Dynamic transcriptome profiling provides insights into rhizome enlargement in ginger (Zingiber officinale Rosc.)

The rhizome is an economically important part of ginger (Zingiber officinale Rosc.). However, the mechanism of ginger rhizome enlargement remains unclear. In this study, we performed an integrated analysis of the hormone content and transcriptome of ginger at three rhizome enlargement stages: initial enlargement (S1), middle enlargement (S2), and peak enlargement (S3). With rhizome enlargement, the levels of the hormones zeatin (ZT), gibberellic acid (GA), indole acetic acid (IAA), and jasmonic acid (JA) were significantly increased, and this increase was positively correlated with rhizome diameter. Transcriptomic analysis identified a large number of differentially expressed genes (DEGs); the number of DEGs were 2,206 in the transition from S1 to S2, and 1,151 in the transition from S2 to S3. The expression of several genes related to hormone biosynthesis and signalling and cell division or expansion, and transcription factors was significantly altered, which suggests that these genes play essential roles in rhizome enlargement. The results of correlation analysis suggested that the process of ginger rhizome enlargement may be primarily related to the regulation of endogenous cytokinin, GA(3), auxin, and JA biosynthesis pathways and signal transduction; GRAS, HB, MYB, MYB122, bZIP60, ARF1, ARF2, E2FB1, and E2FB2, which may regulate the expression of rhizome formation-related genes; and CYC2, CDKB1, CDKB2, EXPA1, and XTH7, which may mediate cell division and expansion. These results provide gene resources and information that will be useful for the molecular breeding in ginger.