Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

Abstract

Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.

Abiotic stress miRNomes in the Triticeae

“…Species and genotype specific miRNA families are more likely to target specific enzymes associated with special pathways than conserved miRNAs. Deng and colleagues showed that miR-n05 was responsive to salt stress in barley and targeted the transcript for the enzyme enolase which functions in carbohydrate metabolism in plants by catalyzing the conversion of 2-phosphoglycerate to phosphoenolpyruvate (Van der Straeten et al 1991; Deng et al 2015). An understanding of both conserved and genotype or species specific miRNA and their targets is crucial for interpreting abiotic stress interrelated molecular mechanisms in the Triticeae .…”

“…Salinity stress may arise due to the accumulation of salt in the soil over time as a consequence of climatological events, primary salinity, or through human activities which cause an imbalanced soil in salt content and generate the salinity stress, secondary salinity (Parihar et al 2015). Each year, more than 900 million ha of land is affected by salinity stress, which carries an associated yield loss (Deng et al 2015). The effect of salinity stress on food production is predicted to increase with the effect of climate change (Wang et al 2003).…”

“…Expression of some conserved miRNA families such as miR156 and miR6213 has been detected as upregulated while miR168, miR444, and miR5048 have shown suppressed expression patterns in response to salinity stress in barley (Lv et al 2012; Deng et al 2015). Also, many miRNA families such as miR171 and miR393 showed induced expression in wheat in response to salinity stress (Gupta et al 2014; Wang et al 2014).…”

“…Also, many miRNA families such as miR171 and miR393 showed induced expression in wheat in response to salinity stress (Gupta et al 2014; Wang et al 2014). Interestingly, miR171 which targets the MYB family of transcription factors was found to be upregulated by salinity stress in both wheat and barley (Wang et al 2014; Deng et al 2015) (Table 2). Importantly, the same miRNA was also upregulated under salt stress in Arabidopsis (Liu et al 2008) which suggests common regulatory mechanisms for salinity tolerance in both monocots and dicots.…”

“…These authors pointed out the central role of these small regulators in the survival of plants under environmental stress. Additionally, many miRNA target transcripts have been connected with stress-responsive transcription factor families, including WRKY and NAC, in the Triticeae (Kantar et al 2010; Kantar et al 2011a; Deng et al 2015). The prominence of miRNA-based gene expression regulation was also shown with several phenotypic and physiological analyses after the expression of stress-responsive miRNAs and/or their target transcripts was altered (Feng et al 2013; Kantar et al 2010).…”