Research Paper
Plant Disease and Biotechnology
Azam Badr Hadad; Farhad Nazarian Firouzabadi; Ahmad Ismaili; Hedayat Bagheri
Volume 7, Issue 19 , November 2017, Pages 1-13
Abstract
Antimicrobial peptides are ancient and conserved molecules which are found in defense mechanisms of almost all living organisms from bacteria to animal and plant species. Identification and introduction of novel antimicrobial peptides, is a cost-effective way to improve crop plants resistance to pathogens ...
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Antimicrobial peptides are ancient and conserved molecules which are found in defense mechanisms of almost all living organisms from bacteria to animal and plant species. Identification and introduction of novel antimicrobial peptides, is a cost-effective way to improve crop plants resistance to pathogens by using recombinant DNA technology. Therefore, an expression construct containing omiganan antimicrobial encoding gene from the cytoplasmic granules of bovine neutrophils, was cloned and transferred to the tobacco leaf disk using Agrobacterium tumefaciens mediated-transformation. The presence of the antimicrobial peptide encoding gene in the genome of transgenic plants was confirmed by PCR analysis. Six putative transgenic lines and a non-transgenic control plant were selected for further molecular analysis. Total protein was extract from transgenic and non-transgenic control plants and used for antimicrobial activity assay against some human; E. coli, Salmonella, Staphylococcus, Bacillus, and plant: Xanthomonas and Pseudomonas pathogens by disc diffusion method. Results of this experiment showed that total protein extract from transgenic lines, as compared to non-transgenic plant, was significantly (P
Research Paper
Biotic and Abiotic stress
Amin Mohammadi purfard; Mohammad- Zaman Nouri; Ali Dehestani Kolagar
Volume 7, Issue 19 , November 2017, Pages 15-24
Abstract
Salinity stress is one of the most important environmental stresses that affects crop production. Salt Overly Sensitive regulation path is an important route in the regulation of ion homeostasis. In this study, the expression patterns of AlSOS1, AlSOS2 and AlSOS3 genes were evaluated in the salt tolerant ...
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Salinity stress is one of the most important environmental stresses that affects crop production. Salt Overly Sensitive regulation path is an important route in the regulation of ion homeostasis. In this study, the expression patterns of AlSOS1, AlSOS2 and AlSOS3 genes were evaluated in the salt tolerant plant, Aeluropus littoralis under 0, 200, 400 and 600 mM sodium chloride and after 0, 8, 16, 24, 48 and 72 h of the stress exposure. Salinity stress significantly increased the expression of all genes compared to the control. In 200 mM NaCl treatment, AlSOS1 and AlSOS2 expression increased in various time courses and peaked at 72 h after the stress exposure. In 400 and 600 mM NaCl treatment, however, the maximum expression of AlSOS1 was observed at 48 h after the stress. AlSOS2 was highly expressed at the salt concentrations of 400 and 600 mM after 48 h and 24 h, respectively. The maximum rate of AlSOS3 transcription was recorded in 400 and 600 mM NaCl after 24 h and 16 h, respectively. Different mechanism of the effect of AlSOS3 on AlSOS2, effect of AlSOS2- AlSOS3 complex on AlSOS1 and differences in the act of the genes are of the reasons for the variations in the gene expression. These results suggest that in severe stress conditions, the reaction of genes would be rapid and with different patterns. AlSOS3 showed a different pattern of the expression comparing to the two other genes which implies differences in the gene regulation mechanism.
Review
Genomics
Reza Ataei; Majid Gholamhoseini; Valiollah Mohammadi
Volume 7, Issue 19 , November 2017, Pages 25-37
Abstract
The phenotypic diversity of many important traits in plants is influenced by several loci, environmental factors and their interactions. Association mapping is one of the methods proposed in recent decades for genetic study and detection of quantitative trait loci (QTLs). Association mapping was used ...
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The phenotypic diversity of many important traits in plants is influenced by several loci, environmental factors and their interactions. Association mapping is one of the methods proposed in recent decades for genetic study and detection of quantitative trait loci (QTLs). Association mapping was used in human genetics and qualitative traits (such as diseases), but recently its use is increasing in the plant science because of advances in high throughput genomic technologies, interests in identifying novel and superior alleles, and improvements in statistical methods. Association mapping through linkage disequilibrium analysis is a purposeful method for identifying marker alleles and quantitative traits association. Unlike linkage mapping, this method identifies the association between phenotypic and polymorphic diversity in the genome by exploiting the diversity of natural populations and taking into account all the events that occurred during the evolution and is a promising approach for overcoming the limitations of linkage mapping. Despite association mapping has high statistical power, the application of this method in structured populations, species with low level of linkage disequilibrium and in traits controlled by rare alleles is complicated and difficult. In this review, we will present a comprehensive view, its application in population, current status and limitation of association mapping in plant science
Research Paper
Bioinformatics
Sohaila Fatemi; Khaled Mirzaei; Mohamed Sedigh Kamangar
Volume 7, Issue 19 , November 2017, Pages 39-50
Abstract
Auxin has an important role in the various stages of plants growth and development. Studies have shown that auxin regulates these processes by auxin responsefactors (ARF) family. ARF proteins due to their central domain, mediate the cellular response to the auxin by activating or repressing the expression ...
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Auxin has an important role in the various stages of plants growth and development. Studies have shown that auxin regulates these processes by auxin responsefactors (ARF) family. ARF proteins due to their central domain, mediate the cellular response to the auxin by activating or repressing the expression of downstream genes. ARF genes in several different plant species have been studied by molecular methods however to better understand the mechanisms of these proteins more studies are needed. In this study with computational methods, we found 27 ARF proteins, which they were scattered on the different parts of Phaseolus vulgaris chromosomes. The phylogenetic analysis of these sequences revealed they were divided into four different classes without any sign of gene-duplication between them. ARF genes expression according to the types of gene and based on the types of tissue respectively showed that they group into the five and two classes. In comparing with other tissues, ARF genes in leaf, young trifoliates, stems, mature pods and young pods tissues have a high level of expression. Of the 27 ARF Phaseolus vulgaris sequences surveyed in this study, nine ARF proteins were gene activator and 17 ARF proteins were gene suppressor.
Research Paper
Plant Disease and Biotechnology
Mohammad Amin Almasi; Galavizh Almasi
Volume 7, Issue 19 , November 2017, Pages 51-63
Abstract
The most common virus affecting lettuce (Lactuca sativa L.) in the field worldwide is Lettuce mosaic virus (LMV), belonging to the family Potyviridea, genius Potyvirus. There are several techniques to detect LMV including serological and molecular assays, but these methods take a long time and requiring ...
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The most common virus affecting lettuce (Lactuca sativa L.) in the field worldwide is Lettuce mosaic virus (LMV), belonging to the family Potyviridea, genius Potyvirus. There are several techniques to detect LMV including serological and molecular assays, but these methods take a long time and requiring sophisticated tools. The aim of this study was to reduce the time required to detect LMV, using loop-mediated isothermal amplification (LAMP) technique. Leaf samples (38 samples) with symptoms similar to LMV were collected from Kurdestan province and were subjected to a serological (DAS-ELISA) test and lastly, four samples were detected as the positive samples. Then, total RNA was extracted and one-step reverse transcription (RT)-LAMP was carried out under isothermal conditions and results were evaluated by agarose gel electrophoresis and hydroxynaphthol blue (HNB) dye. A positive result using the HNB dye was a color change in master-mix from the violet to sky blue. In addition, a novel immunocapture (IC)-RT-LAMP assay for rapid and easy detection (without RNA extraction) of LMV was developed here and its potential compared with other assays. The advantages of RT-LAMP method in compare to other methods include the high specificity, high sensitivity, high rapidity, high efficiency, safety, fascinatingly, no requirement of expensive and tools for amplification, no need to RNA extraction (in IC-RT-LAMP assay), no post-amplification treatment of the amplicons, visual detection and user friendly.
Research Paper
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.
