Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress

Abstract

MicroRNAs (miRNAs) are important molecules that regulate gene expression under salinity stress. Despite their evolutionary conservation, these regulatory elements have been shown to behave differently in different plant species under a particular environmental stress. In this study, we investigated the behavior of salt responsive osa-miR393a and its target gene (TIR1, LOC_Os05g05800) in salt-tolerant (FL478) and salt-sensitive (IR29) rice genotypes. It was found that the mature and precursor sequences of osa-miR393a as well as its cleavage site in TIR1 were conserved among salt tolerant and sensitive genotypes. Promoters of different salt-responsive miRNAs were also found to be less variable between salt-tolerant and salt-susceptible genotypes. Analysis of gene expression, promoter methylation, and cis-element abundance showed that osa-miR393a behaves differently in FL478 and IR29. Salt stress altered the expression pattern of osa-miR393a-TIR1 module in a time-dependent manner in the roots and shoots of two genotypes. Promoter methylation of this regulatory module was also altered at different time points under salt stress. Expression analysis in two genotypes indicated the overall down-regulation of osa-miR393a and up-regulation of TIR1 in FL478 and their reciprocal regulation in IR29. The expression results were complemented by the differential promoter methylation and cis-element abundance of this regulatory module. Together, the results of transcript abundance and promoter methylation of osa-miR393a-TIR1 module signified the association between these two processes which is reported for the first time in plants to the best of our knowledge.

Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)

“…The similarly regulated miRNAs profiles and degrees may represent the fundamental mechanism of adapting to salt shock, and the difference might explain the distinct salt sensitivities [18]. Ganie et al [55] reported significantly different expression patterns of osa-miR393a and its targets between two different rice genotypes. The expression of osa-mi393a in salinity-sensitive genotype tremendously increased from 0 to 24 h under salinity stress, while the target steeply decreased relative to the tolerant genotype.…”

“…The osa-miR393a has been reported to negatively regulate the salinity stress tolerance in rice by repressing the auxin signaling pathway and other mechanisms [49]. Usually, stress induces miRNAs to downregulate their target mRNA [45], and the reciprocal relationship between the expression of osa-miR393a and TIR1 exists at different time points during salt stress [17,55]. In our result, the target of miR393a was a TIR1-like protein which played an important role in abiotic stress response.…”

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

“…The FL478, a salinity tolerant rice cultivar [ 3 ], was used for the gene expression study through qRT-PCR. Seeds were surface sterilized with sodium hypochlorite (3%) and were germinated on the germination papers.…”

“…RNA isolation, cDNA synthesis and qRT-PCR analysis were performed according to the protocol described by Ganie et al [ 3 ]. For qRT-PCR study, 3 biological replicates per sample were used with 3 technical replicates for each biological replicate.…”

“…High salinity stress causes severe impact on millions of hectares of agricultural land worldwide [ 1 , 2 ]. Accumulation of salts in the irrigated soil is one of the prime factors that lowers water availability to root cells of rice plants due to their reduced osmotic potential, hence diminish growth, development and yield of rice [ 3 , 4 ]. Like other plants, the maintenance of osmotic and ionic homeostasis under salinity stress is a key challenge in rice too, which ultimately defines the salinity tolerance level of a particular rice genotype [ 5 ].…”