Expression Analysis of Novel microRNAs in Rice During High Temperature Stress

MicroRNAs (miRNAs) are small non-coding RNAs which play an important role in regulating the genes involved in plant growth and development. Several studies showed that miRNAs are involved in plants response to different kinds of abiotic stresses also. In our previous study, temperature responsive miRNAs were predicted in O.sativa. 27 miRNAs were predicted to be novel in rice using homology search. In continuation to our previous study, expression of 14 novel miRNAs was done in shoot and root of 13 days old seedlings of five different rice cultivars using real time PCR. Expression these miRNAs was analyzed in control and high temperature stress environment. Out of 14 predicted novel miRNAs, two novel miRNAs- miR157a and miR165a showed expression in all five rice cultivars. Interestingly, miR165a showed a differential expression pattern among heat tolerant (N22, IR64 and Rasi) and susceptible (Vandana and Sampada) cultivars suggesting that it might have specific role in high temperature tolerance

PMRD: plant microRNA database

MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops

Overview of the potential of microRNAs and their target gene detection for cassava (Manihot esculenta) improvement

Production and utilization of cassava (Manihot esculenta) is significantly constrained by pests, diseases, poor yields and low nutritional content. Various approaches are currently being applied to mitigate these constraints. However, an aspect of plant developmental genetics little known in cassava is the role that microRNAs (miRNAs) play in gene regulation. miRNAs are 20 - 24 nucleotide long nonprotein-coding RNAs that play important roles in post-transcriptional gene silencing in many organisms. Thorough understanding of the mechanisms involved in miRNAs mediated posttranscriptional gene regulation will have implications for crop production improvement. The potential of miRNAs for cassava improvement and also some data obtained on cassava miRNAs using comparative genomics analysis have been briefly discussed. 17 miRNA families and target genes in cassava that are also conserved in other plant species have been revealed. However, the ESTs representing seven of these miRNA families produced foldbacks that show more than 3 nucleotides not involved in canonical base pairing within a loop or bulge in the mature miRNA: RNA* dimer, thus were not considered miRNA secondary structures. Consistent with previous reports, majority of the target genes identified are transcription factors. Other targets appear to play roles in diverse physiological processes. Furthermore, a detailed description and insight into some of the current bioinformatic resources and approaches applicable to cassava have been discussed. Such information will further enhance the rapid discovery and analysis of more novel miRNAs in cassava towards its improvement.Keywords: Cassava, microRNAs, target genes, improvement, characterizatio

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C-3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5'-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.Peer reviewe

Perspectives on microRNAs and phased small interfering RNAs in Maize (Zea mays L.): Functions and big impact on agronomic traits enhancement

Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed