A cis-regulatory element of the PHYTOCHROME A gene confers the submergence escape capacity for amphibious plants

Submergence is a type of abiotic stress that can severely impact the survival of plants and the yield of crops. Plants not only sense the hypoxic conditions during submergence but also exposed to a range of low-light intensities, depending on the submergence depth and turbidity. However, how light availability affects submergence tolerance remains largely unknown. To clarify the functions of light receptor AtPHYA and transcription factor AtEIN3/EIL1 in the transcriptional response to submergence, we conducted RNA-seq analysis on the wild type Col-0, the atphyA-211 mutant, and the atein3eil1 double mutant. Following a 6-hour submergence stress treatment, we identified 7325 differentially expressed genes (DEGs) in the Col-0 seedlings. The expression of 3748 submergence-induced genes was notably reduced in the atein3eil1 double mutant, while it was significantly enhanced in the atphyA-211 mutant. This suggests that AtPHYA exerts a negative regulatory effect on the expression of genes induced by submergence. The absence of AtPHYA leads to an upregulation of these submergence-induced genes, confirming that AtPHYA negatively modulates their expression. Overall design: Terrestrial-grown plants were either maintained under terrestrial conditions or subjected to submergence for 6 h and leaves tissue was collected. Three replicates were prepared for each condition and each line.