Identification of novel soybean microRNAs involved in abiotic and biotic stresses

Abstract

BackgroundSmall RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing.ResultsThe libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families.ConclusionsValidation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.

Analysis of biochemical variations and microRNA expression in wild (Ipomoea campanulata) and cultivated (Jacquemontia pentantha) species exposed to in vivo water stress

“…miRNAs are critical regulators of gene expression as they respond spontaneously to stress by regulating the existing pool of mRNAs (Leung and Sharp 2007;Sunkar et al 2012). Drought tolerant and sensitive soybean cultivars showed opposite pattern of miRNA expression (Kulcheski et al 2011). Similar to this report, the expression of five miRNA families (miR398, miR408, miR395, miR319 and miR172) differed between I. campanulata and J. pentantha.…”

“…miR169 was observed to respond to only Polyethanol Glycol (PEG)-mediated water deficit in rice while several miRNAs were observed to respond (both up and downregulated) to field like water deficit (Zhao et al 2007;Zhou et al 2010). miRNA expression also varies between closely related species differing in their ability to withstand stress (Kulcheski et al 2011). Differential miRNA expression in tolerant versus sensitive species implies an important role for miRNAs in stress responses in plants.…”

Complexity of miRNA-dependent regulation in root symbiosis

“…In legumes, these miRNAs were identified by the sRNA deep sequencing of various organs (reviewed in [17]) and during pathogen and symbiotic interactions [38,54]. Lelandais-Brière et al [34] and Kulcheski et al [54] identified nine and five novel miRNAs that were predicted to target NBS-LRR disease resistance genes in M. truncatula and G. max, respectively.…”

“…In legumes, these miRNAs were identified by the sRNA deep sequencing of various organs (reviewed in [17]) and during pathogen and symbiotic interactions [38,54]. Lelandais-Brière et al [34] and Kulcheski et al [54] identified nine and five novel miRNAs that were predicted to target NBS-LRR disease resistance genes in M. truncatula and G. max, respectively. Li et al [44] more precisely examined the expression patterns of six miRNAs during soybean nodulation, and among them, miR482 was induced early during nodulation at 6 hpi, reached maximum levels at 6 days after inoculation (dpi) and returned to basal levels at 14 dpi.…”

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

“…Several recent studies have shown that miRNAs that act as post-transcriptional regulators are regulated by drought and other abiotic stresses revealing a new layer of gene regulation that is very important for adapting to stress conditions (Sunkar et al 2007Ghorecha et al 2013). Furthermore, miRNA regulation differs between drought sensitive and tolerant genotypes under stress (Kulcheski et al 2011).…”