Bioinformatics
Mohammad Mohsenzadeh Golfazani; Alireza Tarang; Ramin Seighalani
Abstract
There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance ...
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There is much information about the regulation of gene expression in response to various stresses at the transcriptional level. Nevertheless, there is limited information about this process at the post-transcriptional level. The diversity and complexity of miRNA regulation indicates their importance in biological processes. Many miRNA regulatory modules can form a complex miRNA-mRNA regulatory network. Therefore, research on miRNA-mRNA regulatory networks can provide valuable information for understanding complex biological processes. These data are very important to further study the stress tolerance mechanisms in plants, especially in rapeseed. In this research, the selection of miRNAs related to drought and salinity stress was made by reviewing the articles on abiotic stresses. Then the target genes were identified using the sequences of mature miRNAs and psRNATarget online software. A gene list of 225 identified target genes was prepared using the UniProt database. Their functional pathway was identified utilizing the DAVID bioinformatics database and KEGG database according to default parameters. Investigations showed that these target genes were involved in several biological pathways including ribosome, spliceosome, proteasome, purine metabolism, selenocompound metabolism, and sulfur metabolism. In addition, the STRING database was used to check co-expression genes. Our result indicated the existence of 37 co-expression genes among the identified target genes.
Molecular Plant Breeding
Sajjad Zare; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Hassan Pakniyat
Abstract
Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought ...
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Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought stress in barley leaf and root ESTs were analyzed in Nimruz and spantaneum barley genotypes. Bioinformatics databases were mined for relevant EST libraries and bioinformatics services were used for pre-processing and identify genes with different expressions among libraries. The expression profile of candidate genes was studied, by using Real time-PCR in a factorial-split plot design, including Nimruz as tolerant and Spontaneum as a drought sensitive in pots with three replications. Sampling time was also considered at 0, 24 and 72 hours after drought stress as sub factor. Results of this study led to identification of three highly-expressed miRNAs (ath-miR414, os-miR2102-5p and osa-miR414). The expression analysis showed that miR414 and miR2102 expression was significantly (P< 0.05) increased in both genotypes in response to drought stress. After 72h in Nimruz and Spontaneum, the expression of miR414 reached 2.61 and 2-fold and the expression of miR2102 was 2.4 and 2.8-fold of that of control (Spontaneum at control condition at 0 times), respectively.
Bioinformatics
Reza Mir Drikvand; Seyyed sajad Sohrabi; Seyyed Mohsen ُSohrabi; Kamran Samiei
Abstract
MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation ...
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MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation and response to stresses in plants. Coriander or Coriandrum sativum L. is a plant of Apiaceae family with different nutritional and pharmaceutical applications. Up to now, the genome of this plant has not been sequenced and there is no report of miRNAs identification has been recorded for it. The present study was performed to identify the conserved miRNAs and their target genes in transcriptome of coriander plant. Firstly, Transcriptome of seed and leaf tissues was assembled and non-coding transcripts were identified and considered as miRNA precursor. Finally, among candidate sequences, three miRNAs named csa-miR162, csa-miR169 and csa-miR399 belong to three conserved families were identified after strict filtering. Identified miRNAs showed differential expression between seed and leaf tissues and also role of their target genes in different biological processes was confirmed. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of coriander plant in the present study, these miRNAs can be used as candidate genes to improve qualitative and quantitative yield and resistance to different stresses in this plant.
Molecular Plant Breeding
Mahdieh Safarzadeh; Reza Fotovat; Mohammadreza Azimi; Ehsan Mohsenifard; Behnam Bakhshi
Volume 4, Issue 6 , October 2014, , Pages 21-33
Abstract
Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this ...
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Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this study, the expression patterns of miR159a,b, miR160, miR167a,b and miR171a have been studied in both drought susceptible and drought tolerant varieties in wheat using qRT-PCR. miR159a,b, miR160, miR167a,b and miR171a could play important roles in MYB, ARF, ARF, and SCL, transcription factors regulation, respectively. High conservation among the studied miRNA families was observed in the mature miRNA producer regions by multiplex alignment of pre-miRNAs. Results of qRT-PCR analysis indicated that expressions of miR160 and miR167a,b in tolerant Variety and miR159a,b in susceptible Variety are increased significantly. However, no significant changes in expression were observed for miR171a in both tolerant and sensitive varieties. Presumably, up-regulation miR159a,b in susceptible variety could be resulted to reduction in the expression of MYB genes involved in drought response. On the other hand, up-regulation of miR160 and miR167a,b in tolerant variety, may lead to regulation of auxin and abscisic acid pathways interaction and probably these miRNAs could contribute in stress tolerance in tolerant variety. In addition, no significant change in miR171a expression demonstrated that expression of SCL could be regulated through other mechanisms in plant.
Molecular Plant Breeding
Ehsan Mohseni fard; Mohammad Farsi; Ghasem Hosseini Salekdeh; Amin Mirshamsi Kakhki; Marayam Shahbazi
Volume 3, Issue 5 , February 2013, , Pages 105-115
Abstract
MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several ...
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MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several processes including tissue development, response to biotic and abiotic stress and induction of several other transcription factors and membrane proteins. In this study we selected miRNAs that regulate SPL transcription factors expression in rice. Later, the differential expression of these miRNAs are evaluated using qRT-PCR and Stem-loop primers. Results of shoot differential expression under drought stress showed that miR529 was down-regulated but conversely, miR535 was up-regulated. However, significant differential expression of miR156 was not observed in our study. Likewise, root differential expression under drought condition showed up-regulation of miR535, but miR529 and miR156 did not show any significant differential expression. Although all of these miRNAs are involved in regulating the expression of the same genes, but their diverse differential expressions highlight the complexity of gene-regulatory networks in various environmental conditions. Based on results of this study, it can be suggested that compared to miR535, miR156 and miR529 play more important roles in regulating the development and flowering process via controlling SPL transcription factors whereas, miR535, miR529 and relatively lesser miR156 are responsible for SPL transcription factor regulation under stress.
