Combined transcriptome and metabolome analysis provides insight into the ERF073 – Malic acid network in pakchoi under submergence stress

• The discovery of malic acid accumulated in pakchoi after submergence. • A total of 20 common DEGs were found involving in both stress and recovery stages, including an ethylene responsive transcription factor, ERF073. • During all DAMs, malic acid was up-accumulated in HYD and enriched in map00620, map00620, and map00710 pathways. • We speculated malic acid and ERF073 may correlated with submergence induced resistance of HYD. Pakchoi is sensitive to oxygen deficiency caused by submergence; however, the molecular mechanisms underlying its response to these conditions remains unclear. To determine these mechanisms, two pakchoi cultivars, Heiyoudong (HYD) and Suzhouqing (SZQ), were subjected to submergence for 1 h and 5 h, respectively. Following this treatment, the plants were transferred back to the control conditions for recovery. HYD exhibited higher survival rate than SZQ after recovery. Leaves from 1-h stress, 5-h tress, and subsequent 5-h recovery phases were harvested for metabolome and transcriptome analyses. Data analysis revealed that 206 differentially accumulated metabolites (DAMs) were identified between SZQ and HYD after 1 h stress (S1 vs H1) and 330 DAMs were identified between SZQ and HYD after 5 h stress (S5 vs H5) at stress stage. During recovery stage, 124 and 310 DAMs were found in S1 vs H1 and S5 vs H5, respectively. Additionally, 553 commonly differentially expressed genes (DEGs) were found both in S1 vs H1 and S5 vs H5 at the stress stage, while 458 DEGs were commonly found in the two comparison groups at the recovery stage. Among these DEGs, ERF073 was down-regulated, as further confirmed by qRT-PCR. KEGG pathway analysis revealed that DAMs and DEGs were mainly enriched in metabolic pathways. Taken together, these findings indicate that ERF073 may regulates malic acid accumulation in pakchoi, increasing its resistance to submergence.