriptome analysis combined with qRT-PCR revealed that the auxin response factor genes ZoARF7 and ZoARF23 are likely to act as positive regulators of rhizome bulking. This study provides a theoretical foundation for elucidating the molecular mechanisms underlying hormone-mediated rhizome bulking in ginger.