Abstract
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.
Highlights
Land plants, being strictly aerobic, receive freely diffused molecular oxygen from aerial or underground tissues
Out of 56, 22 known mature miRNA signatures and 2 novel miRNAs were selected. These 24 mature miRNA signatures, and their computational predicted targets were tested by quantitative real time PCR (qRT-PCR) assay in three inbred lines that showed different tolerance to waterlogging
Characterization of Tolerance in Three Inbred Lines Following the screening methods for maize waterlogging tolerance described by Liu et al [26] for each of the three inbred lines Hz32, B73 and Mo17, our results showed that the Hz32 is the most tolerant line while Mo17 is the most sensitive and B73 is in the middle range (Figure 2, Table S1)
Summary
Land plants, being strictly aerobic, receive freely diffused molecular oxygen from aerial or underground tissues. Oxygen deficiency due to short-term waterlogging (hypoxia) or its complete absence (anoxia) often damages roots under transient or sustained flooding conditions [1]. Long-term waterlogging can cause crop yield losses up to 30% when it occurs early in the season [2,3]. Maize survival is mainly dependent on its metabolic, physiological and morphological adaptation strategies. Anaerobically induced polypeptides (ANPs) are selectively synthesized, such as aldolase, enolase, alcohol dehydrogenase (ADH) and lactate dehydrogenase (LDH) [4]. Anaerobic stress induces alteration of metabolic pathways, leading to the accumulation of metabolites such as ethanol, lactates, and CO2, as well as changes in cytosolic pH, reactive oxygen species (ROS) and hormone homeostasis [5,6,7,8]
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