Comparative analysis of maize root sRNA transcriptome unveils the regulatory roles of miRNAs in submergence stress response mechanism

Oxygen limitation under submerged condition induces hypoxic stress and causes a metabolic shift from aerobic respiration to anaerobic fermentation. Submergence stress often limits plant growth and causes substantial yield loss. The present small RNA (sRNA) transcriptome study aims to identify and characterise submergence responsive miRNAs to delineate the response mechanisms of maize seedlings to complete submergence. In this study, we constructed two sRNA libraries from control and submerged maize roots. Deep sequencing revealed 524 known (conserved and non-conserved) and 48 novel miRNAs from two libraries. Out of 188 commonly expressed known miRNAs, 45 miRNAs were found to be differentially expressed (43 down- and 2 up-regulated) in maize roots upon submergence. Submergence responsive miRNAs were found to be associated with diverse biological processes such as plant growth and development (miR172a, miR393b-3p), hormone signalling pathways (miR159c,f, miR160f-5p, miR167d-3p, miR172a, miR393a-5p), redox homeostasis (miR164a,b,c-5p, miR166h, a-3p, miR167e-3p.1), miRNA biogenesis (miR168a, miR168a-5p), chromatin remodeling (miR156a,g, miR159f, miR827-3p), and protein transport (miR156d-3p, miR159c,f, miR169c-3p). Moreover, dynamic correlations between selected miRNAs and their target genes were validated by qRT-PCR. The miR172a mediated upregulation of ERTF RAP2-7 ISOFORM X2 might be a pre-requisite for shifting of aerobic respiration to a less efficient anaerobic fermentation leading to restricted plant growth under flooded condition. To further understand the overall modulation of antioxidant defense system and metabolic adaptation strategy, fine tuning of ascorbate–glutathione cycle, anaerobic fermentation pathway genes, membrane damage, in vivo ROS detection and root MDA accumulation under flooding stress were also investigated in details. Taken together, our findings indicate that deregulation of ROS scavenging system might be the determining factor of meagre performance of maize seedlings under submerged condition. In a nutshell, our study adds new insights into the stress response mechanisms of maize seedlings towards submergence stress at post-transcriptional level.