Journal of Agronomy and Field Innovations

Background: Salinity of soil is one of the main abiotic factors restricting barley (Hordeum vulgare L.) yield worldwide. This phenomenon disrupts ionic and osmotic homeostasis and induces complicated physiological and molecular processes. MicroRNAs (miRNAs) function as post-transcriptional regulators of stress-responsive gene networks, but the genotype-specific miRNA profiles determining salinity tolerance in barley have not been fully studied yet.
Objective: This research analyzed the miRNA expression patterns of salt-tolerant and salt-sensitive barley genotypes in order to identify the miRNAs with a differential expression and their possible targets that are responsible for salinity tolerance.
Methods: Seedlings of CM72 (the tolerant genotype) and Gairdner (the sensitive genotype) seedlings were exposed to 150 mM NaCl for 24 hours, along with non-stressed controls. There were three biological replicates for each treatment. Small RNA libraries for roots and shoots of both genotypes were sequenced on an Illumina platform. Differential expression analysis was performed with DESeq2 (|log2 fold change| ≥ 1, FDR < 0.05). Target prediction, Gene Ontology and KEGG enrichment analyses, and stem-loop RT-qPCR confirmation was carried out.
Results: Forty-eight distinct miRNAs were seen to be differentially modulated by the genotype, with unique patterns related to them: for example, hvu-miR393, hvu-miR156 and hvu-miR171 were upregulated in the salt-tolerant genotype, while hvu-miR168 and hvu-miR396 were downregulated in the salt-sensitive genotype. Enrichment analysis showed that the predicted targets were involved in ion transport, osmotic adjustment, antioxidant defence and hormone signalling pathways. Additionally, the results of RT-qPCR correlated well with the sequencing data (r > 0.85). 
Conclusion: The miRNA reprogramming is genotype dependent and contributes to the observed differences in salinity tolerance of barley while the identified miRNAs and their targets can be potentially used for developing salt-tolerant varieties through marker-assisted selection and biotechnological methods.