Molecular Genetics and Genetic Engineering
Parisa Daryani; Fatemeh Farzaneh Piralger; Nasser Zare; Zahra-Sadat Shobbar; Rasool Asghari Zakaria
Abstract
WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used ...
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WRKY gene family encodes a large group of transcription factors regulating biotic and abiotic stress-responsive genes. In order to identify the WRKY gene family members in rice (Oryza sativa ssp. japonica), multiple searches were done in the related databases. Rice WRKY-conserved sequences were used as the templates for tBLASTN searches in datasets for finding new members. An HMM profile of WRKY domain was also used to find WRKY gene family. Multiple sequence alignment was done using clustalW software, and phylogenetic trees were drawn using MEGA10 software based on a neighbour-joining method with a 1000 repeats bootstrap index. According to the results, 165 members of the WRKY gene family were found in rice, of which 63 were new members. Sequences were divided into three main groups based on the number of WRKY domains and the structure of zinc-finger motifs. Conclusively, there were 21 proteins with two WRKY conserved domains in group I, 53 proteins with one WRKY conserved domain and Cx7Cx23HxC zinc-finger motif in group III and 82 proteins with one WRKY conserved domain and Cx4-5Cx22-23HxH zinc-finger motif in group II. The chromosomal location of OsWRKYs was detected on the rice genome. The different groups were distributed on various chromosomes. The greatest number of OsWRKY genes (32 members) were located on chromosome 1. Following complementary research and identification of promising candidate genes involved in tolerance to each stress, they can be used to increase tolerance to the desired stresses and provide food security using genetic engineering or molecular breeding approaches.
Biotic and Abiotic stress
Mohammad Mohsenzadeh Golfazani; Maryam Pasandideh arjmand; Mojtaba Kordrostami; Habibollah Samizadeh Lahiji; Hassan Hassani kumleh; Mohammad Hossein Rezadoost
Abstract
Increasing of reactive oxygen species (ROS) under iron toxicity is considered as one of the major constraints to rice production. In this study the alterations of SOD, GPX1 and MDHR expression level in two genotypes of rice, Pokkali (as tolerant) and IR64 (as sensitive) were monitored under different ...
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Increasing of reactive oxygen species (ROS) under iron toxicity is considered as one of the major constraints to rice production. In this study the alterations of SOD, GPX1 and MDHR expression level in two genotypes of rice, Pokkali (as tolerant) and IR64 (as sensitive) were monitored under different concentrations of iron levels [(0) (nonstress)], 100, 250, 400 and 500 mg/lit-1Fe-EDTA). The treatments were done when the plants were at 4-leaf stage and lasted for two weeks. Results showed that the expression levels of genes in Pokkali were higher than IR64. The expression level of SOD in IR64, increased at iron concentration increased, while it decreased at higher Fe-level. The expression level of GPX1 was increased in IR64, but decreased in Pokkali. The expression level of MDHR in IR64 was decreased at early stage of Fe-treatment, but then increased. Inversely, in Pokkali MDHR expression reduced constantly under Fe stress. Overall, the relative over expression of genes in Pokkali and presence of different expression levels of them between different concentrations of Fe in tolerant and sensitive genotypes indicate that the gene could remarkably effect on the tolerant level of pokkali by reducing ROS production under Fe-toxicity.
Bioinformatics
Shahrbano Mirdar Mansuri; Nadali Babaeian Jelodar; Zahra-Ssadat Shobbar; Ghorbanali Nematzadeh; Mohammad reza Ghaffari
Volume 7, Issue 19 , November 2017, , Pages 65-76
Abstract
Rice is a glycophyte plant and salinity stress is one of the most important obstacles for the rice production. Understanding complex molecular mechanisms of plant response to salt stress is necessary for developing salt tolerant rice. In this study, microarray data analysis was used for identification ...
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Rice is a glycophyte plant and salinity stress is one of the most important obstacles for the rice production. Understanding complex molecular mechanisms of plant response to salt stress is necessary for developing salt tolerant rice. In this study, microarray data analysis was used for identification of salt stress responsive genes. By analysis of 9 microarray data sets, 13798 differentially expressed genes were found. Gene ontology analysis of up-regulated genes in the salt tolerant genotypes showed that transcription factors enriched against rice genetic background. Based on the hub analysis results, most of the key genes were protein kinases, for example CPK10 and PFK. Amongst the transcription factors, GCN5 identified as the key gene in the hub analysis in this study. Totally, 10 hub genes were identified which belong to regulatory factors, transporters and signal transduction effectors. We hope that the obtained results would be beneficial toward developing the salt tolerant rice.
Bioinformatics
Ehsan Pourabed; Zahra-Sadat Shobbar
Volume 7, Issue 18 , November 2017, , Pages 73-92
Abstract
Rice is one of the most valuable crops, and water deficiency is the most important constraint to rice production. Due to the complexity and multigenic characteristics of the drought tolerance trait, the objective of the current research were reconstruction of the involved gene networks and identification ...
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Rice is one of the most valuable crops, and water deficiency is the most important constraint to rice production. Due to the complexity and multigenic characteristics of the drought tolerance trait, the objective of the current research were reconstruction of the involved gene networks and identification of the key genes in rice plants using microarray data analysis. To achieve the goal, all the differentially expressed genes (DEGs) with fold changes ≥+2.5 and ≤-2.5 at drought stress compared to normal conditions were identified among all the microarray data-series in rice using Genevestigator online tools. Totally, 101 DEGs were identified and their gene regulatory as well as protein-protein interactions (PPIs) networks was reconstructed. The hub genes (genes with the most interactions) were distinguished using nine Cyto-hubba computational algorithms on Cytoscape software. Based on the hub analysis results, 14 unique (non-redundant) genes were identified as the most effective genes in response to drought stress and their co-expression networks were constructed. According to the gene ontology analysis of the DEGs, their co-expressed genes and the hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) roles in drought tolerance mechanism. Amongst the TFs, ABA-responsive binding factors (AREBs), AP2, bZIP, WRKY and MYB gene families were observed. We hope that the obtained results would be beneficial toward finding the smart strategies for drought tolerance improvement.
Bioinformatics
ِSedigheh Akhtartavan; Majid Talebi
Volume 6, Issue 15 , December 2016, , Pages 53-67
Abstract
Drought is one of the major environmental stresses that greatly affects growth and development of plants. The plants reaction against this stress is associated with showing massive changes in complex gene networks. In the present study, the changes of gene expression patterns in two sensitive and tolerant ...
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Drought is one of the major environmental stresses that greatly affects growth and development of plants. The plants reaction against this stress is associated with showing massive changes in complex gene networks. In the present study, the changes of gene expression patterns in two sensitive and tolerant genotypes of rice (as C3 plant) and maize (as C4 plant) were investigated using maize genome arrays containing 17,734 probe sets and the rice genome containing 57/381 probe set. The microarray data were taken from the GEO/NCBI database on both stress and control conditions to identify the genes involved in responses to the stress. The results indicated that 1861 (10.49%) and 1753 (8.9%) genes in the sensitive and tolerant maize, respectively, and 9252 (16%) and 7971 (13.8%) genes in the sensitive and tolerant rice, respectively, changed significantly after drought stress at the level of one percent. From of these genes, 1012 and 175 genes in the sensitive and tolerant genotype leaf of rice and maize, were significantly up-regulated, respectively. The Venn diagram showed that 663 genes of rice and 158 genes of maize, have significantly down-regulated. Rice plant, as a C3 plant, showed five times wider reaction to drought stress in compared with maize plant, as a C4 plant. The functional grouping of the up-regulated genes in two species revealed that functional group of ribosomal proteins and phosphatases in maize plant have the most abundant categories, whereas the functional groups of metal-binding, stress response, response to biological stimuli and signals in rice plant contained the highest percentage of the genes.
Biotic and Abiotic stress
Behnam Bakhshi; Mohmmad Reza Bihamta; Ghasem Hosseini Salekdeh; Masoud Tohidfar
Volume 3, Issue 5 , February 2013, , Pages 93-102
Abstract
Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating ...
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Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating plant gene expression in biotic and abiotic stress. In this study, we selected five miRNAs for promoter analysis and evaluation of differential expression of them under drought stress in roots. Three of them including miR162, miR169 and miR172 are conserved in many plants and the others including miR1425 and miR1880 are rice specific miRNAs. In addition, upstream screening of MIRNA genes showed that upstream region of some MIRNA genes like MIR172 are enriched with important regulatory elements like DRE and ABRE. Quantitative Realtime-PCR was used in this study for analyzing differential expression of evaluated miRNAs. Studying the differential expression of miRNAs in roots under drought condition showed that miR169 was up-regulated but conversely, miR172 was down-regulated. The rest of miRNAs in our study did not show significant differential expression under drought stress. It can be concluded that NF-YA and AP2 as the most important target genes for miR169 and miR172 respectively can play critical roles in response to drought stress. .
Proteomics
Ghasem Hosseini Salkade; Davood Nasr Abadi
Volume 1, Issue 1 , March 2012, , Pages 1-11
Abstract
Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. ...
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Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. To further understand the mechanism of plant response to salinity we employed a proteomic approach to profile the protein changes of rice 3th leaf and root under salt stress. Plants were grown in Yoshida nutrient solution and salt stress imposed after 25 days. Plants were treated by 100¬mM NaCl for 10. After that 3th leaves and total root were collected from control and salt stressed plants. The Na+ and K+ content of leaves/roots and several yield components changed significantly in response to short-term salt stress and their proteome patterns were analyzed using 2-DE in triplicates. The expression pattern of proteins significantly changed in all leaves/roots in response to stress. More than 488 and 345 protein were detected repeatedly in root and leaf 2Dgels respectively by software package. 107 proteins in root and 86 proteins in leaf of two genotypes showed significant response to stress. 3 protein in leaf gels and 2 protein in root gels were selected and identified by ESI-Q-TOF. The most important were Ferritin, Rubisco activase and ascorbat¬peroxidase in leaf and Peroxidase and Ascorbat¬peroxidase in root. All of them were enzyme and involved in detoxification and removal of reactive oxygen species (peroxidase, ascorbat¬peroxidase) Iron homeostasis (ferritin) or activation of other enzymes (rubisco¬activase).
