Research Paper
Bioinformatics
Abbas Saidi; Zohreh Hajibarat
Abstract
Calmodulin is a regulated protein of calcium and is a small intracellular protein that binds to calcium ions and mediates many of its intracellular actions. Calmodulin-binding transcription factors (CAMTAs) are recognized as one of the stress-responsive proteins. In this study, CAMTA genes were selected ...
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Calmodulin is a regulated protein of calcium and is a small intracellular protein that binds to calcium ions and mediates many of its intracellular actions. Calmodulin-binding transcription factors (CAMTAs) are recognized as one of the stress-responsive proteins. In this study, CAMTA genes were selected in maize. In this study, CAMTA family genes in maize were selected and chromosomal distribution, gene structure, domain patterns, and phylogenetic tree of CAMTA genes in maize were analyzed to further evaluate. To identify expression levels in different plant tissues, CAMTA gene expression analysis in response to heat stress and germination was studied. ZmCAMTA1 and ZmCAMTA2 genes were expressed in heat stress. Gene structure was similar in most proteins in each group, confirming the phylogenetic classification of CAMTA. Prediction of cis-elements in the promoter region of genes showed that bZIP and AP2 / ERF had the highest cis-elements in the promoter region of ZmCAMTA genes. In leaf tissue, ZmCAMTA1 gene was up-regulated expression in response to heat stress. ZmCAMTA2 gene was up-regulated in stem tissue in response to heat stress. The ZmCAMTA2 gene in response to increased expression germination showed that this study could be considered as a useful resource for future comparative studies of ZmCAMTA in different plant species and provide useful information for finding candidate genes in response to stress.
Research Paper
Molecular Plant Breeding
Somayeh Ebrahimi; Ahmad Ismaili; Seyed Sajad Sohrabi; Hasan Torabi Podeh
Abstract
Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock ...
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Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock transcription factors (HSFs) in the molecular mechanism of response to various abiotic stresses has been confirmed; therefore, this study used the analysis of RNA sequencing data to identify, classify and evaluate changes in HSF expression in lentil under water-deficit stress, and finally, the expression of some transcripts were examined using qRT-PCR. From the total assembled transcripts of lentil, 35 transcripts belonging to three HSF classes were identified. Also, according to the results, the expression of 14.28% of the identified transcripts, which often belonged to class A, is altered in lentil under water-deficit stress. The expression of 14.28% of the identified transcripts, most of which belonged to class A, is altered in lentil under water-deficit stress. In general, the results show that changes in the expression of some transcripts of one HSF gene take precedence over those of other transcripts of that gene in response to drought stress; therefore, it is of particular importance to study alternative splicing in response to this environmental factor in lentil. The HSF genes identified in this study can be used in future experiments to understand better the molecular mechanism of water-deficit stress tolerance in lentil.
Research Paper
Molecular Genetics and Genetic Engineering
Sepideh Charkhandaz; Karim Sorkheh
Abstract
The yield and acceptable quality of the oil of canola make this plant as one of the most important plants for providing edible oil. Due to the hot and dry climate in Iran and water necessary for seed germination, discovery of the solution to improve germination and seedling establishment is required. ...
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The yield and acceptable quality of the oil of canola make this plant as one of the most important plants for providing edible oil. Due to the hot and dry climate in Iran and water necessary for seed germination, discovery of the solution to improve germination and seedling establishment is required. Seed priming and treatment of seedlings with the extract of the seaweed Ascophyllum nodosum is one of the solutions for uniform germination and establishment of seedlings. The currently study have been explore the effect of application of Ascophyllum nodosum seaweed extract on seed germination and changes in the relative expression pattern of some important key genes related to gibberellic acid and brassinosteroids biosynthesis pathway using qRT-PCR. For this purpose, germination indexes were measured by the application of treatment 1% v/v treatment of Ascophyllum nodosum extract in four levels of treatment (0, 10, 15 and 30 days) until flowering stage. The leaf of sampling in each treatment was performed in three biological replications. The results of this study showed the effectiveness of seaweed extract treatment on increasing germination and seed vigor percentage, so that 100% germination of treated seeds obtained on the 3-day. The relative expression of algae extract showed an increase in the expression of EXP, ATI, ENTKO, AEC and BINSP genes, which are all important and as the key genes in the germination process compared to the control treatment. The use of seaweed extract treatment showed the highest expression in ATI (4.39) and ENTKO (5.70) genes in 30-day treatment, respectively. The lowest expressions for GIB and EXP genes in all three treatments (10, 15 and 30 days) were obtained. Also, there was the highest positive correlation between EEN and GIB (1), ENTKO and BINSP (0.98), AEC and BINSP (0.96) genes at the 5% significantly level. The correlation of these genes due to the use of algae extract ultimately led to a positive effect on the germination process of rapeseed seeds. Also, the results of heat map showed the genes of EXP and AEC (-0.57), GIB and ATI (-0.50) genes and XEN and ATI (-0.49) have a negative correlation at an error level of 5% and the increase of one led to the decrease of the other. This indicates that’s the activity of the final product of each of these genes is able to affect the germination process and promoting plant growth and development.
Research Paper
Molecular Plant Breeding
Mohammad Hassan Kaffash Moghaddam; Forough Sanjarian; Alaeddin Kordnaeeje; Mehrdad Chaichi; Amir Mohammad Naji
Abstract
Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, ...
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Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, it is promising to identify the native drought-tolerant germplasms and molecular mechanisms used to enhance drought stress resistance. The aim of this study was to investigate the expression level of eight selected genes related to drought tolerance NCED, ABF, HKT, PAL, bHLH, ABC transporter and lipoxygenase in two native germplasms of Iranian winter wheat, one is sensitive and the other is drought tolerant. For this purpose, drought treatment was applied on native germplasms in a completely randomized design with three replications and two levels of treatment in the greenhouse. Selected gene fragments were amplified, gene expression was measured by Reverse Northern Blot and quantified using total lip software. Analysis of variance of the mean relative expression of each gene compared to the internal control gene showed that drought stress had a significant effect on the expression of all genes except bHLH gene. Biplot based on the first and second components made it possible to isolate genotypes in dehydration stress based on the expression of the seven genes evaluated. This method can be used in screening and identifying tolerant genotypes in landrace population of wheat.
Research Paper
Bioinformatics
Maryam Ramezani; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Seyed Sajad Sohrabi
Abstract
Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds ...
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Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds biosynthesis pathways. MicroRNAs (miRNAs) play an important role in different processes such as growth and development, cell proliferation, response to stresses and biosynthesis metabolite. As far as the bioinformatic data are concern, the genome/transcriptome of kelus has not been sequenced. The present study was performed to identify the conserved miRNAs and their target genes in the kelus leaf transcriptome. After pair-end sequencing with the Illumina HiSeq 2500 platform, clean reads were assembled. In total, 4658 unigenes were found to contain potential miRNAs sequences. Following strict filtering criteria, five miRNAs belonging to five conserved miRNA families (miR156-3P, miR408, miR169, miR171 and miR398) were identified among candidate sequences. Results of this study revealed that the target genes of the identified miRNAs were involved in various metabolic pathways, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, peroxisome degradation, and fatty acid degradation. By affecting genes associated with six metabolic pathways, miR408 was identified as the most influential conserved microRNA in the kelus leaf transcriptome. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of kelus, these miRNAs can be used as candidate genes for breeding kelus quantitative and qualitative traits.
Research Paper
Bioinformatics
Solmaz Azizi; Nasser Zare
Abstract
Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in the apoptotic (programmed cell death) pathway and biotic and abiotic stress responses in plants. In the present study, we identified 95 LOX homologous genes from four Fabaceae species (Cicer arietinum, Glycine max, Phaseolus vulgaris, ...
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Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in the apoptotic (programmed cell death) pathway and biotic and abiotic stress responses in plants. In the present study, we identified 95 LOX homologous genes from four Fabaceae species (Cicer arietinum, Glycine max, Phaseolus vulgaris, Medicago truncatula), which could be divided into 9-LOX, 13-LOX type I, and type II subgroups according to their phylogenetic relationships with Arabidopsis, rice, barley, and foxtail millet. LOX genes are distributed unevenly across the chromosomes, and their coding enzyme is active in the cytoplasm and chloroplast. These genes are intron rich, have six to nine introns, and are conserved in gene structure and intron phase. All identified genes have the conserved lipoxygenase and PLAT/LH2 domains. Several cis-acting elements related to hormones and stresses, such as ERE, MYB, and MYC in the LOXs promoters, indicated the role of these genes in plant development and responses to environmental stresses. In addition, different miRNA molecules were identified that regulate the post-transcriptional expression of LOXs genes through cleavage or inhibition of translation. Transcriptome data-based gene expression analysis showed that Glycine max LOXs expression pattern differed under abiotic stress conditions, and GmLOX4, GmLOX21, GmLOX25, GmLOX5, GmLOX22, GmLOX24, GmLOX14, GmLOX16, GmLOX7, and GmLOX26 were highly expressed in response to salt, drought, cold and heat stresses, indicating that they can improve the tolerance of Glycine max to abiotic stress. This study provides valuable information for a better understanding of the function of LOX genes and further exploration of the LOX gene family in Fabaceae.
