Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi; Esmaeil Bakhshandeh; Markus Kuhlmann
Abstract
From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. ...
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From prokaryotes to higher eukaryotes, protein phosphatase 2Cs (PP2Cs) play a critical role in the stress response. For the purpose of identifying the AlPP2C gene and examining its expression, Aeluropus littoralis, a salt-secreting halophytic grass belonging to the Poaceae family, was genome-wildly analyzed. Based on the unique structure of the PP2C domain, 34 AlPP2C genes were discovered and classified into ten evolutionary branches based on homology with Arabidopsis thaliana. According to exon-intron structural analyses, they possessed a wide range of exon counts. AlPP2Cs shared similar motif organization in the same evolutionary branches based on motif distribution. The motifs ABRE, MBS, DRE, STRE, and LTR, which are related with stress, were discovered in the promoter region of the AlPP2C. AlPP2Cs displayed varied expression patterns in leaf and root tissues in response to salt stress and recovery conditions, according to transcriptome analyses. The AlPP2C4 gene is only expressed in the root tissues. These results expand our understanding of the PP2C gene family and provide valuable information for future research on PP2Cs molecular function and biological processes studies.
Biotic and Abiotic stress
Maryam Chalekaei; Ali Dehestani; Ali reza Abbasi; Seyyed Hamidreza Hashemi-petroudi
Abstract
In this study, the type and frequency of regulatory elements in the promoter regions of DVL gene family in Aeluropus littoralis were studied. Relative expression of AlDVL8 gene as a member of this family was also measured under the salinity stress, salicylic acid, gibberellic acid and cytokinin. The ...
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In this study, the type and frequency of regulatory elements in the promoter regions of DVL gene family in Aeluropus littoralis were studied. Relative expression of AlDVL8 gene as a member of this family was also measured under the salinity stress, salicylic acid, gibberellic acid and cytokinin. The results of the promoter study indicated that, this gene family has different regulatory elements for responding to stresses and hormones. Some of these regulatory elements are present in the promoter region of all genes, possibly indicating the general role of DVLs. Some others are present only in the promoter region of some genes that may be related to their specific activity. Treatments other than cytokinin increased gene expression in the shoot at 3, 12, and 24 hours and decreased expression at 6 hours. Cytokinin treatment at all times increased gene expression. In the root, almost the reverse trend of gene expression was observed, so that at 6 hours, increased gene expression was observed in all treatments, and at 12 and 24 hours, decreased expression was observed in all treatments. The results of this study showed that the expression of AlDVL8 gene in shoot and root organs was induced by experimental treatments and its expression was inverse in these two different tissues. Due to the changes in hormones during stress, expression induction of this gene family, and the presence of stress-responsive elements in the promoter regions of these genes, this gene family can be suggested as a candidate for stress tolerance.
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi
Abstract
Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family ...
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Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family in plant responses to salt stress, identification of these genes in the Aeluropus littoralis, halophyte plant, was considered in this study. In total, 36 non-redundant ERF genes were identified in A. littoralis genome. The phylogenetic tree classified the AlERF gene family into six distinct groups (B1 to B6) based on hemology with the Araboidopsis thaliana. Gene structure analysis revealed that AlERF genes contained zero to two introns. Domain search and conserved motif analyses in AlERF protein sequences determined that 2 motifs (1 and 2) out of the identified 10 motifs participate in the AP2/ERF domain structure. Based on transcriptome data and heatmap diagram, AlERF6.3 gene was expressed more in root tissue under salinity stress, and the least expression level was observed in AlERF6.7 gene in leaf tissue under recovery conditions. The different expression patterns of genes in leaf and root tissues under salt stress suggested different regulatory mechanisms in the gene expression. The results of this study, as the first report on the ERF gene family in A. littoralis, provides basic information for further studies of the functional characteristics of AlERF genes.
Biotic and Abiotic stress
Nazanin Amirbakhtiar; Zahra-Sadat Shobbar; Ahmad Ismaili; Farhad Nazarian Firouzabadi; Mohammad reza Ghaffari
Volume 8, Issue 21 , June 2018, , Pages 81-94
Abstract
Salt stress is considered as one of the most important constraints in wheat production worldwide, thus for, research toward development of tolerant varieties is of great importance. Discovering genes and molecular mechanisms involved in salt tolerance are the primary steps in molecular breeding for salinity. ...
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Salt stress is considered as one of the most important constraints in wheat production worldwide, thus for, research toward development of tolerant varieties is of great importance. Discovering genes and molecular mechanisms involved in salt tolerance are the primary steps in molecular breeding for salinity. In this study, taking advantage of the data deposited in NCBI Gene Bank, two salinity-related microarray data sets of bread wheat were analyzed to identify salt responsive genes. Bioinformatics’ analyses indicated that 3096 and 2060 genes were salt responsive genes in root and shoot, respectively. Gene ontology analysis of salt responsive genes showed that these genes were enriched for response to chemical stimulus, response to oxidative stress, transport, regulation of transcription and carbohydrate metabolic process in biological process category in both tissues. Furthermore, the differentially expressed genes in metabolic process category were enriched for catalytic activity, binding and oxidoreductase activity in both tissues. In order to determine the key genes involved in salt tolerance, hub analysis was performed on the salt responsive genes identified in the root. Based on the achieved results, the role of regulatory genes including protein kinases, protein phosphatases and transcription factors such as MYB and WRKY, was highlighted in inducing salt tolerance.
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.
Biotic and Abiotic stress
Amin Azadi; Mohsen Mardi; Eslam Majidi Harvan; Seyed Abolghasem Mohammadi; Foad Moradi
Volume 6, Issue 16 , March 2017, , Pages 61-73
Abstract
So far, many quantitative trait loci (QTLs) have been detected for yield and its components in wheat under normal conditions. In order to identify QTLs associated with concentrations of sodium and potassium in bread wheat under salt stress conditions, a population consisted of 186 recombinant inbred ...
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So far, many quantitative trait loci (QTLs) have been detected for yield and its components in wheat under normal conditions. In order to identify QTLs associated with concentrations of sodium and potassium in bread wheat under salt stress conditions, a population consisted of 186 recombinant inbred lines from a cross between Roshan ×SuperHead#2 were evaluated. Salinity treatments were performed using a hydroponic system in a greenhouse. Normal conditions (10 mM NaCl) and salinity (150 mM NaCl) were considered and stress was conducted in stages. The molecular genetic map of the population consisted of 23 simple sequence repeat (SSR) and 428 diversity arrays technology (DArT) markers. Three QTLs for each of sodium and potassium concentration traits and a QTL for potassium to sodium ratio were detected on chromosomes 4A, 2B, 3B, 7B and 2D using composite interval mapping approach. The QNa.abrii-3B, with a LOD score of 5.9, explained 8.3 % of the phenotypic variation for sodium concentration under salt stress conditions and gwm247 marker showed a strong linkage with this QTL. In addition, two novel QTLs for sodium concentration were detected on chromosomes 2B and 2D and QNa.abrii-2D explained 9.2 % of the phenotypic variation for this trait under salt stress conditions. Proceed with future researches, there is probability of identifying QNa.abrii-2B and QNa.abrii-2D as two homoeologous group in wheat, beside Nax1 gene.
Biotic and Abiotic stress
Samira Shakeri; Seyed kamal Kazemitabar; Seyed hamidreza Hashemi
Volume 4, Issue 8 , March 2015, , Pages 1-10
Abstract
Analysis of gene expression is considered as an essential part of functional genomics studies in all living organisms. Real-time PCR technique is very strong one to study the expression of a gene. However, despite its reliability, it has a set of specific problems, such as internal control gene selection ...
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Analysis of gene expression is considered as an essential part of functional genomics studies in all living organisms. Real-time PCR technique is very strong one to study the expression of a gene. However, despite its reliability, it has a set of specific problems, such as internal control gene selection which are suitable for normalization of the data. The study about selection reference of genes in sesame plant, at different developmental stages and under salinity stress of were studied. For this purpose, four internal control genes consists of eIF4- A, UBQ5, Alpha-Tubulin and Beta-Actin which are commonly used as housekeeping genes in plants, are selected and the stability of its expression in different salinity levels (zero and 75 mM) and different growth stages in five time periods (0 h, 6 h, 1 day, 4 days, 8 days and 16 days) in leaf tissue were examined. Study of the expression of reference genes using geNORM software showed that, in developmental stages and salinity in the leaf tissues, eIF4-A and Beta-Actin genes have more stable expression than other investigated genes. Using these genes can be useful in normalization of gene expression by Real-Time PCR analysis. The results can be used as reference genes for gene expression analysis in the Real-Time PCR.
Biotic and Abiotic stress
V Ghasemi omraan; A Bagheri; GH Nematzadeh; A Mirshamsi; Nadali Babaeian Jelodar
Volume 2, Issue 2 , September 2012, , Pages 27-37
Abstract
Salinity, predominantly NaCl, limits plant growth and impairs agricultural productivity. In higher plants, Na+ efflux and compartmentalization are achieved by Na+/H+ antiporters located in both the plasma and vacuolar membranes. Here we investigated the expression pattern of the genes AlNHX ...
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Salinity, predominantly NaCl, limits plant growth and impairs agricultural productivity. In higher plants, Na+ efflux and compartmentalization are achieved by Na+/H+ antiporters located in both the plasma and vacuolar membranes. Here we investigated the expression pattern of the genes AlNHX and AlSOS1 under 250 mM NaCl treatment after 6h and 1, 3, 8 and 17 days time intervals by Real Time-PCR technique. The transcript levels of AlNHX and al AlSOS1 were up-regulated by salt stress in all tissues. The AlSOS1 expression remarkably increased in leaves after 6 h and the AlNHX transcript abundance reached to the maximum level after 24 h. In node and internode tissues the transcript levels of AlNHX and AlSOS1 increased sharply 24 h after salt treatment and then gradually decreased within 3 and 8 days and finally after 17 days reached to a steady-state in which the mRNA content was similar to that of control plants. The transcript abundance of both genes in roots slightly increased Upon salt treatment and after 3 days reached to their maximum levels and this expression continued until 8 days and then decreased to a basal expression similar to control for AlNHX gene but in AlSOS1 decreased to reach a new steady-state in which the mRNA content was about 2-fold that of control plants.
