Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel)

MicroRNAs have been shown to be involved in regulating plant’s response to environmental stresses, including salinity. There is no report yet on the miRNA-mediated posttranscriptional regulation of salt stress response of a grass halophyte by miRNAs. Here we report on the deep-sequencing followed by expression validation through (s)qRT-PCR of a selected set of salt-responsive miRNAs and their targets of the salt marsh monocot halophyte smooth cordgrass (Spartina alterniflora Loisel). Expression kinetics study of 12 miRNAs showed differential up/down-regulation in leaf and root tissues under salinity. Induction of expression of six putative novel microRNAs with high read counts in the sequence library suggested that the halophyte grass may possess different/novel gene posttranscriptional regulation of its salinity adaptation. Similarly, expression analysis of target genes of four selected miRNAs showed temporal and spatial variation in the up/down-regulation of their transcript accumulation under salt stress. The expression levels of miRNAs and their respective targets were coherent, non-coherent, or semi-coherent type. Understanding the gene regulation mechanism(s) at the miRNA level will broaden our fundamental understanding of the biology of the salt stress tolerance of the halophyte and provide novel positive regulators of salt stress tolerance for downstream research.