Research Paper
Bioinformatics
Sepideh Sanjari; Reza Shirzadian-Khorramabad; Zahra-Sadat Shobbar; Maryam Shahbazi
Volume 8, Issue 21 , June 2018, Pages 1-15
Abstract
Sorghum, in spite of its great tolerance to drought stress, suffers from grain yield loss due to pre and post flowering -drought stress conditions. NAC TFs play key roles in Sorghum drought adaptation. In this study, NAC protein family data was collected from databases. Then, hidden Markov model profiles ...
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Sorghum, in spite of its great tolerance to drought stress, suffers from grain yield loss due to pre and post flowering -drought stress conditions. NAC TFs play key roles in Sorghum drought adaptation. In this study, NAC protein family data was collected from databases. Then, hidden Markov model profiles of NAM domain (PF02365) was obtained from Pfam database and used to find the putative NAC members against Sorghum proteins. Totally, 183 protein sequences encoded by 131 gene loci were identified. The unrooted phylogenetic tree was constructed based on NAC domains of Sorghum and 11 known NAC domains of other plants using the Neighbor-Joining method, which classified the family into 15 subfamilies. 13 members of the NAC protein family of Sorghum joined to the SNAC subfamily of other plants, which are expected to be involved in abiotic stress tolerance. 14 different stress and hormone responsive regulatory elements were predicted in promoters of SNAC subgroupgenes. To study the expression pattern of these genes, two extreme Sorghum cultivars including Kimia and Sepideh were planted based on Split-plot Randomized Complete Block Design with three replications in the field. Irrigation was performed in two levels including normal irrigation and drought stress (water holding from anthesis). Based on the SbSNAC expression pattern, we predict that some members are involved in response to drought stress at post-flowering stage as positive (3 members) and negative transcriptional regulators (3 members). As well, some of them play role in leaf senescence (2 members) and metal remobilization processes (2 members).
Research Paper
Bioinformatics
Sara Dezhsetan; Mahdi Behnamian; Sahar Fathi Ajirlou; Mohammad Ali Ebrahimi; Beniamin Yazdani
Volume 8, Issue 21 , June 2018, Pages 17-35
Abstract
NAC gene family is one large family of plant-specific transcription factor that plays various roles in plant developmental stages and stress responses. The possibility of bioinformatics studies on NAC gene family in barley was provided with completion of the genome sequencing of Hordeum vulgare cv. Morex ...
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NAC gene family is one large family of plant-specific transcription factor that plays various roles in plant developmental stages and stress responses. The possibility of bioinformatics studies on NAC gene family in barley was provided with completion of the genome sequencing of Hordeum vulgare cv. Morex project. In this research using genome scanning, 73 non-redundant NAC-encoding genes in total were identified from the genomic sequences of Hordeum vulgare cv. Morex. A composite phylogenetic tree was constructed with HvNAC protein sequences and a number of known rice and Arabidopsis NAC protein sequences and tree was classified into 15 distinct subgroups. It is revealed the uneven distribution of the HvNAC genes on barley chromosomes. Most members of NAC genes were not located in groups (singletons) and few members of this family were located in groups with two or three genes. Most detected cis elements in upstream and downstream of HvNAC genes were involved in response to light, response to abiotic stresses and relatively low in response to biotic stresses. In silico gene expression analysis revealed that HvNAC genes were expressed in a wide range of tissues and is not highly expressed in developmental stages. Also, the HvNAC genes partly is expressed in stress conditions, especially in abiotic stresses and relatively less expressed in biotic stresses. This bioinformatics information provide a framework for genomics and functional studies of this gene family in barley.
Research Paper
Bioinformatics
Seyyedeh Maryam Yousef Mousavi; Bahram Maleki Zanjani; Abbas Bahari
Volume 8, Issue 21 , June 2018, Pages 37-45
Abstract
Flour and dough properties are influenced by gluten protein and starch content during bread baking process. Gluten, the most important protein of Wheat endosperm, is composed of glutenin and gliadin. Identification of the cultivars genetic structure is one of the plant breeding requirements. So HMW-GS ...
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Flour and dough properties are influenced by gluten protein and starch content during bread baking process. Gluten, the most important protein of Wheat endosperm, is composed of glutenin and gliadin. Identification of the cultivars genetic structure is one of the plant breeding requirements. So HMW-GS gene was sequenced for two varieties namely Khazar 1, Golestan and F1 progenies. Amino acid sequence of parental varieties and F1 progenies started with EGEAS sequence (these five amino acid well known as start amino acid sequences for HMW-GS). Results show that the number of amino acids in N-terminal and C-terminal of HMW-GS were equal in parents and F1 progenies (with 104 and 42 amino acids respectively). Results also showed that the cysteine amino acid numbers in C-terminal for all three cases were the same, whereas the number of cysteines was different in N-terminal of HMW-GS. Phylogenetic tree was constructed based on amino acid sequence data of HMW-GS between parents and F1 progenies as well as the number of HMW-GS amino acid sequences in NCBI database. Considering differences observed for Amino acid sequence of parental varieties and F1, it can be concluded that the more variation in later generations could potentially be used in bread wheat breeding programs to improve bread- baking quality.
Research Paper
Medicinal plant Biotechnology
Mansoore Kermani; Bahare Karimi; Elham Azizi; Ali Masoumi
Volume 8, Issue 21 , June 2018, Pages 47-57
Abstract
Stevia rebaudiana bertoni is a natural sweetener that is sweeter than sugar; however it does not have any calorie and can be used for diabetic patients. The sweet taste of stevia is because of the steviol glycosides (SGs) accumulated in the leaves. Rebaudioside A-F and Stevioside are the main compounds ...
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Stevia rebaudiana bertoni is a natural sweetener that is sweeter than sugar; however it does not have any calorie and can be used for diabetic patients. The sweet taste of stevia is because of the steviol glycosides (SGs) accumulated in the leaves. Rebaudioside A-F and Stevioside are the main compounds of stevia. KO and UGT85C2 genes are two important genes involved in biosynthesis pathway of steviol and steviolmonoside that are precursors of other SGs. Due to the very low germination rate of stevia seeds, tissue culture is the fastest way for propagation of it. Therefore, optimizing the composition of the culture medium is necessary to increase of pharmaceutical ingredients in stevia. This experiment was conducted to study the effect of different concentrations of KH2PO4 (0, 4.25, 8.5, 17, 34 µM) on the expression of KO and UGT85C2 genes using semi- quantitative RT-PCR technique as well as soluble sugar content and antioxidant activity of stevia. Analysis of variance showed a significant difference between the treatments (p≤0.01) for all measured parameters. Mean comparison using LSD (p≤0.05) showed that UGT85C2 and KO genes possessed the highest expression level in 4.25 and 17 µM KH2PO4respectively. Also, the stevia showed the highest content of soluble sugars and antioxidant activity in 34 µM KH2PO4. According to our results it seems that total steviol glycosides increased after adding KH2PO4into the culture medium, but its effect on different glycosides was not the same and probably changed the ratio of different SGs in this plant.
Research Paper
Bioinformatics
Reza Mir Derikvand; Seyyed Mohsen Sohrabi; Kamran Samiei
Volume 8, Issue 21 , June 2018, Pages 59-70
Abstract
Plant defensins are a large family of cysteine-rich antimicrobial peptides. These peptides are small molecules with molecular mass between 5 and 7kD and eight conserved cysteines that are involved in disulfide bond formation. In the present study, some members of defensin gene family were isolated and ...
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Plant defensins are a large family of cysteine-rich antimicrobial peptides. These peptides are small molecules with molecular mass between 5 and 7kD and eight conserved cysteines that are involved in disulfide bond formation. In the present study, some members of defensin gene family were isolated and characterized from lentil genotypes. All coding sequences of the defensin genes of dicotyledon plants were retrieved from GenBank. The retrieved coding sequences were aligned against lentil EST library and the resulted sequences were pooled and assembled. The resulted contigs and singletons were aligned against GenBank nr database using BLASTn tool. The contigs and singletons with the full open reading frame were used to primer design. In the next step, DNA extraction was performed from Gachsaran, Mahali, Filip2003-2L, Filip2003-9L, Filip2005-2L and Filip2006-10L genotypes. Finally, by using PCR, genomic sequence of defensins were amplified, cloned into pTZ57R/T plasmid and sequenced. The results showed complete identity among the isolated defensins from all genotypes. The identified genes also contain conserved introns with variable length that comprised of regulatory elements for response to different factors and conditions. For first time in this study, genomic sequences of three members of defensin gene family were isolated from lentil genotypes and structures and features of them were determined.
Review
Genetic Engineering and Gene Transformation
Masoumeh Fallah Ziarani; Masoud Tohidfar
Volume 8, Issue 21 , June 2018, Pages 71-79
Abstract
Today, Change the color of the flower due to its commercial importance is one of the goals of the researchers. Creation of the variation in flower color of ornamental plants can be highly profitable for the country and facilitate the way for export to other parts of the world. In the past, efforts have ...
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Today, Change the color of the flower due to its commercial importance is one of the goals of the researchers. Creation of the variation in flower color of ornamental plants can be highly profitable for the country and facilitate the way for export to other parts of the world. In the past, efforts have been do in the traditional way and genetic engineering for change the color of the flower, but with slowdown. With the discovery of Crispr's system, the ability to make targeted changes at the genome level took less time. In order to target change by Crispr, the target gene and area must be identified, that is done by bioinformatic tools. The desired change through the design of gRNA is done. In following, the normal protein and mutated protein were checked for the function. Today, donor DNA is used to enhance the performance of the Crispr system. In this system, by homologous recombination can be enhanced Crisper's performance by replaces a healthy gene or knocked out and prevented the creation of non-specific changes in the genome.
Research Paper
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.
