Identification and Expression Analysis of microRNAs at the Grain Filling Stage in Rice(Oryza sativa L.)via Deep Sequencing

Abstract

MicroRNAs (miRNAs) have been shown to play crucial roles in the regulation of plant development. In this study, high-throughput RNA-sequencing technology was used to identify novel miRNAs, and to reveal miRNAs expression patterns at different developmental stages during rice (Oryza sativa L.) grain filling. A total of 434 known miRNAs (380, 402, 390 and 392 at 5, 7, 12 and 17 days after fertilization, respectively.) were obtained from rice grain. The expression profiles of these identified miRNAs were analyzed and the results showed that 161 known miRNAs were differentially expressed during grain development, a high proportion of which were up-regulated from 5 to 7 days after fertilization. In addition, sixty novel miRNAs were identified, and five of these were further validated experimentally. Additional analysis showed that the predicted targets of the differentially expressed miRNAs may participate in signal transduction, carbohydrate and nitrogen metabolism, the response to stimuli and epigenetic regulation. In this study, differences were revealed in the composition and expression profiles of miRNAs among individual developmental stages during the rice grain filling process, and miRNA editing events were also observed, analyzed and validated during this process. The results provide novel insight into the dynamic profiles of miRNAs in developing rice grain and contribute to the understanding of the regulatory roles of miRNAs in grain filling.

Profiling microRNA expression during multi-staged date palm ( Phoenix dactylifera L.) fruit development

“…For instance, the expression of pda-nov-miR044, pda-novmiR166, pda-nov-miR168, pda-nov-miR178, pda-nov-miR197, pdanov-miR213, and pda-nov-miR228 is positively correlated with their targets (Supplementary Fig. S2B; Supplementary Table S1), which may be due to a similar feedback regulation between co-expressed miRNAs and their targets as previously reported in Arabidopsis and rice [9,35]. However, the concrete molecular mechanisms of these examples remain to be demonstrated experimentally in details.…”

“…Although a miRNA and its target mRNAs are expected to show negative correlation, many studies have reported that this may not always be the case [9,35]. In our data, we observed examples of such cases.…”

High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

“…Generally, small RNAs in the 21 nt class represent miRNAs. The same phenomenon was also observed in peanut [14], soybean [15], maize [16], rice [17,18], and Medicago truncatula [19].…”

The pivotal role of small non-coding RNAs in the regulation of seed development

“…Interestingly, different studies in rice have reported that most of the deeply conserved miRNAs are found down-regulated along the grain filling process, whereas less conserved miRNAs are up-regulated (Lan et al 2012;Yi et al 2013). Therefore, novel miRNAs were proposed to target starch synthesis genes by translational inhibition and thus contribute to rice grain filling (Lan et al 2012).…”

“…Therefore, novel miRNAs were proposed to target starch synthesis genes by translational inhibition and thus contribute to rice grain filling (Lan et al 2012). Work with two different rice cultivars has already contributed with some miRNA (and respective target) candidates involved in carbohydrates metabolism: miRn45-5p [putative sucrose-phosphate synthase (SPS)]; miR1861 [Os01g63810,a starch-binding domain (SBD) containing protein involved in starch degradation, and Os10g32810, a b-amylase]; miR1436 [starch synthase (SS)]; miR1862d (SS); miR1428e-3p [sucrose non fermenting-1-related kinase 1 (SnRK1b)]; Osa-53 (Os02g58480, a sucrose synthase); Osa-56 (Os03g42650, a vegetative storage protein) (Peng et al 2013;Yi et al 2013).…”