Waterlogging of plants leads to low
oxygen levels (
hypoxia) in the roots and causes a metabolic switch from aerobic respiration to anaerobic fermentation that results in rapid changes in gene transcription and
protein synthesis. Our research seeks to characterize the
microRNA-mediated gene regulatory networks associated with short-term waterlogging.
MicroRNAs (
miRNAs) are small non-coding RNAs that regulate many genes involved in growth, development and various biotic and abiotic stress responses. To characterize the involvement of
miRNAs and their targets in response to short-term
hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature
miRNA signatures (22 known and 2 novel mature
miRNAs, representing 66
miRNA loci) and their 92 predicted targets in three inbred Zea mays lines (waterlogging tolerant Hz32, mid-tolerant B73, and sensitive Mo17). Based on our studies, miR159, miR164, miR167, miR393, miR408 and miR528, which are mainly involved in root development and stress responses, were found to be key regulators in the post-transcriptional regulatory mechanisms under short-term waterlogging conditions in three inbred lines. Further, computational approaches were used to predict the stress and development related cis-regulatory elements on the promoters of these
miRNAs; and a probable
miRNA-mediated gene regulatory network in response to short-term waterlogging stress was constructed. The differential expression patterns of
miRNAs and their targets in these three inbred lines suggest that the
miRNAs are active participants in the signal transduction at the early stage of
hypoxia conditions via a gene regulatory network; and crosstalk occurs between different biochemical pathways.