Proteomics
Ghasem Hosseini Salkade; Davood Nasr Abadi
Volume 1, Issue 1 , March 2012, , Pages 1-11
Abstract
Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. ...
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Rice is an excellent model cereal for molecular biology and genetics research. Salinity is a major factor limiting rice production world wide. The analysis of stress-responsiveness in plants is an important route to the discovery of genes conferring stress tolerance and their use in breeding programs. To further understand the mechanism of plant response to salinity we employed a proteomic approach to profile the protein changes of rice 3th leaf and root under salt stress. Plants were grown in Yoshida nutrient solution and salt stress imposed after 25 days. Plants were treated by 100¬mM NaCl for 10. After that 3th leaves and total root were collected from control and salt stressed plants. The Na+ and K+ content of leaves/roots and several yield components changed significantly in response to short-term salt stress and their proteome patterns were analyzed using 2-DE in triplicates. The expression pattern of proteins significantly changed in all leaves/roots in response to stress. More than 488 and 345 protein were detected repeatedly in root and leaf 2Dgels respectively by software package. 107 proteins in root and 86 proteins in leaf of two genotypes showed significant response to stress. 3 protein in leaf gels and 2 protein in root gels were selected and identified by ESI-Q-TOF. The most important were Ferritin, Rubisco activase and ascorbat¬peroxidase in leaf and Peroxidase and Ascorbat¬peroxidase in root. All of them were enzyme and involved in detoxification and removal of reactive oxygen species (peroxidase, ascorbat¬peroxidase) Iron homeostasis (ferritin) or activation of other enzymes (rubisco¬activase).
A Hashemi; GH Nematzadeh; GH Hosseini Salekde; A Hosseini; M.R Hajirezaei
Volume 2, Issue 2 , September 2012, , Pages 1-14
Abstract
Two rice lines, IR29 and FL478, which differed in salinity tolerance, were investigated for physiological and metabolic responses
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Two rice lines, IR29 and FL478, which differed in salinity tolerance, were investigated for physiological and metabolic responses
Plant Disease and Biotechnology
M.R Safarnejad; M Basirat; M.A Ebrahimi; H Safarpour; S Nazari; B Mahmoudi; S Ataie Kachoie
Volume 2, Issue 3 , January 2013, , Pages 1-12
Abstract
Rhizomania is one of the most important Sugar beet diseases throughout the world. The disease is caused by beet necrotic yellow vein virus (BNYVV). The Polymyxa betae (Keskin) is the only natural transmitting agent of the disease between the plants. The fungus is an obligate parasite and could not be ...
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Rhizomania is one of the most important Sugar beet diseases throughout the world. The disease is caused by beet necrotic yellow vein virus (BNYVV). The Polymyxa betae (Keskin) is the only natural transmitting agent of the disease between the plants. The fungus is an obligate parasite and could not be cultured in the media, then detection of fungus is done normally by microscopic observation. In order to facilitate detection process, present study is done to develop specific antibodies against this fungus by applying recombinant protein. The Glutathione-S-transferase (GST) as a specific immunogenic protein is a critical enzyme expressed in zoospores, sporangia and resting spores and could be a good candidate to develop a serological test for P. betae. For this aim, the DNA region encoding fungal GST gene was isolated and cloned into pET28a bacterial expression vector. Large scale expression of the recombinant protein was performed in Escherichia coli (Migula). Purification was carried out by applying immobilized metal affinity chromatography under native conditions. The purified recombinant GST protein was used for immunization of rabbit. Purification of immunoglobulin was performed by affinity chromatography using protein A column. The purified antibodies were applied for efficient detection of infected plant in serological assays.
Biotic and Abiotic stress
Sepideh Torabi; Ghasem Hosseini Salekdeh
Volume 3, Issue 4 , September 2013, , Pages 1-14
Abstract
R Rice is one of most important crops feeding about half of the world population. Phosphorous is one of limiting factors of rice growth and its deficiency substantially decreases rice yield. In this study, we aimed to identify biochemical mechanisms of rice adaptation to phosphorous deficiency in leaf ...
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R Rice is one of most important crops feeding about half of the world population. Phosphorous is one of limiting factors of rice growth and its deficiency substantially decreases rice yield. In this study, we aimed to identify biochemical mechanisms of rice adaptation to phosphorous deficiency in leaf and root. We compared the metabolites in parental lines, Nipponbare, and its near isogenic line (NIL6-4) containing a major QTL for phosphorous uptake (PUP1) on chromosome 12. Phosphorous deficiency resulted in significant decrease in number of tillers and fresh weight in both parental line and its near isogenic line, however, this reduction was more pronounced in the parental line. Analysis of the level of several soluble sugars and activity of enzymes involved in energy production revealed that phosphorous deficiency could lead to some changes in glycolysis pathway in rice near isogenic line so that the plant could cope with the ATP shortage. It is most likely that enhancement of this biochemical pathways may increase rice adaptation to phosphorous deficiency and consequently increase plant production with less phosphorus fertilizer required.
Genetic Engineering and Gene Transformation
Hossein Maleki; Ali Hatef Salmanian; Jafar Amani; Alaodin Kordenaiej; Mahyat Jafari
Volume 3, Issue 5 , February 2013, , Pages 1-9
Abstract
E. coli O157:H7 is an important zoonotic pathogen that causing severe gastrointestinal disease such as hemorrhagic diarrhea and hemolytic uremic syndrome. The first step of bacterial pathogenicity is, attaching to the host cell. EspA is a protein molecule and forms as filamentous structure ...
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E. coli O157:H7 is an important zoonotic pathogen that causing severe gastrointestinal disease such as hemorrhagic diarrhea and hemolytic uremic syndrome. The first step of bacterial pathogenicity is, attaching to the host cell. EspA is a protein molecule and forms as filamentous structure that is transiently expressed on the outer membrane surface and interacts with the host cell during the early stage adhesion and forms bacterial biofilm, this filamentous structure make it a strong immunogenic. Tir is bacterial protein that translocated to host cell after expression in the bacteria by type III secretion system (T3SS) and integrated in to host cell membrane. Intimin can attach to the host cell by conducting to Tir. The purpose of this study is constructing bivalent gen which contains virulence factor mention before and transferring in to target plant in order to production edible vaccine against E. coli O157:H7.After bioinformatics investigation the two bivalent gen construction (espA-Tir,) were attached by peptide linker, and the gens were constructed. After codon optimization based on tobacco; construction were cloned in expression vector which contains CaMV35s promoter. After transformation and regeneration, the expressions of transgenes were showed in analysis.
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.
Proteomics
Mohammad Reza Azimi; Ghasem Hosseini Salekdeh
Volume 4, Issue 7 , December 2015, , Pages 1-13
Abstract
Water shortage is one of the most important environmental factors in limiting plant production worldwide. Molecular breeding may help to develop drought tolerant plants. Proteomics approach can help in comprehensive analysis of stress responsive genes and identification of drought signaling pathways. ...
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Water shortage is one of the most important environmental factors in limiting plant production worldwide. Molecular breeding may help to develop drought tolerant plants. Proteomics approach can help in comprehensive analysis of stress responsive genes and identification of drought signaling pathways. These drought tolerance candidate genes or their regulatory genes may be further analyzed for their possible implication in increase plant tolerance to drought stress. In this studied we analyzed the changes in proteome of wheat flag leaf in response to drought. We compared a drought tolerant with drought susceptible genotypes under normal and stress well-watered and stress conditions. Stressed plants were exposed to 50% field capacity before anthesis. Out of 900 proteins analyzed across two dimensional gels, 57 protein spots showed significant differences in response to stress. Of these, 42 protein spots could be identified using mass spectrometry analysis. Differentially expressed proteins and enzymes could be grouped in different functional groups. Our results showed that tolerant genotype may use various mechanisms particularly the up-regulation of genes involved in oxidative stress defense in flag leaf. This may help the tolerant genotypes to better remove reactive oxygen species generate by stress in flag leaf and maintain its physiological and photosynthetic activities.
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.
Molecular Plant Breeding
Marouf Khalili; Seyed Abolghasem Mohammadi
Volume 5, Issue 9 , June 2015, , Pages 1-14
Abstract
Seed germination (capacity, time, and synchronization) is a manifest characteristic of the standard germination test of a cultivated variety. In order to identify genomic regions associated with seed germination, 149 bread wheat recombinant inbred lines and their parents RojoYecora and No. 49 were conducted ...
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Seed germination (capacity, time, and synchronization) is a manifest characteristic of the standard germination test of a cultivated variety. In order to identify genomic regions associated with seed germination, 149 bread wheat recombinant inbred lines and their parents RojoYecora and No. 49 were conducted in an alpha lattice design with two replications at the University of Mahabad during 2013-14, under normal and moisture stress conditions. Different traits including index of germination speed, final germination percentage, germination speed, germination rate, and average daily germination were measured. In this study, 340 pairs of microsatellite primers were used to determine the parental polymorphism. Furthermore, 7 retrotransposon-based markers on LTR regions of barely retrotransposons, and their twenty-eight combinations at IRAP technique, as well as, 63 combination of this primer with anchored ISSR primers at REMAP technique were used for population screening. QTL analysis using composite interval mapping (CIM) for each trait in each environment and mean of two environments were accomplished. For all studied traits, transgressive segregation was observed. In general, eleven QTLs were detected for all traits. Total phenotypic variance explained by these QTLs varied from 11.82 to 21.42 percent. The highest LOD value for QTL controlling germination speed (LOD =6.65) was obtained on chromosome 4BQSg-Normal. The results revealed that QTLs of index of germination rate and germination speed related to the quantity and quality of seed germination had desirable performance in all three environments. However, detected stable and cluster QTLs may be used in marker assisted selection (MAS) programs.
Genomics
Fariba Morsali Aghajari; Reza Darvishzadeh; Naser Abbaspour
Volume 5, Issue 10 , September 2015, , Pages 1-16
Abstract
In order to study the effect of salinity on yield and physiological traits of sunflower and genetic analysis of these traits under salinity conditions, a factorial experiment based on completely randomized design with three replications were performed outside the greenhouse in an open air area under ...
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In order to study the effect of salinity on yield and physiological traits of sunflower and genetic analysis of these traits under salinity conditions, a factorial experiment based on completely randomized design with three replications were performed outside the greenhouse in an open air area under natural environmental conditions. The studied factors were included 2 salinity stress levels (normal and 6 dS/m) and sunflower recombinant inbred lines (102 lines derived from the cross PAC2 ×RHA266 together with parental lines). Traits such as grain yield per plant, chlorophyll content, net photosynthetic rate, leaf relative water content, Na+ and K+ concentrations were measured after flowering. The effect of salinity was significant on grain yield, leaf relative water content, Na+ and K+ concentrations as well as on Na+/K+ and K+/ Na+ ratios. For all traits, significant differences were observed between the genotypes studied. Genetic analysis of studied traits was done using a linkage map comprising 221 molecular markers (210 SSR/11 SNP) with an average distance of 7.44 cM between markers via composite interval mapping (CIM) procedure. Totally, 10 and 8 QTLs were detected for studied traits under normal and salt stress conditions, respectively. The phenotypic variance explained by QTLs (R2) ranged from 10.4%- 34.4%. The results showed the existence of co-localized QTLs for some of the studied traits under normal and salt stress conditions including Na+.S.4.1 with Na+/K+.S.4.1, Chl.NS.6.1 with K+.S.6.1. Using co-localized QTLs in different environmental conditions and different years could enhance the efficiency of marker-assisted selection in plant breeding programs.
Genetic Engineering and Gene Transformation
Atena Mozafari; Rouhollah Kazemi; Jafar Amani; Mahyat Jafari; Ali Hatef Salmanian
Volume 5, Issue 11 , December 2015, , Pages 1-13
Abstract
Diarrheal diseases have been considered as one of the most major world health problems in all age categories. Among all the pathogens caused to diarrhea, entrohemorrhagic Escherichia coli (EHEC) and Vibrio cholerae are the most important agents. E. coli O157:H7 as the most important serotype of EHEC ...
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Diarrheal diseases have been considered as one of the most major world health problems in all age categories. Among all the pathogens caused to diarrhea, entrohemorrhagic Escherichia coli (EHEC) and Vibrio cholerae are the most important agents. E. coli O157:H7 as the most important serotype of EHEC bacteria caused diarrhea by producing STX2 toxin. In vibrio cholerae the cholera toxin (CTX) also is the main virulence factor that leads to diarrhea. Both of these toxins are belong to AB5 family and due to non-toxicity and natural immunogenic characteristic of B subunit, it could be introduced as an appropriate candidate for immunogenicity against these toxins. Plant seeds are an effective biological bioreactor for production of recombinant immunogenic antigens and also foreign proteins can be expressed in plants with the native structure. In this research, the production of recombinant protein composed of binding subunits of STX2 and cholera toxin was evaluated in canola seed as an oral vaccine candidate. The SC construct composed of (stx2B and ctxB) was subcloned to plant vector under the control of canola seed specific promoter (fae) and transformed to Agrobacterium tumefaciens. Then the recombinant vector was transformed to plant host via Agrobacterium mediated transformation. Transgenic plants was evaluated and the amount of chimeric protein expressed in transgenic canola seed was determined by semi quantitative ELISA and subsequently the amount of chimeric proteins was estimated 40 milligram per 1 gram seed. The results showed that the canola seed can efficiently produce recombinant protein.
Plant Disease and Biotechnology
Elham Zamani; Forogh Sanjarian; Ebrahim Mohammadi-goltapeh; Naser Safaie
Volume 6, Issue 13 , May 2016, , Pages 1-12
Abstract
Induced resistance is one the ways by which plants cope with the biotic stresses. Pathogenesis-related proteins (PRs), including chitinase and β-1,3-glucanase are synthesized by plant in response to pathogenic infection. In present work, we have carried out inoculation experiment in wheat to investigate ...
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Induced resistance is one the ways by which plants cope with the biotic stresses. Pathogenesis-related proteins (PRs), including chitinase and β-1,3-glucanase are synthesized by plant in response to pathogenic infection. In present work, we have carried out inoculation experiment in wheat to investigate the effect of salicylic acid (SA) and Pseudomonas flourescens on Septoria tritici Bloch (STB) symptoms. Subsequently, the expression profiles of chitinase and β-1,3-glucanase were analyzed with semi-quantitative RT-PCR at 0, 4, 14 and 24 days after inoculation in both treated and control plants. Results showed that the expression of both chitinase and β-1,3-glucanase genes increased in interaction with Z. tritici and the application of SA and P. flourescens. On the other hand, the application together had no significant effect on gene expression. Briefly, it can be concluded that increment of chitinase and β-1,3-glucanase expression level with the application of SA and P. flourescens would play role induction of plant defense against STB.
Plant Disease and Biotechnology
Jalal Gholamnezhad; Forogh Sanjarian; Ebrahim Mohammadi Goltapeh; Naser Safaei; Khadijeh Razavi
Volume 5, Issue 12 , February 2016, , Pages 1-10
Abstract
As a rule the reference genes used in gene expression analysis have been selected for their housekeeping roles, but the variation observed in most of them is a major obstacle to their effective use. It is widely supported to identify and validate stable reference genes, since no single biological gene ...
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As a rule the reference genes used in gene expression analysis have been selected for their housekeeping roles, but the variation observed in most of them is a major obstacle to their effective use. It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. In this study, suitability of seven wheat housekeeping genes for normalization of mRNA expression in wheat leaves infected by Mycosphaerella graminicola was investigated. Expression level of Actin, Rubisco, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Translation Elongation Factor 1α (TEF-1α), α-Tubollin, eukaryotic release factors 1 and 3 (ERF1 and ERF3) genes were examined by reverse northern dot blot method. Expression stabilities of the reference genes were statistically analyzed by Ecxel and SAS softwares. α-Tubolin, TEF-1α and Actin were the three most stable genes whereas the expression of Rubisco and GAPDH had the least stability. The presented comprehensive data on changes in expression of various wheat housekeeping genes in wheat- M. graminicola phatosystem facilitate selection of reference genes for Reverse northern dot blot method.
Bioinformatics
Manzar Heidari; Zahra-Sadat Shobbar; Parisa Koobaz; Mohammad javad Heydari
Volume 6, Issue 14 , August 2016, , Pages 1-15
Abstract
Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. ...
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Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. EST libraries data under normal and drought stress conditions were downloaded from NCBI databank. Preprocessing, clustering and assembly of the EST sequences were done using EGassembler software. Generated contig and singleton sequences were used as template for BLASTx analysis against rice protein database and functional category assignment using CLC Protein Workbench software and AgriGO. The identified proteins in the normal and drought libraries were allocated to 70 and 82 functional categories, respectively. IDEG6 were used to identify significant differences between functional categories in control and drought stress libraries. Gene ontology analysis, revealed significant differences in 20 groups of molecular function, 35 groups of biological processes and 12 groups of the intracellular components. In order to find the significant differential expression between the two libraries, 4012 ESTs with unigene accession numbers were implemented through applying an algorithm by MATLAB software and were analyzed by IDEG6 software, where 42 genes were found to be differentially expressed between drought and normal conditions (31 up-regulated and 11 down-regulated genes). The up-regulated genes were involved in environmental and oxidative stress response, homestasis, proteolysis and glycolysis, while photosynthesis related genes were down-regulated.
Biotic and Abiotic stress
Khadijeh Noroozi; Reza Fotovat; Farid Shekari; Ehsan Mohsenifard
Volume 6, Issue 15 , December 2016, , Pages 1-11
Abstract
Soil salinity is one of the major abiotic stresses that dramatically reducing crop productivity in the world. Recent studies indicate that the application of exogenous salicylic acid (SA) as a key molecule in the signal transduction pathway participates in the signaling of abiotic stresses. The role ...
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Soil salinity is one of the major abiotic stresses that dramatically reducing crop productivity in the world. Recent studies indicate that the application of exogenous salicylic acid (SA) as a key molecule in the signal transduction pathway participates in the signaling of abiotic stresses. The role of salicylic acid in salinity signalling is, however, unclear. In the present study, two barley (Hordeum vulgare L.) varieties (Reyhan and Nosrat) contrasting in their salinity tolerance were used to assess the role of various SA concentrations on the expression of Receptor-like kinases (RLKs) genes. The results demonstrated that that salinity and salicylic have a significant effect on seedling traits of barley cultivars. Salinity stress and salicylic acid increased the expression of Hv3ARK, IdiRLK2 genes in the cultivar Nosrat but in the other cultivar the relative expression of the genes were different. These results suggest the involvement of a number of RLKs in SA-mediated abiotic stress responses.
Proteomics
Maryam Jamshidnia; Sayed Kamal Kazemitabar; Christian Lindermayr; Hamid Najafi Zarini
Volume 6, Issue 16 , March 2017, , Pages 1-12
Abstract
Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in ...
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Recently, transient gene expression has been developed to provide a more rapid means of assessing plant tissues as a protein production platform without the labor-intensive and time-consuming process of generating stably transformed transgenic plants. This study reports the expression of HDA19 gene in two species of tobacco plants (Nicotiana tabacum and Nicotiana bentamiana) by means of transient transformation. Specific primers were designed and used for PCR amplification and cloning of HDA19 gene in the plant expression vector pB2GW7. The recombinant construct was transferred into Agrobacterium tumefaciens strain GV3101, and was used for Agrobacterium mediated transformation of tobacco plants. The presence of the desired gene in transgenic lines was confirmed through colony PCR. The expression of the protein in transgenic lines was confirmed by immune-dot blot assay and ELISA. Although the transformation of the two species was confirmed by immune-dot blot assay and SDS-PAGE, recombinant protein production in Nicotiana tabacum plants was confirmed by ELISA and it was estimated 400 µg per gram wet weight of tobacco leaves. According to the results, this species is the appropriate host for the production of recombinant HDA19, one of the histone deacetylases, rather than Nicotiana bentamiana.
Molecular Phsoiology
Batool Sabertanha; Baratali Fakheri; nafise Mahdinezhad; Zohre Alizade
Volume 7, Issue 17 , July 2017, , Pages 1-13
Abstract
This study aimed to investigate the effect of drought stress and silver nanoparticles on beta-carotene hydroxylase (bch) gene expression and carotenoid production in saffron. The experiment was implemented in two levels including normal irrigation and full drought stress on nine ecotypes of saffron in ...
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This study aimed to investigate the effect of drought stress and silver nanoparticles on beta-carotene hydroxylase (bch) gene expression and carotenoid production in saffron. The experiment was implemented in two levels including normal irrigation and full drought stress on nine ecotypes of saffron in three levels: control (distilled water), 55 and 110 ppm of silver nanoparticles levels. This study was conducted in split plot factorial experiment based on randomized complete block design with two replications at research field of Birjand University and biotechnology institute of Zabol University.In order to examine gene expression pattern, after taking leaf samples from all treatments, RNA extraction, cDNA synthesis and determination of temperature gradient, Real time polymerase chain reaction (Real-Time PCR) was used. Then, Data were analyzed using EX and SAS 9.2 software. The main effects of treatments with nine ecotypes of saffron, silver nanoparticle and drought stress and their interaction effects for bch gene expression and amount of carotenoid were significant at 1% probability level. The maximum bch gene expression and the amount of carotenoid was observed in 55 ppm of silver nanoparticles under drought stress in Ghaen ecotype (1478.62 & 21.37 µg.g-1, respectively). Therefore, drought stress and silver Nanoparticles up to 55ppm increased bch gene expression and carotenoid production.
Tissue culture and Micropropagation
Pegah Moradi Dezfouli; Mohammad Sedghi; Mehran Enayati Shariatpanahi; Bahram Alizade
Volume 7, Issue 18 , November 2017, , Pages 1-14
Abstract
In this research, Hayola F1 hybrids were used to produce rapeseed doubled haploid lines using microspore embryogenesis. To study general combining ability (GCA) of, the induced doubled haploid (DH) rapeseed lines, a top cross analysis was conducted using 28 doubled haploid lines and top cross parent ...
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In this research, Hayola F1 hybrids were used to produce rapeseed doubled haploid lines using microspore embryogenesis. To study general combining ability (GCA) of, the induced doubled haploid (DH) rapeseed lines, a top cross analysis was conducted using 28 doubled haploid lines and top cross parent of Hayola 420. Produced hybrids of doubled haploid lines × Hayola 420 were sown in research farm in 2015 growing season. Plant height, number of pods per branch and sub branches, number of seeds per pod, pod length, number of sub branches, length of main branch, 1000-seeds weight, single plant yield, number of days to flowering, number of days to seeding, number of days to physiological maturity, and oil yield were recorded in all top cross progeny to investigate GCA of DH lines. Results of analysis of variance showed a significant difference among all top cross hybrids for all investigated traits at 1% probability level. Based on means comparison analysis using multiple range Duncan test at 1% probability level, top cross hybrids of DH1, DH8, DH10, DH11, DH13, and DH21 were more differ than other top cross hybrids for all investigated characteristics. The highest mean of seed yield and oil yield was related to the top cross progeny of DH21 × Hayola 420. Results of top cross analysis showed that the highest positive and significant GCAs for single plant seed yield, number of pods per plant, and 1000-seeds weight were corresponded to DH1, DH10, and DH21, therefore these three DH lines can be used as elite parental lines in future breeding programs of rapeseed.
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
Bioinformatics
Hajar Nasrollahi; Farshid Talat; Iraj Bernousi; Mehdi Badri Anarjan
Volume 7, Issue 20 , March 2018, , Pages 1-12
Abstract
Diploid genome contains 8 genomes designated as A, B, C, D, E, F, G and K which have been identified in the genus Gossypium. The genome of A is limited only in two species as G. herbaceum and G.arboreum, and it is transferred from G. herbaceum to other species. The chloroplast genome (CP) of G. herbaceum ...
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Diploid genome contains 8 genomes designated as A, B, C, D, E, F, G and K which have been identified in the genus Gossypium. The genome of A is limited only in two species as G. herbaceum and G.arboreum, and it is transferred from G. herbaceum to other species. The chloroplast genome (CP) of G. herbaceum has 160,140 bp lengths with protected quadripartite structure. Single copy regions of chloroplast genome are separated by two inverted repeat regions with a large copy region with 88,709 bp also the single copy region and each small inverted repeat regions have 20,221 and 25,605bp. The plastidic' s genome has 113 single copy genes and 19 duplicated copy genes. Single copy genes are encoding of 79 genes for protein production, four ribosomal RNA genes and 31 transfer RNA genes. Result showed that among all plastid genes only 18 genes appeared to have 1-2 intron/s and when compared with chloroplast genome of two allotetraploid species. Ycf15 gene as the only duplicated gene, rpl22 was in G. herbaceum and in the two species has studied G. herbaceum, G. barbadense. But ycf15 gene in G. barbadense and both ycf15 and rpl22 genes were lost in G. barbadense and G. hirsutum. Though the high level of SSR protection in the chloroplast genome. SSRs are useful for genetic variation analysis since they have high efficiency against genomic SSRs.
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).
Molecular Plant Breeding
Seyed Sajad Sohrabi; Ahmad Ismaili; Farhad N azarian Firouz-Abadi; Hossein Fallahi
Volume 8, Issue 22 , September 2018, , Pages 1-14
Abstract
Development and improvement of lentil breeding programs to deal with adverse environmental factors in comparison to other legumes has more challenges due to poor pool of genetic resources. EST-SSR (EST-Simple Sequence Repeats) markers are one of the most commonly used molecular markers in many plant ...
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Development and improvement of lentil breeding programs to deal with adverse environmental factors in comparison to other legumes has more challenges due to poor pool of genetic resources. EST-SSR (EST-Simple Sequence Repeats) markers are one of the most commonly used molecular markers in many plant breeding programs due to polymorphism in genes coding regions. Hence, in the present study, for the development of EST-SSR markers, assembly process of RNA sequences of lentil under cold stress and normal condition was used. In order to apply cold stress, lentil plants treated at 4 °C condition. Total RNA was extracted from plant samples and was sequenced. 8905 microsatellite locations in 7211 unigene derived from lentil RNA sequences data was identified that 1293 unigene of them contained more than one SSR marker location. The most abundant type of EST-SSR marker was found to be of single nucleotide type. In this study, A/T, AG/CT and AAG/CTT motifs had the highest frequency among the one, two and three nucleotide motifs, respectively. The results of blast of unigene containing SSR showed that 80% of the unigenes had a similar record in the non-redundant protein database. The functional annotation of the unigenes showed that unigene containing SSR marker are subordinate to the critical stress-responsive terms such as binding, cell, cell parts and metabolic. Also, according to the results of this study, it can be stated that most of the identified EST-SSR markers were found in genes that play an important role in responding to cold stress, and UTR regions is often possible position. Hence, more analysis of these areas in candidate gene transcripts in response to cold stress is more important.
Bioinformatics
Zahra Hajibarat; Abbas Saidi; Zohreh Hajibarat
Abstract
Flower initiation is an important factor influencing plant yield. Environmental factors significantly affect flowering initiation. Bioinformatic analysis was performed on MADS-box transcription factors which are considered as important components in the flower formation. Brachpodium is a new experimental ...
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Flower initiation is an important factor influencing plant yield. Environmental factors significantly affect flowering initiation. Bioinformatic analysis was performed on MADS-box transcription factors which are considered as important components in the flower formation. Brachpodium is a new experimental model which used to understand the genetic, cellular mechanism and molecular biology of plants. In this study, 43 sequences of Brachypodium MADS-box genes were analyzed using phylogeny relationships, conserved motifs, chromosomal location, detection of transcription factor binding sites, and amino acid composition. The aim of this study was to better identify molecular mechanisms related to flowering. In this study, results showed that MADS-box genes distribute on all Brachypodium chromosomes, while gene clusters were located on all chromosomes except chromosome five. Analysis of the amino acid composition revealed that lucine, serine, and glutamate, with the highest amount, and tryptophan, with the least amount, elicit appreciable flowering. Based on the phylogeny analysis the genes were divided to four clusters. Tajima test indicated the presence of balancing selection in MADS-box sequences and as a result polymorphism is conserved in the sequences. Thus, the total diversity in MADS-box genes were high. Overall, our results provided useful information for the survey of flowering response genes, thereby detection of molecular mechanism and intergenic relationships facilitate flowering pathway.
Biotic and Abiotic stress
Mohammad Mohsenzadeh Golfazani; Maryam Pasandideh arjmand; Mojtaba Kordrostami; Habibollah Samizadeh Lahiji; Hassan Hassani kumleh; Mohammad Hossein Rezadoost
Abstract
Increasing of reactive oxygen species (ROS) under iron toxicity is considered as one of the major constraints to rice production. In this study the alterations of SOD, GPX1 and MDHR expression level in two genotypes of rice, Pokkali (as tolerant) and IR64 (as sensitive) were monitored under different ...
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Increasing of reactive oxygen species (ROS) under iron toxicity is considered as one of the major constraints to rice production. In this study the alterations of SOD, GPX1 and MDHR expression level in two genotypes of rice, Pokkali (as tolerant) and IR64 (as sensitive) were monitored under different concentrations of iron levels [(0) (nonstress)], 100, 250, 400 and 500 mg/lit-1Fe-EDTA). The treatments were done when the plants were at 4-leaf stage and lasted for two weeks. Results showed that the expression levels of genes in Pokkali were higher than IR64. The expression level of SOD in IR64, increased at iron concentration increased, while it decreased at higher Fe-level. The expression level of GPX1 was increased in IR64, but decreased in Pokkali. The expression level of MDHR in IR64 was decreased at early stage of Fe-treatment, but then increased. Inversely, in Pokkali MDHR expression reduced constantly under Fe stress. Overall, the relative over expression of genes in Pokkali and presence of different expression levels of them between different concentrations of Fe in tolerant and sensitive genotypes indicate that the gene could remarkably effect on the tolerant level of pokkali by reducing ROS production under Fe-toxicity.
Bioinformatics
Zahra Aminfar; Babak Rabiei; Masoud Tohidfar; Mohammad Hossein Mirjalili
Abstract
Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol ...
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Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol phosphate (MEP) pathway in plastids. To perform a meta-analysis of two pathways of MVA and MEP, expression data of the microarray experiments in different tissues, developmental stages, biotic and abiotic stresses were used in Arabidopsis thaliana as a model plant. The transcriptom meta-analysis was carried out using Genevestigator as a large database containing transcriptomics data of GEO in NCBI and ArrayExpress in EBI. The results of the meta-analysis showed that the transcription of genes encoding the enzymes of MVA and MEP pathway did not coordinate and they had different expression patterns in developmental stages, various tissues and conditions. MVA pathway genes show the highest expression in the roots and reproductive organs, while the MEP pathway genes are expressed in photosynthetic tissues. The results obtained here can help to understand how the underlying pathway gene networks are organized and regulated in different conditions, tissues and developmental stages.
