Profiling the expression domains of a rice-specific microRNA under stress

Abstract

Plant microRNAs (miRs) have emerged as important regulators of gene expression under normal as well as stressful environments. Rice is an important cereal crop whose productivity is compromised due to various abiotic stress factors such as salt, heat and drought. In the present study, we have investigated the role of rice-specific Osa-miR820, in indica rice cultivars showing contrasting response to salt stress. The dissection of expression patterns indicated that the miR is present in all the tissues but is enriched in the anther tissues. In salinity, the miR levels are up-regulated in the leaf tissues but down-regulated in the root tissues. To map the deregulation under salt stress comprehensive time kinetics of expression was performed in the leaf and root tissues. The reproductive stages were also analyzed under salt stress. It emerged that a common regulatory scheme for Osa-miR820 expression is present in the salt-susceptible Pusa Basmati 1 and salt-tolerant Pokkali varieties, although there is a variation in the levels of the miR and its target transcript, OsDRM2. The regulation of Osa-miR820 and its target were also studied under other abiotic stresses. This study thus captures the window for the miR-target correlation and the putative role of this regulation is discussed. This will help in gaining useful insights on the role of species specific miRs in plant development and abiotic stress response.

Protocol for Artificial MicroRNA Mediated Over-Expression of miR820 in Indica Rice

“…The expression levels of mature miR820 were analysed using stem-loop end point PCR as described earlier [27]. Presence of miR820 was confirmed by sequencing, proving the functionality of this construct in vivo system.…”

“…While there is absolute similarity between the mature Osa-mR820 sequences, their precursor sequences share more than 90% similarity. As reported earlier the digital expression status of Osa-miR820 family, in the leaf and panicle tissues of PB1, revealed that the 24-nt species accumulated to a higher level as compared to the 21-nt species [27]. Therefore, to decipher the functional role of the 21-nt Osa-miR820 species we adopted the amiR approach, to allow its over-expression in indica rice over and above the endogenous levels.…”

“…A careful analysis of the targets of Osa-miR820 using psRNA target finder identified a putative NAC domain protein 77 as a potential target [27]. This indicated a disturbance in the auxin pathway.…”

“…It was proposed to be encoded by CACTA transposon family, with its expression being controlled epigenetically at its own locus [24] [25]. Recently, it was shown to be down-regulated under drought [26], salt [27] and arsenic [28] stress. The pre-miR820 can be processed by either DCL1 or DCL3 to yield 21-nt and 24-nt long mature miRs, respectively [18].…”

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

“…The date palm was also characterized by the group to host a large population of conserved and novel miRNAs, functioning at the post-transcriptional level to regulate abiotic stress tolerance. Recently, Sharma et al (2015) showed a correlation between miR820 and its target de novo methyltransferase (DRM2) in the salt susceptible rice cultivar, Pusa Basmati (PB), and the salt tolerant counterpart, Pokkali (PK). Time kinetics of miR820 indicated its up-regulation in the leaves and down-regulation in the roots with increased exposure of PB and PK to salt stress.…”