Fig. 3: Combined transcriptome and metabolome analysis to identify the target genes of ethylene pathway.

a Venn diagram illustrating the number of differentially expressed genes (DEGs) in the axillary region of seedlings of the Csein2 mutant and Csein3/Cseil1 double mutant compared with the wild-type (WT) 15 days after germination (DAG); the DEGs in 15 DAG seedlings after ethylene treatment (1 mM) and control (mock) treatment; and the shared DEGs across these comparison groups. Relative expression levels of critical genes downstream of ethylene signaling that control branch (b) and tendril (c) development in the WT 24 h after ethylene treatment (1 mM), as well as in the Csein2 and Cseil1/Csein3 plants. The data are presented as the means ± SEs (n = 3 independent plants). Significant differences in means between various mutants and the wild-type (WT) were determined using one-way ANOVA followed by Dunnett’s multiple comparisons test and are indicated by asterisks (*P < 0.05, **P < 0.01). (d) Determination of the levels of hormones known to be involved in branching in the axillary region of 15 DAG WT seedlings 24 h after ethylene treatment (1 mM), as well as in the Csein2 and Cseil1/Csein3 plants. The data are presented as the means ± SEs (n = 6 biological replicates of the Csein2 mutant, Csein3/Cseil1 double mutant, and WT were used to quantify the levels of ABA and IAA, and n = 5 biological replicates of the Csein2, Csein3/Cseil1, and WT were used to quantify the levels of SL and BR). Each biological replicate consisted of pooled axillary regions from 5 independent plants. Significant differences in the means between various mutants and the WT were determined using one-way ANOVA followed by Dunnett’s multiple comparisons test, and P values are indicated above the corresponding boxes. Source data are provided as a Source Data file.