Genetic Engineering and Gene Transformation
Nahid Ahmadi; Hasan Rahnama
Volume 3, Issue 4 , September 2013, , Pages 77-85
Abstract
Transient expression of foreign genes in plant tissues is a valuable tool for plant biotechnology and to shorten the time for gene functional analysis. Transient expression is a fast, flexible, simple and easy method that could be used in fully differentiated plant tissues. 2A11 promoter is a tomato ...
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Transient expression of foreign genes in plant tissues is a valuable tool for plant biotechnology and to shorten the time for gene functional analysis. Transient expression is a fast, flexible, simple and easy method that could be used in fully differentiated plant tissues. 2A11 promoter is a tomato fruit specific promoter whose expression occurs in fruit significantly. Cloning of fruit-specific promoter (2A11) is the main purpose of this study. 2A11 promoters were amplified from genomic DNA of tomato by PCR using specific primers. The promoter fragments were cloned into cloning vector PTZ57R/T. Recombinant plasmids were transferred into E. coli XLI-blue strain. Fragments of the interest were digested using restriction enzymes BamH1 and HindIII and were then purified and substituted in CaMV35S promoter in binary pBI121. Binary pBI121 was selected for cloning of 2A11 promoters as it is an ideal vector for agroinfiltration due to the presence of the CaMV35S promoter and the GUS reporter gene within its T-DNA region. Recombinant plasmids were transformed into Agrobacterium tumefaciens LBA4404 strain with freeze and thawing method. The expression of GUS gene was analyzed in tomato with agroinfiltration method. The results showed that, 2A11 promoter was found as efficient as CaMV35S promoter in expression of GUS gene specifically in tomato fruit. Then, we can use this promoter for tissue specific expression of recombinant proteins in tomato fruits.
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.
Molecular Plant Breeding
maasoumeh Habibi; Asadollah Abiar Fini; Neda Mirakhorli; Mohsen Mardi
Volume 3, Issue 5 , February 2013, , Pages 85-92
Abstract
Bread wheat (Triticumaestivum) is one of the most important world food crops that are exposed to many pathogen. During the previous expression-profiling experiments, in addition to major resistant genes to disease in wheat, some defense-related genes such as S-Like RNase gene have been identified. Here ...
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Bread wheat (Triticumaestivum) is one of the most important world food crops that are exposed to many pathogen. During the previous expression-profiling experiments, in addition to major resistant genes to disease in wheat, some defense-related genes such as S-Like RNase gene have been identified. Here to study expression pattern of this gene in several fungal wheat diseases, some bioinformatics and laboratory studied were performed. In bioinformatics studies, several microarray libraries infected with Fusarium, Spike blight and Stripe rust were considered. In laboratory experiments Septoria tritici bloth was studied. So the level of expression was measured at 8 time interval, from 0h to 6 days after inoculation by Mycosphaerella graminicola in Wangshuibai as a resistant wheat cultivar and Falat as a susceptible wheat cultivar by semi quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The results show that the maximum expression of this gene, depending on types of disease and resistant cultivars, is obtained up to 24 hours after the inoculation. Thus, according to this results it can be concluded that this gene plays an important role in resistance to diseases and ,along with the main gene, increase and maintain resistance to many fungal diseases in wheat. Also this gene was confirmed by Nucleotide Blast.
Cytogenetic
Mehran Gholami; Masoomeh Jamalomidi; Koorosh Falakro
Volume 3, Issue 4 , September 2013, , Pages 87-97
Abstract
Tea (Camellia sinensis L.) is an important beverage crops containing caffeine worldwide. Releasing cultivars with high yield and quality demands knowledge about tea genetics and cytogenetics. Karyotypical study of nine tea genotypes was carried out using squash method on root tips. The best microscopic ...
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Tea (Camellia sinensis L.) is an important beverage crops containing caffeine worldwide. Releasing cultivars with high yield and quality demands knowledge about tea genetics and cytogenetics. Karyotypical study of nine tea genotypes was carried out using squash method on root tips. The best microscopic slides was first obtained using root tip of tea cuttings pretreated by α-bromo Naphthaline for 8 h, fixed by farmer solution and then stained with hematoxilin. Eight morphological traits were taken into consideration, each within three meiotic chromosomes using Micromeasure software. Analysis of variance showed significant differences (1%) among genotypes, chromosomes and the interactions, for all of the measured parameters. All studied teas were diploid and had 2n=2X=30 metacenteric and submetacenteric chromosomes. Total length of chromosomes ranged from 1.10 to 4.42 μm. Also, in terms of total length of chromosomes, genotypes 4 and 8 had the highest correlation and genotypes 2 and 9 had the lowest. Moreover some cytogenetic statistics was used in order estimate the karyotypic symmetry of genotypes. The results obtained showed that the genotypes 1 and 2 had the most asymmetric and genotypes 3 and 8 had the most symmetric, based on the TF%. Ordination based on principal components analysis (PCA) revealed presented that more than 97% of total diversity with two components was described. Centromeric index and long arm length had the most roles in the components, respectively. Cluster analysis using UPGMA method, also grouped the genotypes in four clusters and 100 promising clones were separated from the others, similar to result of PCA Bi-plot, relatively.
Biotic and Abiotic stress
Behnam Bakhshi; Mohmmad Reza Bihamta; Ghasem Hosseini Salekdeh; Masoud Tohidfar
Volume 3, Issue 5 , February 2013, , Pages 93-102
Abstract
Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating ...
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Drought stress is one of the most important abiotic stresses that deteriorates rice agriculture of Iran. One of the best ways to establish drought stress tolerance in plants is miRNA mediated post transcriptional gene regulation. MiRNAs are small 19-24 nt regulatory RNAs and play important role in regulating plant gene expression in biotic and abiotic stress. In this study, we selected five miRNAs for promoter analysis and evaluation of differential expression of them under drought stress in roots. Three of them including miR162, miR169 and miR172 are conserved in many plants and the others including miR1425 and miR1880 are rice specific miRNAs. In addition, upstream screening of MIRNA genes showed that upstream region of some MIRNA genes like MIR172 are enriched with important regulatory elements like DRE and ABRE. Quantitative Realtime-PCR was used in this study for analyzing differential expression of evaluated miRNAs. Studying the differential expression of miRNAs in roots under drought condition showed that miR169 was up-regulated but conversely, miR172 was down-regulated. The rest of miRNAs in our study did not show significant differential expression under drought stress. It can be concluded that NF-YA and AP2 as the most important target genes for miR169 and miR172 respectively can play critical roles in response to drought stress. .
Tissue culture and Micropropagation
Hamed Ebrahimizadeh; Mahmoud Lotfi; Shiva Azizinia; Farangis Ghanavati
Volume 3, Issue 4 , September 2013, , Pages 99-108
Abstract
Production of haploid plants was studied in summer squash via induction of parthenogenic embryos. Female flowers were pollinated with anthers irradiated by different doses of gamma ray (25, 50, 75, 100 and 200 Gray) and induced embryos were rescued and cultured in specific medium. The results achieved ...
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Production of haploid plants was studied in summer squash via induction of parthenogenic embryos. Female flowers were pollinated with anthers irradiated by different doses of gamma ray (25, 50, 75, 100 and 200 Gray) and induced embryos were rescued and cultured in specific medium. The results achieved showed that the highest number of embryos was obtained in 50 and 75 Gray doses (82%), however, no embryo was produced at 200 Gray. Gamma ray doses and embryo stage had significant effect on frequency of embryo and plant regeneration. Highest embryo regeneration and haploid formation (27 plant regeneration and 11 haploids formation, respectively) were recorded at 50 Gray. All amorphous embryos produced only diploid plant, though 29.17, 33.33, 57.14, 66.67, 100 and 100 percent of plants derived from cotyledon, heart, torpedo, arrow-tip, torpedo-tip and globular embryos respectively, were haploid. Based on this study, out of the 7744 extracted seeds, 127 embryos and 44 plants were regenerated; among those 17 plants were identified as haploid plants using chloroplast counting, Flow-Cytometry technique and morphologic traits evaluations.
Molecular Plant Breeding
Ahmad Esmaili; Behnaz Talebi; Reza Drikvand; Mohammad Ali Ebrahimi; Tahmasb Hossienpour
Volume 3, Issue 5 , February 2013, , Pages 103-111
Abstract
In order to study of genetic diversity of barley genotypes, 14 pair’s primers of SSR were used in 20 genotypes. After genomic DNA extraction and PCR reaction, Primers produce 266 polymorph bands and mean of polymorph band per primer was 19. The highest value of polymorphic information content (PIC) ...
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In order to study of genetic diversity of barley genotypes, 14 pair’s primers of SSR were used in 20 genotypes. After genomic DNA extraction and PCR reaction, Primers produce 266 polymorph bands and mean of polymorph band per primer was 19. The highest value of polymorphic information content (PIC) belonged to Hvm60 and Hvm20 primers (0.88 and 0.73, respectively) and the lowest value of PIC was belonged to Bmac0032 primer (0.32) and mean of PIC for all primers were 0.6. Jacard similarity coefficient was calculated and ranged from 0.3 to 0.96 among genotypes. The highest genetic similarity (0.96) belonged to genotypes no. 6 and 5 and the lowest (0.3) was belonged to genotypes no. 13 and 10. Clustering dendrogram based on UPGMA method classified genotypes to 5 main groups. Results of PCOA classification were similar to results of cluster analysis. Evaluation of genotypes by SSR molecular marker could discriminate two row and six row genotypes and also hulled and hulless genotypes. In other hand the similar parents in pedigree of some genotypes (e.g. between 3 and 12 and between 14 and 18) had an important effect on this classification. Results of this study revealed that this molecular marker has a valuable potential for evaluation and discrimination of barley genotypes.
Reza Moradi; Samira Shabazi; Hossein Ahari Mostafavi; Mohammad Ali Ebrahimi; Hamed Askari; S. Mahyar Mirmajlesi
Volume 3, Issue 4 , September 2013, , Pages 109-117
Abstract
In this study, effects of gamma irradiation doses on spore germination of Trichoderma harzianum and its effects on morphological and antagonistic capability of the mutants to control Rhizoctonia solani have been evaluated. Spore suspension of Trichoderma was gamma-radiated by 0, 50, 100, 150, 200, 250, ...
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In this study, effects of gamma irradiation doses on spore germination of Trichoderma harzianum and its effects on morphological and antagonistic capability of the mutants to control Rhizoctonia solani have been evaluated. Spore suspension of Trichoderma was gamma-radiated by 0, 50, 100, 150, 200, 250, 300, 350, 400 and 450 Gry Gamma ray and the effects on mycelial growth were evaluated by irradiation with 0, 400, 800, 1200, 2000 and 2500 Gry. The results obtained showed that 450 Gry gamma radiations completely blocked the spore germination and 250 Gry was found as the optimum dose to induce mutation in Trichoderma. Furthermore, gamma irradiation could change the morphological characteristics such as: colonies shape and color, sporolation and mycelia growth rate. Dual culture test proved that, the mutated isolates had statistically more antagonistic capability against R. solani than its parental strains. According to the findings of the present study, bio-control capability of Trichoderma could be improved through gamma radiation.
Molecular Plant Breeding
Ehsan Mohseni fard; Mohammad Farsi; Ghasem Hosseini Salekdeh; Amin Mirshamsi Kakhki; Marayam Shahbazi
Volume 3, Issue 5 , February 2013, , Pages 105-115
Abstract
MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several ...
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MicroRNAs (miRNAs) play important roles in numerous processes in plants including development, tissue proliferation, differentiation, hormone signaling and responses to biotic and abiotic stresses. SPL, the plant-specific transcription factors, are regulated by miRNAs and play important roles in several processes including tissue development, response to biotic and abiotic stress and induction of several other transcription factors and membrane proteins. In this study we selected miRNAs that regulate SPL transcription factors expression in rice. Later, the differential expression of these miRNAs are evaluated using qRT-PCR and Stem-loop primers. Results of shoot differential expression under drought stress showed that miR529 was down-regulated but conversely, miR535 was up-regulated. However, significant differential expression of miR156 was not observed in our study. Likewise, root differential expression under drought condition showed up-regulation of miR535, but miR529 and miR156 did not show any significant differential expression. Although all of these miRNAs are involved in regulating the expression of the same genes, but their diverse differential expressions highlight the complexity of gene-regulatory networks in various environmental conditions. Based on results of this study, it can be suggested that compared to miR535, miR156 and miR529 play more important roles in regulating the development and flowering process via controlling SPL transcription factors whereas, miR535, miR529 and relatively lesser miR156 are responsible for SPL transcription factor regulation under stress.
Plant Disease and Biotechnology
Fatemeh Hosseini; Reza Pourrahim; Mojdeh Maleki; Shirin Farzadfar
Volume 3, Issue 4 , September 2013, , Pages 119-131
Abstract
Potato virus A is one of the most important viruses infecting potato in the world. During spring and summer of the year 2011, a total of 280 symptomatic and 463 random leaf samples, and 1186 tuber samples were collected from potato fields located in Khorasan-e-razavi and Markazi provinces, Iran and tested ...
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Potato virus A is one of the most important viruses infecting potato in the world. During spring and summer of the year 2011, a total of 280 symptomatic and 463 random leaf samples, and 1186 tuber samples were collected from potato fields located in Khorasan-e-razavi and Markazi provinces, Iran and tested for PVA infection using DAS-ELISA method. Based on the results obtained, PVA infection was recorded in 39 and 11 % of symptomatic leaf samples, 23 and 6 % of random leaf samples and 17 and 13 % tuber samples in Markazi and Khorasan-e-Razavi provinces, respectively. Morever, biological properties of the selected PVA isolates were studied using host range studies on 10 plant species. Four PVA isolates were selected and their coat protein (CP) gene was amplified by specific primers using RT-PCR and their nucleotide sequences were determined (KF152950-3). The CP sequences of four Iranian and 37 Non-Iranian (from other parts of the world) PVA isolates were compared and a phylogenetic tree was reconstructed using Neighbor Joining-NJ method with 1000 bootstrap value. The PVA isolates in the phylogenic tree were clustered in two main groups (I and II) where group I had two subgroups (IA and IB). Three Iranian PVA isolates (Ar2, Kh4 and F2 all from Markazi province) were grouped in IA subgroup and showed highest similarity with two isolates from Germany and Netherlands (Y11427 and X91968) and the other Iranian PVA isolate (Gh4 from Khorasan-e-Razavi P.) was grouped in IB subgroup showing the highest similarity with an isolate from China (DQ309063). Comparison of the deduced amino acid (aa) sequences of CP among the four Iranian and the other PVA isolates revealed substitution of 2 to 7 aa mainly in N terminal of CP. This is the first phylogenetic study on Iranian PVA isolates and also the first report of PVA infection in Markazi province. This study showed variation among PVA isolates in Iran. These data could to be considered in potato breeding programs in order to achieve PVA resistant cultivars.
Molecular Plant Breeding
Hossein Jafary; Mohammd Naghi Ansari; M.A. Ebrahami; Mehdi Taheri; Ebrahim Dorostkar
Volume 3, Issue 5 , February 2013, , Pages 117-127
Abstract
Peroxidase and Catalyse are two important enzymes involved in reaction of many crop species to salt tolerance. Assessment of activity of these enzymes in the seedlings of barley during salt stress and using quantitative data for mapping of QTLs involved in salt tolerance has been addressed in this study. ...
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Peroxidase and Catalyse are two important enzymes involved in reaction of many crop species to salt tolerance. Assessment of activity of these enzymes in the seedlings of barley during salt stress and using quantitative data for mapping of QTLs involved in salt tolerance has been addressed in this study. Parents of four barley mapping populations were exposed to the different concentrations (0 mM, 100mM and 200 mM) of salt (NaCl) and the level of activity of Catalase and Proxidase were quantified in the seedlings stage. There was a high variation in enzymatic activities of parents of OWB population (Dom and Rec) in 200mM of NaCl. In order to map QTLs involved in salt tolerance in OWB, 94 doubled haploid lines were exposed to 0 mM and 200mM of NaCl and the activity of Catalase and Peroxidase were quantified. Mapping of QTLs was performed using MAPQTL5 software. The results showed that the position of QTLs depends on both concentration of salt and on the type of enzyme. For Peroxidase activity there was no QTL mapped despite a high variation between individuals of mapping population while for Catalase in the concentration of 200 mM of NaCl, two QTLS in Chromomes 3(3H) and 4(4H) were mapped. Two other minor QTLs with LOD values slightly lower than the threshold were mapped in chromosomes 5(1H) and 7(5H). The results showed that quantification of the level of activity of Catalase can be used as quantitative data for mapping of QTLs involved in salt tolerance in barley
Genomics
Mohammad Ebrahimi
Volume 3, Issue 4 , September 2013, , Pages 133-148
Abstract
Today with appropriate understanding of economical, ecological, cultural and social importance of biodiversity, significant progresses have been made toward identification, quantification, finding distribution patterns and genetic relationships of this diversity. In addition, analysis of genetic variation ...
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Today with appropriate understanding of economical, ecological, cultural and social importance of biodiversity, significant progresses have been made toward identification, quantification, finding distribution patterns and genetic relationships of this diversity. In addition, analysis of genetic variation of various aspects such as distribution of allelic diversity, genetic structure and kinship relationships between and within populations, individuals and species is one of the main concerns in biological sciences. In this regard, and with respect to the importance of identification, preservation and maintenance of these genetic pools, to ensure the permanent existence of them and using those resources as a tool for facilitating management strategies and breeding processes, the efficiency of some different genetic and genomic methods including genome and transcriptome based microsatellites have been evaluated in some crop plants, i.e. saffron, and some species belonging to genus Prunus and Punica. Through the development of different molecular markers used in the above-mentioned studies, genome-based microsatellite markers have significantly improved our knowledge on the processes related to habitat segmentation and small populations, distribution of allelic diversity, patterns of germplasm management and finally genetic relationships in the field of genetic conservation. Recently, availability of next generation sequencing tools provided access to huge amount of transcriptomic and genomic sequences. This has allowed us to, a) investigate the diversity of gene functions caused by habitat segmentation, b) assess diversity of responses to biotic and abiotic stresses as well as environmental changes and, c) identify suitable markers to be used in studies such as marker-assisted selection. Here we discuss how the integration of genomic and transcriptomic variations backed up with new bioinformatic tools could improve the identification of relative influences of genetic and environmental threats and open up new frontiers in conservation studies.
Molecular Plant Breeding
Saeed Bagherikia; Ghasem Karimzadeh; Mohammad Reza Naghavi
Volume 3, Issue 5 , February 2013, , Pages 129-138
Abstract
The chromosomal arm 1RS of rye (Secale cereale L.) is a valuable resource for improving the properties of wheat (Triticum aestivum L.) which has been translocated with the short arm of a wheat group-1 chromosome (1AL.1RS, 1BL.1RS, 1DL.1RS). This arm carries rust resistance genes; Lr26 for leaf rust (Puccinia ...
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The chromosomal arm 1RS of rye (Secale cereale L.) is a valuable resource for improving the properties of wheat (Triticum aestivum L.) which has been translocated with the short arm of a wheat group-1 chromosome (1AL.1RS, 1BL.1RS, 1DL.1RS). This arm carries rust resistance genes; Lr26 for leaf rust (Puccinia triticina), Sr31 stem rust (P. graminis) and Yr9 for stripe rust (P. striiformis). These genes were located 6.6 cM from the Sec-1. This close linkage has been used as a marker for identification of rust resistance genes. In this study, the presence of Sec-1 was examined in 66 Iranian cultivars and 70 abroad regional accessions, using rye-specific primer “O-SEC”. The rust resistance gene by the presence of Sec-1 was verified in 15 (23%) Iranian cultivars and 2 (3%) abroad accessions. Moreover, because of the rye-specific primer can distinguish between 1AL.1RS and 1BL.1RS translocations, the presence of these genes were identified in 14 (21%) cultivars and 2 (3%) abroad accessions in chromosome 1B. Also among all cultivars and accessions, the presence of the resistance genes was verified in chromosome 1A of "Sholeh" cultivar (1.5%). On the whole, the presence of rust resistance genes in Iranian wheat cultivars appeared to be better than abroad wheat accessions. This is because many Iranian wheat materials are commercial cultivars and in their pedigree have cultivars carrying rust resistance genes. The results of this study can be used for the production of new wheat cultivars in breeding programs.
Molecular Plant Breeding
Nahid Raanaian; Ali reza Abbasi; Hassan Zeynali-Khanghah
Volume 3, Issue 4 , September 2013, , Pages 149-156
Abstract
Exposing plants to both biotic and abiotic stresses could lead to increased reactive oxygen species and in turn could induce oxidative stress. In order to increase scavenging capacity of oxidative agents, the different plant antioxidant activities also are arising. Among those, vitamin E includes a group ...
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Exposing plants to both biotic and abiotic stresses could lead to increased reactive oxygen species and in turn could induce oxidative stress. In order to increase scavenging capacity of oxidative agents, the different plant antioxidant activities also are arising. Among those, vitamin E includes a group of Fat-soluble antioxidants, which their synthesis is limited to photosynthetic organisms including plants, alga and cyanobacteria. In this study, the coding region of Arabidopsis Tocopherol cyclase gene; which catalyzes 2,3-dimethyl-5-phytyl-1,4-benzoquinone (DMPBQ) into γ –tocopherol; was introduced into pBin vector containing the coding region of GFP protein. Then, the obtained construct was transformed into tobacco plant through agrobacterium-mediated method. Leaves of 2-3 weak old seedlings were selected as explant and direct regeneration was performed. In order to confirmation of transgenic plants, PCR by using specific primers was carried out. Due to the fact that the pBin vector contains the kanamycin resistant gene, seeds belonging to the T0 transgenic plants were planted on medium containing kanamycin and green seedling were selected as transgenic T1 plant. In order to evaluate the effects of transferred gens on physiological parameters, mature T1 transgenic plant as well as the wild type plants were subjected to drought stress and relative water content was measured.
Molecular Plant Breeding
Ahmadreza Masomi; Hossein Askari; Abbas Saeidi; Masood Soltani-Najafabadi
Volume 3, Issue 5 , February 2013, , Pages 139-146
Abstract
Soil and water salinity is one of the limiting factors for rice cultivation in the worldwide. Among crops, rice is very sensitive to salinity but the sensitivity is higher at the seedling and heading stages. Study of gene expression patterns besides away of cellular proteins function, could be useful ...
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Soil and water salinity is one of the limiting factors for rice cultivation in the worldwide. Among crops, rice is very sensitive to salinity but the sensitivity is higher at the seedling and heading stages. Study of gene expression patterns besides away of cellular proteins function, could be useful to create of resistance plants to stress such as salinity. In this study, expression of the Coumaroyl coenzyme A -3hydroxylase (C3H) gene and physiological processes was surveyed under salinity stress in Oryza sativa cv. IR65192-4B cultivar, by Complete Randomized Design (CRD) in three replicates and qRT-PCR technique. Physiological results showed that, salinity stress reduced root length in 100mM but not significant in 0 and 50 mM NaCl. In addition, reduction of root dry weight was significant under salinity. On the other hand, data analysis of C3H gene expression shown, expression altered in differentages of the rice roots under one level of NaCl, and also, is variable in one age but in different of NaCl concentrations. Weak gene performance in one branch can lead the loss of other branches efficiency. Therefore, this point must be consider to create of salt resistance plant because can play a major role in overall resistance.
Bioinformatics
Mozhdeh Arab; Hamid Najafi zarrini; Ghorbanali Nematzadeh; Seyyed Hamidreza Hashemi-petroudi
Abstract
Calcium-dependent protein kinase (CPK), as a member of Ser/Thr kinases superfamily, plays a vital role in responding and adapting to biotic and abiotic stresses. The halophyte plant, Aeluropus littoralis, has been considered an attractive model to improve genetic resources of crops and plant stress genomic ...
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Calcium-dependent protein kinase (CPK), as a member of Ser/Thr kinases superfamily, plays a vital role in responding and adapting to biotic and abiotic stresses. The halophyte plant, Aeluropus littoralis, has been considered an attractive model to improve genetic resources of crops and plant stress genomic research. In order to identify the A. littoralis CPK gene family, the whole genome sequences were used to analyze the phylogenetic relationships, exon/intron structure, protein motif/domain organization and the prediction of protein-protein interaction networks. Fourteen AlCPK genes were identified in A. littoralis that were homologous to nine Arabidopsis thaliana CPK genes. The protein domain analysis of AlCPK showed that all studied genes belong to the CPK family due to having several EF-hand (except for AlCPK29.2, which does not have an EF-hand domain) and Kinase domains. AlCPK29.2 protein had the lowest molecular weight and aliphatic index, the highest instability index and gravy among the studied proteins. Gene structure analysis showed that most of AlCPKs (69.8%) have more than seven exons. Besides, AlCPK8 protein was predicted with two N-myristoylation and two palmitoylation motifs, while CPK34.1 protein lacked N-myristoylation, and palmitoylation motif and AlCPK5.1 protein had three palmitoylation motifs. Transcriptome analysis of 34 members of the AtCPK gene family in five abiotic stresses showed that AtCPK genes had diverse expression at different treatments, which could be evidence for AtCPK tissue/ stress-specific expression. The ABF4 gene was identified as one of the components of ABA signaling in AlCPK protein-protein interactions. The findings of this research can be used to classify the roles and pathways of the stress response by studying AlCIPK gene expression under different abiotic stresses.
Molecular Plant Breeding
Marjan Jannatdoust; Reza Darvishzadeh; Sattar Tahmasebi Enferadi; Maryam Monazzah
Abstract
Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways ...
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Salinity is a major abiotic stress that limits the growth and productivity of plants in many parts of the world due to increased use of poor-quality water for irrigation and soil salinity. Plant adaptation or tolerance to salinity stress involves alteration in physiological processes and metabolic pathways and activating molecular or gene networks. In this study, 2DE technique was used to identify proteins responsive to salinity stress in maize. Two maize lines with different responses to salinity stress; R10 (tolerant) and S46 (sensitive) were selected. In the eight-leaf stage, salinity stress treatment of 8 dS/m was applied to plants for 20 days and then leaf proteins were extracted. Spots with more than a 1.5-fold increase or decrease in their expression were isolated and sequenced by mass spectrometry. Functional classification of protein spots per line after MS/MS revealed that the differentlly expressed proteins have different metabolic activities. In the tolerant line (R10), 5 spots including Pyruvate orthophosphate dikinase proteins, ATP synthase subunit beta, Germin-like protein, Chlorophyll a-b binding protein, Triosephosphate isomerase, and 40S ribosomal protein, respectively showed an increased expression level. Moreover, in the sensitive line (S46), one spot showed an increased expression level that related to Proteasome subunit beta proteins, and two spots including Chlorophyll a-b binding protein and Ribulose bisphosphate carboxylase small chain protein showed a decreased expression level. The proteins identified in this study and the possible related biochemical pathways provide new information on the response of maize lines (R10 and S46) to salinity stress.
Bioinformatics
Alireza Payriz; Leila Nejadsadeghi; Daryoosh Nabati Ahmadi
Abstract
MicroRNAs are main groups of small, non-coding molecules that regulate gene expression in animals and plants. Ajwain (Trachyspermum ammi) is plants known for their medicinal properties. To date, no miRNAs have beenidentified in T. ammi. Therefore, in the present study, a computational approach based ...
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MicroRNAs are main groups of small, non-coding molecules that regulate gene expression in animals and plants. Ajwain (Trachyspermum ammi) is plants known for their medicinal properties. To date, no miRNAs have beenidentified in T. ammi. Therefore, in the present study, a computational approach based on homology search through Blastx algorithm against mirbase database was used to predict miRNA and their target genes. The parameters of GC percentage, minimum folding free energy, minimum folding free energy index and secondary structure were determined and the sequences of miRNA precursor candidate were identified. In order to investigate the expression of selected genes using Real time PCR, an experiment was performed in a completely randomized design on the ajwain Arak ecotype at three levels of 0, 12 and 24 hours after methyl jasmonate application. A total of nine miRNAs including miR156, miR160, miR166, miR168, miR171, miR172, miR396, miR477 and miR827 were identified. It was estimated that they regulate 931 of T. ammi genes, which belong to several gene families with different biological functions. Jasmonate and its derivatives are plant signaling molecules. Therefore, miR160 and miR166 expression was evaluated by Real time PCR technique. The results showed that pri-miR160 and pri-miR166 was up-regulated in response to methyl jasmonate treatment, that indicated pri-miR160 and pri-miR166 were associated with hormone transfer.
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.
Bioinformatics
Anahita Panji; Ahmad Ismaili; Seyyed Mohsen Sohrabi
Abstract
Antimicrobial peptides are a part of the innate immune system in plants. They are present in all tissues and a wide range of plant species, and their antimicrobial effect against plant and animal pathogens and cancer cells has been proven. Snakins are a group of low molecular weight cysteine-rich plant ...
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Antimicrobial peptides are a part of the innate immune system in plants. They are present in all tissues and a wide range of plant species, and their antimicrobial effect against plant and animal pathogens and cancer cells has been proven. Snakins are a group of low molecular weight cysteine-rich plant antimicrobial peptides involved in the defense against biotic and abiotic stresses, hormone pathways, and plant growth and development. In the present study, laboratory and bioinformatic methods were used to investigate the characteristics of the snakin gene family members and to evaluate their expression changes in four seed development stages (3, 8, 13, and 18 days after pollination) in barley plants. The results showed the presence of 11 snakin genes in the genome of barley. The protein sequences of the identified snakins contained the GASA functional domain. These snakins had a signal peptide and had extracellular accumulation. Due to their high abundance of hydrophobic amino acids, they were hydrophobic and produced complex secondary structures. Phylogenetic analysis was performed between barley, rice, and arabidopsis snakins as two monocot and dicot models, leading to three classes. Also, six disulfide bonds and antimicrobial properties were computationally confirmed in all identified proteins. Expression analysis showed different expression patterns for snakin gene family members in different stages of seed development and also exhibited different trends in each stage. The snakin genes can use to produce transgenic plants and to produce a new generation of natural antibiotic agents to protect humans, plants, and animals.
Bioinformatics
Maryam Mehdizadeh hakkak; Masoud Tohidfar; Mohammad Hossein Mirjalili
Abstract
Squalane is an unsaturated triterpene that has wide applications in pharmaceuticals. In this research, the production of squalene and its bioinformatic analysis in four species of unicellular and multicellular eukaryotes and prokaryotes were investigated in order to determine the difference of this gene ...
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Squalane is an unsaturated triterpene that has wide applications in pharmaceuticals. In this research, the production of squalene and its bioinformatic analysis in four species of unicellular and multicellular eukaryotes and prokaryotes were investigated in order to determine the difference of this gene in eukaryotes and prokaryotes. The results of phylogenetic analysis showed that algae as multicellular eukaryotes, yeast as single-celled eukaryote and bacteria as single-celled prokaryote were placed in one group and plants were placed in a separate group. GC percentage of SQS protein was evaluated by GC Content Calculator, as well as aliphatic index and instability index by protparam. The results showed that the SQS gene is in a range from unstable to stable. The analysis of the presence of signal sequences and the analysis of the detection of the final location of the protein showed that the possibility of transferring the SQS protein to the mitochondria, chloroplast and secretory pathway is very low and it is not among the signal proteins. It was also found in Gymnema sylvestre that this protein has three protected domains. The comparison of the secondary structure of the protein confirmed the existence of alpha sheets. 3D modeling of this protein in plant was done by homology modeling method and using Swiss Model database after selecting a suitable model with high similarity which was extracted from PDB database. In order to validate the structure of the drawn three-dimensional model and stereochemical analysis, the Ramachandran diagram was drawn and the dihedral angles were calculated. The results of structural quality evaluation showed that the proposed models have good quality and stability. The study of the protein structure can help to understand the function of the protein, and studying the details of its structure can be useful in the studies of the active site of the protein and docking.
Plant Disease and Biotechnology
Abbas Saidi; Zahra Hajibrat; Ahmad Mosuapour Gorji; Rahim Ahmadvand
Abstract
Potato is one of the most important sources in the supply of food and industrial raw materials not only in Iran but also in the world which its yield is affected by various pathogens. Among these pathogens, PVY, PVX and nematode are the main factors of yield reduction. The molecular mechanism underlying ...
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Potato is one of the most important sources in the supply of food and industrial raw materials not only in Iran but also in the world which its yield is affected by various pathogens. Among these pathogens, PVY, PVX and nematode are the main factors of yield reduction. The molecular mechanism underlying disease resistance in potato remains largely unknown. In this study, analysis of gene expression profiles from the GEO data of three pathogen infections in potato was performed and morphological traits under four stresses were investigated. For this purpose, 501 common genes with different expression (DEGs) were studied in two experiments. Functional enrichment analysis showed that DEGs are more involved in nitrogen and primary metabolic cycle, GTP binding and GTPase binding, which are continuously up-regulated after inoculation with different pathogens. Based on the analysis of morphological traits under four stresses, PVY and PVX/PVY interaction left a significant difference with other stresses (PVX and nematode) on these traits. Potato microarray data extracted from GEO database were used for weighted gene co-expression network analysis (WGCNA). Based on the results of the network, 2 groups (modules) of genes were obtained whose expression profiles were highly correlated with each other in response to the above-mentioned four stresses. The results of this experiment provide valuable insight into the pathways and genes affected by PVY, PVX, PVX/PVY and potato nematode viruses, which may facilitate to identify genes resistant to many diseases in potato.
Bioinformatics
Aboozar Soorni; Sepehr Meratian Esfahani; Badraldin Ebrahim Sayed-Tabatabaei
Abstract
Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental ...
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Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental factors are changed to produce the most effective substance in medicinal plants, but in newer approaches that are based on plant genetics, higher yields are observed. One of these approaches is the use of miRNAs. These miRNAs control gene expression after transcription by mRNA analysis or inhibition of their translation, and play different roles in biological and metabolic processes in plants and animals. One of the simplest and least expensive methods for identifying miRNAs is the use of bioinformatics tools and methods. To identify distinct miRNA in different species of thyme, a study based on homology search was conducted using transcriptomic data of thyme. First, this information was refined and then aligament performed against all known miRNAs in the miRBase database. After screening of results based on factors such as length and e-value level, the secondary structure of miRNAs was analyzed with UNAfold tool. Target genes were identified using psRNATARGET tool and phylogenetic relationships were investigated using maximum likelihood method and RaxML tool. In total 64 distinct candidate’s miRNAs were identified in different species of thymus and 14 miRNAs included miR172 and miR396 played an important role in terpenes synthesis and it has been proven in previous studies. The phylogenetic tree was able to show the relationship between miRNAs in different species.
Bioinformatics
Masoud Tohidfar; Yousef Saeedi Honar; Naser Farrokhi
Abstract
Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of ...
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Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients.
Biotic and Abiotic stress
Navid Taherifar; Hengameh Taheri
Abstract
Heat stress has detrimental effects on the growth and performance of plants through biochemical, physiological, morphological, and molecular changes. Plants have developed complex mechanisms to balance growth and tolerance to stress, allowing them to effectively defend against more severe stresses by ...
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Heat stress has detrimental effects on the growth and performance of plants through biochemical, physiological, morphological, and molecular changes. Plants have developed complex mechanisms to balance growth and tolerance to stress, allowing them to effectively defend against more severe stresses by remembering mild stress and forming heat stress memory, known as thermopriming. To investigate the role of thermopriming in inducing the transcription response of HSFA2, HSFA1b and MIPS2 genes, the changes in the transcriptional level of the genes were studied at different times after priming and return stress in canola seedlings using the qRT-PCR technique. The results showed that the expression of these genes was not stable during the recovery period after the initial mild stress (memory phase), while their transcription level immediately after facing the second severe stress was induced at a much higher level in primed plants (P+T treatment) compared to non-primed plants (T treatment) which continued until 48 hours after return stress. Also, morphological analysis of seedlings at 7 and 14 days after release from the second stress showed that thermopriming increase the growth indices and heat tolerance in these plants through strengthening the expression of stress memory genes. Since the HSFA1b, HSFA2 and MIPS2 genes have maintained their expression level until days after the return stress, these genes can be the key components of the transcriptional memory of heat stress and be used in breeding programs and the development of heat tolerant varieties.
