It has been well documented that ethylene accumulation is a key signal for flooding. Our transcriptome **data** show that several ethylene biosynthesis genes, such as S-adenosyl-L-methionine (SAM) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO), were upregulated in the submerged roots. These results agree with previous studies showing that waterlogging stress promotes ethylene biosynthesis [52]. However, although ethylene biosynthesis genes were upregulated, waterlogging stress did not affect the downstream genes in the ethylene pathway, such as ETR, CTR1, and EIN3. Furthermore, although the increased EBF transcription could lead to EIN3 inhibition, this inhibition did not decrease the transcription of ERF TFs. Hence, we speculate that an EIN3-independent pathway might be involved in activating ERF TF transcription since there is growing evidence of the EIN3/EIL1-independent mediated pathway in the ethylene pathway. For example, the double knockout ein3ein1 Arabidopsis mutants were able to respond to ethylene under stress [53]. However, further studies are required to verify this.