Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus

Abstract

Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.

Keywords: abiotic stress; miRNA; regulatory network; sunflower (Helianthus annuus).

Figure 1

Expression patterns of miRNAs and their target genes under drought stress. Sunflower seedling at the six leaf stages grew on soil (¾ river sand and ¼ soil) under normal conditions and leaves and roots of them were harvested as control then they treated by withholding the water for 12, 24 and 48 h. (A) Expression patterns of miRNAs in the leaf. (B) Expression patterns of miRNAs in the root. (C) Expression patterns of target gene in the leaf. (D) Expression patterns of target genes in the root.

Figure 2

Expression patterns of miRNAs and their target genes under heat stress. Plants treated at 42 ± 1°C for 1.5, 3, and 6 h. (A) Expression patterns of miRNAs in the leaf. (B) Expression patterns of miRNAs in the root. (C) Expression patterns of target gene in the leaf. (D) Expression patterns of target genes in the root.

Figure 3

Expression patterns of miRNAs and their target genes under salt stress. Plant subjected under NaCl treatment in two concentration, 75 and 150 mM. (A) Expression patterns of miRNAs in the leaf (B) Expression patterns of miRNAs in the root. (C) Expression patterns of target gene in the leaf. (D) Expression patterns of target genes in the root.

Figure 4

Expression patterns of miRNAs and their target genes under cadmium stress. Plants treated with cadmium in 5 and 20 mg/L concentration. (A) Expression patterns of miRNAs in the leaf. (B) Expression patterns of miRNAs in the root. (C) Expression patterns of target gene in the leaf. (D) Expression patterns of target genes in the root.

Figure 5

Clustering of miRNAs expression profiles. Heat map diagram of miRNA expression prepared with two-way unsupervised hierarchical clustering of miRNAs expression under different abiotic stress. miRNAs are given in the rows and each columns represent a sample. The miRNA clustering tree is shown on the left (cluster I, II and III). Abbreviations: L, Leaf; R, Root; h, Hour; D, Drought stress; S, Salt Stress; Cd, Cadmium stress.

Figure 6

miRNA-mediated gene regulatory sub networks in response to abiotic stress. miRNA-target-abiotic stress interaction are shown. (A) Feedback loop between miR160, its target and abiotic stress. (B) Feedback loop between miR167, its target and abiotic stress and abiotic stress. (C) Feedback loop between miR172, its target and abiotic stress. (D) Feedback loop between miR398, its target and abiotic stress.

Figure 7

miRNA-mediated gene regulatory sub networks in response to abiotic stress. miRNA-target-abiotic stress interaction are shown. (A) Feedback loop between miR403, its target and abiotic stress. (B) Feedback loop between miR842, its target and abiotic stress.