Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing

Abstract

Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive Hassawi-3 and the salt-tolerant ILB4347 genotypes of faba bean, growing under salt stress. A total of 527 miRNAs in Hassawi-3 plants, and 693 miRNAs in ILB4347 plants, were found to be differentially expressed. Additionally, 284 upregulated and 243 downregulated miRNAs in Hassawi-3, and 298 upregulated and 395 downregulated miRNAs in ILB4347 plants growing in control and stress conditions were recorded. Target prediction and annotation revealed that these miRNAs regulate specific salt-responsive genes, which primarily included genes encoding transcription factors and laccases, superoxide dismutase, plantacyanin, and F-box proteins. The salt-responsive miRNAs and their targets were functionally enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, which showed that the miRNAs were involved in salt stress-related biological pathways, including the ABC transporter pathway, MAPK signaling pathway, plant hormone signal transduction, and the phosphatidylinositol signaling system, among others, suggesting that the miRNAs play an important role in the salt stress tolerance of the ILB4347 genotype. These results offer a novel understanding of the regulatory role of miRNAs in the salt response of the salt-tolerant ILB4347 and the salt-sensitive Hassawi-3 faba bean genotypes.

Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove (Sonneratia apetala Buch.-Ham.)

“…totally, 73 miRNAs (56 known miRNAs and 17 novel) were found to be regulated by salinity ( p < 0.01, Q < 0.05; Figure 5 ; Supplementary Data S3 ). Earlier studies have demonstrated that miR156, miR159, miR160, miR168, miR169, miR171, miR172, miR393, and miR396 were the major salt stress-regulated miRNAs in plants ( Alzahrani et al, 2019 ). All of these were also identified in our study, indicating the existence of common salt stress-related miRNAs.…”

MicroRNAs Mediated Plant Responses to Salt Stress

“…It was found that Hassawi-3 and ILB4347 differentially expressed 527 and 693 miRNAs, respectively. There was also a significant increase in 284 miRNAs in Hassawi-3 under control and a reduction in 243 miRNAs in ILB4347 plants during stress conditions [ 131 ].…”

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

“…Alzahrani et al (2019) [ 116 ] uncovered 1220 salt-responsive miRNAs by small RNA sequencing of two contrasting faba bean ( Vicia faba ) genotypes for salinity stress response (ILB4347 tolerant and Hassawi-3 sensitive). The Hassawi-3 genotype had 284 upregulated and 243 downregulated miRNAs, while ILB4347 had 298 upregulated and 395 downregulated miRNAs in the control and under salinity stress.…”

“…The Hassawi-3 genotype had 284 upregulated and 243 downregulated miRNAs, while ILB4347 had 298 upregulated and 395 downregulated miRNAs in the control and under salinity stress. The target gene(s) were predicted to encode TFs, laccases, superoxide dismutase, plantacyanin, and F-box proteins in addition to genes involved in hormone signal transduction, phosphatidylinositol signalling, and the MAPK signalling pathway [ 116 ].…”