miRNA Regulatory Networks Underlying the Root–Leaf Synergism in Salt Tolerant Pokkali Rice

Pokkali is one of the rice varieties that have adapted to grow under highly saline conditions. Several studies have shown that plant’s response to salt stress is a multigenic trait involving the coordinated action of signaling molecules, ion transporters, enzymes, and transcription factors. In earlier studies, we have reported that the adaptability of Pokkali rice to excess salt involves genetic regulations by a panel of microRNAs (miRNAs). The miRNAs are crucial primary regulators of gene expression that may act at the transcriptional or post-transcriptional levels in a sequence-specific manner. In this study, we have analyzed and compared the small RNA and transcriptome datasets of roots and leaves of Pokkali plants grown in the presence of salt. The expression profiles in the absence of salt, in both roots and leaves, were used for comparative controls. The miRNA nodes involved in root–leaf synergism were identified and validated. The analysis highlighted the role of osa-miR156a, osa-miR164a, osa-miR167a, osa-miR169a,b, osa-miR396a,b, osa-miR398b, and osa-miR399d. These miRNAs operated in stringently regulated genetic networks. The analysis also revealed that osa-miR167a and osa-miR399d are important part of synergistically interacting nodes to regulate growth of Pokkali plants in the presence of salt.