Research Paper
Biotic and Abiotic stress
Saleh Naderi; Baratali Fakheri; Sedigheh Esmailzadeh Bahabadi
Volume 4, Issue 6 , October 2014, Pages 1-9
Abstract
Basil (Ocimum basilicum L.), a medicinal plant of the Lamiaceae family, is used in traditional Iranian medicine. Essential oils of basil are composed of phenylpropanoids. Chavicol o-methyl and eugenol o-methyl are the most important components in essential oil of basil. Chitosan, main compound of fungal ...
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Basil (Ocimum basilicum L.), a medicinal plant of the Lamiaceae family, is used in traditional Iranian medicine. Essential oils of basil are composed of phenylpropanoids. Chavicol o-methyl and eugenol o-methyl are the most important components in essential oil of basil. Chitosan, main compound of fungal species could be used as biotic elicitor to improve secondary metabolites. In the present study, the effect of chitosan on methylchavicol content, chavicol o-methyl transfrase gene expression and enzymes activity of catalase, ascorbate peroxidase was evaluated. The plants were treated at pre flowering stage with 2 g/L chitosan and harvested after 1, 2, 3, and 5 days. Essential oils analysis showed that methylchavicol increased under chitosan compare to untreated plants. Chavicol o-methyl transfrose gene expression and antioxidant enzymes activity increased significantly after chitosan. Totally, changes in gene expression in different harvest stages are consistent with methylchavicol changes. Thus, chitosan increased methylchavicol by increasing CVOMT gene expression.
Research Paper
Biotic and Abiotic stress
Marjan Bahrabadi; Farhad Shokouhifar; Mohammad Ali Ebrahimi
Volume 4, Issue 6 , October 2014, Pages 11-20
Abstract
Synthetic pathogen-inducible promoters are suitable alternatives for native promoters in plant genetic manipulation to the purpose of resistant crop production. An ideal pathogen-inducible promoter would only be activated in response to target pathogens. Furthermore, it should express the transgene locally ...
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Synthetic pathogen-inducible promoters are suitable alternatives for native promoters in plant genetic manipulation to the purpose of resistant crop production. An ideal pathogen-inducible promoter would only be activated in response to target pathogens. Furthermore, it should express the transgene locally and temporarily. The absence of these characteristics in native promoters have drawn the attentions toward design and construction of synthetic promoters. Some components like cis-regulatory elements are used in construction of synthetic promoters and this provides high flexibility in determining the expression quantity and the inducibility type. One of the most common methods for a synthetic inducible promoter analysis is using Agrobacterium-mediated transient expression system. With this method, Functional analysis of the promoter can be performed in a short time by application of biotic and abiotic treatments and assaying the transgene expression. In this study, the SP-DD synthetic pathogen inducible promoter (containing of two copies of Box D cis-element derived from parsley PR2 promoter) fused with an intron-containing ß-glucuronidase reporter gene was transferred to tobacco leaves (Nicotiana benthamiana) by agroinjection. The promoter function was evaluated in response to salicylic acid treatment and environmental stresses like heat, cold and UV radiation. The results showed that the SP-DD synthetic promoter induced the ß-glucuronidase gene expression in response to salicylic acid and the expression amount increased over time from 2 hours to 24 hours post applicaion. Besides, the promoter showed slight sensitivity in response to heat and cold stresses but the ultraviolet radiation stress had no effect on the promoter induction.
Research Paper
Molecular Plant Breeding
Mahdieh Safarzadeh; Reza Fotovat; Mohammadreza Azimi; Ehsan Mohsenifard; Behnam Bakhshi
Volume 4, Issue 6 , October 2014, Pages 21-33
Abstract
Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this ...
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Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this study, the expression patterns of miR159a,b, miR160, miR167a,b and miR171a have been studied in both drought susceptible and drought tolerant varieties in wheat using qRT-PCR. miR159a,b, miR160, miR167a,b and miR171a could play important roles in MYB, ARF, ARF, and SCL, transcription factors regulation, respectively. High conservation among the studied miRNA families was observed in the mature miRNA producer regions by multiplex alignment of pre-miRNAs. Results of qRT-PCR analysis indicated that expressions of miR160 and miR167a,b in tolerant Variety and miR159a,b in susceptible Variety are increased significantly. However, no significant changes in expression were observed for miR171a in both tolerant and sensitive varieties. Presumably, up-regulation miR159a,b in susceptible variety could be resulted to reduction in the expression of MYB genes involved in drought response. On the other hand, up-regulation of miR160 and miR167a,b in tolerant variety, may lead to regulation of auxin and abscisic acid pathways interaction and probably these miRNAs could contribute in stress tolerance in tolerant variety. In addition, no significant change in miR171a expression demonstrated that expression of SCL could be regulated through other mechanisms in plant.
Research Paper
Molecular Plant Breeding
Parvaneh Mahmodi; Ahmad Moeini; Seyed Mojtaba Khayam Nekoie; Mohsen Mardi; Ghasem Hosseini Salekdeh
Volume 4, Issue 6 , October 2014, Pages 35-46
Abstract
Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing ...
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Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing has risen as a cost-effective and powerful method for transcriptome study. De novo assembly of transcripts provides main solution to transcriptome analysis for organisms without reference genome. Precise sequencing and assembly of transcriptome reliable data are necessary for the downstream analysis. Accordingly, this work was analyzed by two of the most popular software's Trinity and SOAPdenovo for saffron stigma transcriptome to study the effective programs for transcriptome assembly. The results showed that the mean sequence length and the number of unigenes obtained by Trinity were more than SOAPdenovo (Trinity: 689, SOAPdenovo: 624). Translation of the better results produced by the appropriate assembler to protein led to a significant increase in the number of its records obtained at databases. Furthermore, these unigenes might help to identify more metabolite pathways. Assembled unigenes by Trinity had no lacking distance and were about twice the unigenes assembled by SOAPdenovo. As a general conclusion, it seems that selection of an appropriate software and its parameters is not easy without comprehension understanding of different software operation and their setting. Thus, comparison of the different softwares efficiency on the different organisms could provide some practical suggestions and choose an appropriate software.
Research Paper
Molecular Genetics and Genetic Engineering
Masoud Tohidfar; Ebrahimi Ghorishi; Bartali Fakheri; Motahareh Mohsenpour
Volume 4, Issue 6 , October 2014, Pages 47-59
Abstract
Abiotic stresses such as drought and salinity are the first factor of YIELD decrease in the world. In this study, betaine aldehyde dehydrogenase gene (badh) is used as both an abiotic stress marker gene and one of the abiotic stress tolerance candidate genes along with Flavodoxin (fld) in construction ...
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Abiotic stresses such as drought and salinity are the first factor of YIELD decrease in the world. In this study, betaine aldehyde dehydrogenase gene (badh) is used as both an abiotic stress marker gene and one of the abiotic stress tolerance candidate genes along with Flavodoxin (fld) in construction of chloroplast vector for rice. Thereby, adding the appropriate enzyme role to let gene cassette enter to the center. The first two parts of a specific target areaof Plastom rice (FR) the rice genome using PCR that they can be re-attached in cloning. Then, the gene cassetes were designed for fld and badh genes in regulatory regions of the chloroplast. So that the fld genes and with rbcl 5'UTR and badh genes with T7gene10 5'UTR were cloned the strong chloroplastsic promoter Prrn and the terminator rbcl 3'UTR. Finally, The complete two-gene cassettes fld/badh with the regulatory regions is separated from targeting chloroplast metabolism of rice in two sides cloned. The two specific chloroplast vector called pFrFB(-) and pFrFB(+) are potential to be attached to gene that are resistant to drought and salinity targeted with two different orientations relative to the inner regions of the chloroplast genome of rice plants and are able to be the goal of creating high resistance to salinity, drought and chill in transferring genes to use the chloroplast of rice plant via gene gun.
Research Paper
Genomics
Marjan Jannatdoust; Reza Darvishzadeh; Mohammad Ali Ebrahimi
Volume 4, Issue 6 , October 2014, Pages 61-72
Abstract
In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) ...
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In this study, genetic variability among and within 50 confectionery sunflower populations was investigated using 10 microsatellite markers (SSR). The number of alleles per locus ranged from 2 to 3 with an average of 2.1. The number of effective alleles per locus was estimated from 1.948 (locus ORS785) to 1.468 (locus ORS1088) with an average of 1.825. The highest expected heterozygosity (0.484) was estimated for ORS785 locus and the lowest one (0.268) estimated for ORS1088. The mean of expected and observed heterozygosity was 0.435 and 0.722, respectively. Polymorphic information content varied between 0.572 in ORS785 locus and 0.334 in ORS1088 with an average of 0.503. A principal co-ordinates analysis (PCoA) showed that the first two Eigen-values explained 31.71% of the cumulative variation. Cluster analysis based on complete algorithm and Nei genetic distance grouped the studied populations in 3 main classes. Analysis of molecular variance revealed that the high part of total variation was due to within populations. So it will be better to do selection within populations in breeding programs.
Research Paper
Biotic and Abiotic stress
Seyyedeh farzaneh Fatemi ardestani; Ghorbanali Nematzadeh; Hossein Askari; Hamidreza Hashemi
Volume 4, Issue 6 , October 2014, Pages 73-83
Abstract
Soil salinity limits crop production by creating osmotic stress and disruption of ion homeostasis, leads to damage at the molecular level and finally cell death. In this study, gene expression analysis based on cDNA-AFLP technique was used to compare the expression profiles of KCl stress at three levels: ...
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Soil salinity limits crop production by creating osmotic stress and disruption of ion homeostasis, leads to damage at the molecular level and finally cell death. In this study, gene expression analysis based on cDNA-AFLP technique was used to compare the expression profiles of KCl stress at three levels: 0 (control), 200mM and 400mM, in Aeluropus littoralis which is the closest family to cereal. Among 34 isolated ESTs, 27 ESTs were obtained with the average length of 280 bp. The nucleotide sequences were compared with those in the GenBank database. Approximately 80% of the ESTs show homology to nucleotide or amino acid sequences in the GenBank database and 6 ESTs show no significant similarity in the GenBank database which considered as novel genes. Finally, 27 ESTs were recorded in NCBI database which are included potassium transporter, ribosomal protein, NADH dehydrogenase and golgin. The result of this research is very important to understand molecular basis and resistance mechanisms of drought stress for breeding and genetic engineering to improve crop resistance against stress and the production of resistant plants. EST classification based on responses to stress, will facilitate performance analysis, characterization of responsive genes in plant roots of Aeluropus littoralis to stress in future studies on this herb that is a member of the Poaceae family.
Research Paper
Molecular Plant Breeding
Zohreh Hajibarat; Abbas Saidi; Reza Talebi; Zahra Hajibarat
Volume 4, Issue 6 , October 2014, Pages 85-94
Abstract
Identification of genetic diversity and classification of genetic resources (germplasm) are of important and essential activities in breeding and management of plant genetic resources. In order to study of genetic diversity of chickpea genotypes, 38 pair’s primers of SSR were used on 18 landrace and ...
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Identification of genetic diversity and classification of genetic resources (germplasm) are of important and essential activities in breeding and management of plant genetic resources. In order to study of genetic diversity of chickpea genotypes, 38 pair’s primers of SSR were used on 18 landrace and 30 improved varieties. After genomic DNA extraction and PCR reaction, primers produced 117 polymorphic bands and the mean of polymorphic band per primer was 3.5. The highest value of polymorphic information content (PIC) belonged to TAA170 primer (0.77) and the lowest value of PIC belonged to Cstms5 primer (0.08). Mean of PIC for all primers was 0.48. Calculated Jacard similarity coefficient ranged from 0.47 to 0.94 among genotypes. In order to assess genetic relationships, cluster analysis was performed by method NJ with Splitstree (ver 4.13.1) software. Results of this study revealed that SSR molecular markers has a valuable potential for evaluation and discrimination of chickpea genotypes.
Research Paper
Molecular Genetics and Genetic Engineering
Somayeh Khosrojerdi; Maryam Hashemi; Maryam Mousivand
Volume 4, Issue 6 , October 2014, Pages 95-105
Abstract
Cellulases can hydrolysis cellulose into glucose units which act in a synergistic manner of three enzymes endo-beta -1, 4-glucanase, cellobiohydrolase and beta-glucosidase. Nowadays, cellulases are used in various industries including animal feeds, textile, sewage treatment, brewery industries and biofuel ...
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Cellulases can hydrolysis cellulose into glucose units which act in a synergistic manner of three enzymes endo-beta -1, 4-glucanase, cellobiohydrolase and beta-glucosidase. Nowadays, cellulases are used in various industries including animal feeds, textile, sewage treatment, brewery industries and biofuel production. Demand for cellulolytic enzymes with unique catalytic properties is growing more rapidly than ever before. In this study, Bacillus subtilis A14h with cellulase production potential was identified using biochemical and molecular (16SrDNA gene) methods.The optimum conditions of B. subtilis A14h cellulase activity was evaluated in the presence of two type of substrates (carboxymethyl cellulose and beta-glucan), temperatures range of 30-70°C,and pH 4.6. Also, endo 1, 4-beta glucanase gene amplified using specific primers, sequencing outcome was recorded in the NCBI database. Sequence analysis and construction of phylogenetic trees was performed using vector NTI and Mega.4 softwares.The results showed that the isolate belongs to the Bacillus subtilis species. The phylogenetic analysis and comparison of the amino acid sequence of endo -1, 4-beta glucanase gene showed that the enzyme catalytic region belongs to glycosyl hydrolases family 5 and the non catalytic region was placed in the CBM3 family. The B. subtilis A14h cellulase was most closely related to the cellulase of B.subtilis strains. The results showed that the highest enzyme activity equal to 1464.25 U/ml was obtained in the presence of beta-glucan substrate at 55° C.
