Genetic Engineering and Gene Transformation
Zahra Ghorbanzadeh; Mehrbano Kazemi Alamouti; Leila Pourhang; Seyyed Mohammad Mousavi Pakzad; Elahe Moatamed; Mona Mapar; Aliakbar Ebadi; Mohammad Reza Ghaffari; Ghasem Hosseini Salekdeh; Behzad Ghareyazie; Motahhareh Mohsenpour
Abstract
Improvement of the root architecture lead to higher grain yield and seed quality. This is achieved via improvement of the plant growth, better establishment in soil, higher absorption of water and nutrition resulting in the biosynthesis of the essential amino acids and hormones. It increases the efficiency ...
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Improvement of the root architecture lead to higher grain yield and seed quality. This is achieved via improvement of the plant growth, better establishment in soil, higher absorption of water and nutrition resulting in the biosynthesis of the essential amino acids and hormones. It increases the efficiency of the nutrition usage and the stress tolerance. Drought conditions are a serious challenge in Iran; therefore, improving crop tolerance has a major importance. In this study, we investigate the presence of DRO1 gene, which is involved in the modification of the root growth angle, in rice cultivar Hashemi and compared to the Kinandang Patong cultivar. We further analyze the simultaneous presence of DRO1 and a second gene, OsCKX4, which is involved in the improvement of root structure. DRO1 and OsCKX4 are cloned together in a single construct under the control of the ubiquitin and the root specific promoters, respectively. The resulting construct, pUhrCkDro is transformed into the Agrobacterium tumefactions strain EHA105 and used for the gene transformation into Hashemi cultivar. Putative transgenic plants, survived on 50 mg. L−1 Hygromycin during tissue culture steps, are transplanted into the Yoshida solution and then into the pots until they set seeds. Construct specific and gene specific PCR analysis are used to confirm the transgenic plants. Transgenic plants show stronger root structure compared to the non-transgenic ones. Molecular analysis in the T1 and T2 generations leads to the homozygous events. The multi-genic construct used in this study, can be introduced into other crops for the aim of root structure improvement and drought tolerance. It is hoped that the production of transgenic rice with enhanced root structure results in improving drought tolerance, reducing water consumption and enhancing yield under drought stress conditions.
Plant Disease and Biotechnology
Son ay Baghdadi; Abdolhossein taheri; saeed nasrollahnejad; Farzad Aliramaji; leila fahmideh
Abstract
In order to detection and differentiation of two complications of disorder and lack of podding in soybeans, while visiting 185 soybean fields in Golestan and Mazandaran provinces, only from the summer cultivation of 17 fields from five different places in Golestan province, plants with signs of disorder ...
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In order to detection and differentiation of two complications of disorder and lack of podding in soybeans, while visiting 185 soybean fields in Golestan and Mazandaran provinces, only from the summer cultivation of 17 fields from five different places in Golestan province, plants with signs of disorder and the lack of acute podding were identified and 17 samples were selected from each field and sampling was done from the leaves or stems of the mentioned plants in order to extract RNA and DNA. Then, PCR was performed to detect nepovirus using the degenerate primer of nepovirus and to detect phytoplasma using a pair of general primers and a nested PCR test. The results of electrophoresis confirmed the amplification of the 1800 bp band in the general PCR, the 1250 bp fragment in the nested PCR related to phytoplasma, and also the amplification of the 640 bp band related to a nepovirus. Besides, no band of healthy plants was observed. at the same time, tissue grafting and mechanical inoculation were performed on GPX soybean benchmark plant using the mentioned samples and two types of symptoms appeared. From the sequencing of the disordered samples (production of a small number of seeds and small pods), Tomato ring spot virus strain ep31_63026 and from the sequencing of the samples with non-encapsulation (grassiness and no formation of pods and seeds), Aster yellows phytoplasma from the 16SrI-B group were identified, which confirmed the results of the reference plant. The phylogenetic analysis of sequencing results confirmed the presence of Phytoplasma and Nepovirus only in the summer culture of samples that had symptoms of disorder and lack of podding.
Bioinformatics
Seyyed Mohsen Sohrabi; Ali Akbarabadi; Kamran Samiei; Anahita Panji
Abstract
Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present ...
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Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present study, by using transcriptome (RNA-seq) analysis followed by gene network analysis, the key genes involved in response to bacterial diseases were identified and their various characteristics were investigated. The results of the transcriptome analysis showed that bacterial pathogens have different effects on the transcriptome of tomato. Further analysis revealed 913 common differentially expressed genes among different bacterial treatments. Network analysis identified five key genes named large guanine nucleotide binding protein, mitogen-activated protein kinase 5, mitogen-activated protein kinase 7, heat shock protein 90 kDa and hop-interacting protein. Further analysis of identified key genes showed that all of them contain biotic stress related regulatory elements (w-box, WRE3 and WUN-motif) in their promoter region and have an important role in responding to biotic stresses. The key genes identified in this research can be used in classic breeding programs or in production of disease-resistant transgenic plants after a more detailed examination.
Keywords: Gene networks, Plant breeding, Plant diseases, Tomato, Transcriptome
Molecular Plant Breeding
Mohammad Hassan Kaffash Moghaddam; Forough Sanjarian; Alaeddin Kordnaeeje; Mehrdad Chaichi; Amir Mohammad Naji
Abstract
Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, ...
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Bread wheat is one of the most important crops in the world, which is essential in terms of global food security. However, its production is extremely compromised in agricultural regions affected by water deficiency during part of the growing season and mostly in the later stages of growth. Therefore, it is promising to identify the native drought-tolerant germplasms and molecular mechanisms used to enhance drought stress resistance. The aim of this study was to investigate the expression level of eight selected genes related to drought tolerance NCED, ABF, HKT, PAL, bHLH, ABC transporter and lipoxygenase in two native germplasms of Iranian winter wheat, one is sensitive and the other is drought tolerant. For this purpose, drought treatment was applied on native germplasms in a completely randomized design with three replications and two levels of treatment in the greenhouse. Selected gene fragments were amplified, gene expression was measured by Reverse Northern Blot and quantified using total lip software. Analysis of variance of the mean relative expression of each gene compared to the internal control gene showed that drought stress had a significant effect on the expression of all genes except bHLH gene. Biplot based on the first and second components made it possible to isolate genotypes in dehydration stress based on the expression of the seven genes evaluated. This method can be used in screening and identifying tolerant genotypes in landrace population of wheat.
Bioinformatics
Seyyed Hamidreza Hashemi-petroudi; Samira Mohammadi
Abstract
Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family ...
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Salt stress is one of the abiotic stresses limiting plant growth and development. The ethylene response factor (ERF) is one of the transcription factor family that involved in plant development and responses to biotic and abiotic stresses. Regarding to importance role of genes belonging to ERF gene family in plant responses to salt stress, identification of these genes in the Aeluropus littoralis, halophyte plant, was considered in this study. In total, 36 non-redundant ERF genes were identified in A. littoralis genome. The phylogenetic tree classified the AlERF gene family into six distinct groups (B1 to B6) based on hemology with the Araboidopsis thaliana. Gene structure analysis revealed that AlERF genes contained zero to two introns. Domain search and conserved motif analyses in AlERF protein sequences determined that 2 motifs (1 and 2) out of the identified 10 motifs participate in the AP2/ERF domain structure. Based on transcriptome data and heatmap diagram, AlERF6.3 gene was expressed more in root tissue under salinity stress, and the least expression level was observed in AlERF6.7 gene in leaf tissue under recovery conditions. The different expression patterns of genes in leaf and root tissues under salt stress suggested different regulatory mechanisms in the gene expression. The results of this study, as the first report on the ERF gene family in A. littoralis, provides basic information for further studies of the functional characteristics of AlERF genes.
Molecular Phsoiology
Armin Saed-Moucheshi; Fatemeh Sohrabi; Ali Shirkhani
Abstract
Reactive oxygen species (ROS) produced in organelles such as mitochondria, chloroplast, and peroxisome play an important role in plant signaling and signal transduction pathways. ROSs basically are able to regulate oxidation-reduction (known as redux) reactions, plant growth and defense responses to ...
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Reactive oxygen species (ROS) produced in organelles such as mitochondria, chloroplast, and peroxisome play an important role in plant signaling and signal transduction pathways. ROSs basically are able to regulate oxidation-reduction (known as redux) reactions, plant growth and defense responses to environmental stimuli. Therefore, they affect every aspect at all life cycle stages of plants. ROSs such as hydrogen peroxide, superoxide, hydroxyl radicals, and singlet oxygen act as secondary messengers in plant cells to regulate a diverse range of protein functions (with post-translational modifications) and gene expression. They are produced naturally during the plant responses to environmental conditions and intra-/inter-cellular communications. Recent researches are indicating that ROS compounds play a key role in the plants response under both biotic and abiotic stresses. Biotic stresses such as fungi, viruses, mites, insects and other organisms, along with abiotic stresses such as drought, salinity and heavy metals, increase the production of ROS in plant cells. Plants possess various mechanisms to deal with the destructive effects of ROS increased production. ROS removal in plants is usually performed by two main groups of enzymatic and non-enzymatic antioxidant molecules. Antioxidant molecules play important roles in plant tolerance under stressful conditions by neutralizing ROS and converting them into water molecules. However, under severe stress conditions, plants are not able to eliminate the entire content of extra produced ROS molecules; as a result, the high amount of ROS causes oxidative stress in plants leading to various damages to the main components of the cells, such as proteins, lipids, DNA, carbohydrates, and ultimately cell death. There are still many unanswered questions regarding the plant specific responses to oxidative stress and regulation of cell communication during stress conditions. This review article tries to introduce the origin, location, and pathways of ROS production along with their types and effects on the cellular signal transduction system in stimulating adaptive responses of plants under stress conditions. Moreover, this review discusses the effectiveness of antioxidants systems in maintaining cell homeostasis and neutralizing the negative impacts of oxygen free radicals in plants.
Bioinformatics
Maryam Ramezani; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Seyed Sajad Sohrabi
Abstract
Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds ...
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Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds biosynthesis pathways. MicroRNAs (miRNAs) play an important role in different processes such as growth and development, cell proliferation, response to stresses and biosynthesis metabolite. As far as the bioinformatic data are concern, the genome/transcriptome of kelus has not been sequenced. The present study was performed to identify the conserved miRNAs and their target genes in the kelus leaf transcriptome. After pair-end sequencing with the Illumina HiSeq 2500 platform, clean reads were assembled. In total, 4658 unigenes were found to contain potential miRNAs sequences. Following strict filtering criteria, five miRNAs belonging to five conserved miRNA families (miR156-3P, miR408, miR169, miR171 and miR398) were identified among candidate sequences. Results of this study revealed that the target genes of the identified miRNAs were involved in various metabolic pathways, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, peroxisome degradation, and fatty acid degradation. By affecting genes associated with six metabolic pathways, miR408 was identified as the most influential conserved microRNA in the kelus leaf transcriptome. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of kelus, these miRNAs can be used as candidate genes for breeding kelus quantitative and qualitative traits.
Bioinformatics
Mahin Pouresmaeil; Maghsoud Pazhouhandeh
Abstract
Today, the genome sequence of most organisms has been identified, and this information is useful in understanding the function and characteristics of organisms. In the meantime, there is unprocessed information that can be used to study unknown proteins and genes with the advancement of technology and ...
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Today, the genome sequence of most organisms has been identified, and this information is useful in understanding the function and characteristics of organisms. In the meantime, there is unprocessed information that can be used to study unknown proteins and genes with the advancement of technology and the use of bioinformatics tools. In this research, the sequence of a gene with unknown function from Arabidopsis thaliana with accession number of X91953.1 in NCBI database was used to investigate and study its structure and possible function. This gene is related to chromosome number one in Arabidopsis thaliana and with 676 base pairs, it produces a protein with 150 amino acids and a molecular weight of approximately 15 kD. By using bioinformatics servers, the characteristics of both gene and protein sequences were investigated and it was found that it has 18 types of regulatory motifs, the functions of some of which are known, which can be related to the response to light and the activity of Cis elements for expression in the meristem. The analyzes showed that this protein has 38 motifs, three of them are conserved with high frequency. This protein has a signal peptide at its Nt and is leaked into the extracellular space. Therefore, its presence in the intercellular space is more likely than the nucleus and intracellular organelles. There is also a regulation site of a microRNA on its transcript and this microRNA is active in response to salinity and also in the embryo. This unknown protein has about 90% homology with another protein in Arabidopsis with accession number of UPF0540 (At1g62000), which can be used for further studies to identify the role of the desired protein. This protein is expressed in 10 different tissues, mainly in embryo and seed endosperm. Based on all the analyzes carried out, two functions of seed coat differentiation and the biosynthesis of secreted substances due to light can be predicted for this protein. In the continuation of this work, laboratory methods are recommended for testing the functions attributed to this gene.
Molecular Plant Breeding
Leila Farhadi; Ali Arminian; sajad Rashidi Monfared
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific ...
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MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific name (Camelina Sativa L.) is an oil-medicinal plant belonging to the Brassicaceae family. First the RNA was extracted from C. sativa leaf and sent to the Beijing genome institute for RNA-sequencing. Then the data were assembled denovo with Trinity software after removing the reads with lower quality than the threshold level and trimming them. Detection of miRNAs was then performed by miRDeep2 software. Accordingly, we identified 33 miRNAs from the leaf dataset, and their secondary structures were evaluated. The target genes of the detected miRNAs were identified by the psRNAtarget website. Examining the target genes showed that a total of 1415 genes are regulated by these microRNAs, which belong to several gene families with different biological functions, including the genes of proteins that bind to the Squamusa promoter, the protein kinase family, etc. Comparing the expression of microRNA carrying genes (TPM) in the two studied doubled haploid lines, showed that except for miR296 and miR474 which were more expressed in line number 1, the other miRNAs had higher expression in line number 2. Considering the lower amount of oil production in line number 1 compared to line number 2, this indicates the relationship of these two microRNAs with oil production. miR483 was not expressed in any of the lines. miR113 and miR206 had the highest expression levels among all microRNAs. The higher expression of micro RNAs in line 2 probably indicates the higher activity of the silencing mechanism at the transcription level for the target genes in this line compared to line number 1.
Molecular Plant Breeding
nadali bagheri; zeinab Masoudi Jozchal
Abstract
Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) ...
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Grain length is one of the most important characteristics in rice breeding, which affects the yield and quality of the grain. In this study, the genetic diversity of grain length and width and 1000 seed weight were evaluated in the F2 population resulting from the crossing of L44 line (maternal parent) and IR-229R genotype (paternal parent). Also, molecular markers correlated with grain length were used to identify genotypes with longer grain length in the F2 population. The results of the evaluation of morphological traits showed that the average length of rice grain in the second generation L44 × IR-229R population is 11.16 mm, which is close to the average grain length in the mother genotype L44 (11 mm). Also, 10 genotypes showed longer seed length than the paternal parent, and among these genotypes, 6 genotypes (numbers 8, 10, 76, 82, 91 and 96) had greater seed width and 1000 seed weight than the population average. In the molecular evaluation, it was found that primers RM488 and RM234 (correlated with rice grain length on chromosome 1 and 7, respectively) showed polymorphism between parent’s genotypes. In examining the grain length trait with markers RM488 and RM234, genotypes 76, 82, 91 and 101 with grain length of 12.96, 12.66, 12.79 and 12.53 mm respectively were identified as long seed genotypes.
Bioinformatics
Zahra Pakbaz; Asa Ebrahimi; Martina Rickauer; Cecile Ben; Abdollah Mohammadi
Abstract
Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family ...
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Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family are scarcely known. Therefore, in this study we provided an extensive evaluation of MTP genes in three important members of this family including: Glycine max, Medicago truncatula and Phaseolus vulgaris by providing phylogenetic assessments, chromosomal distributions, gene structures and expression in different tissue. According to the results 14, 12 and 23 MTP genes respectively were found in M. truncatula, P. vulgaris and G. max. 13 duplicated MTP genes in G. max were found meanwhile we did not find any duplication in the MTP genes of M. truncatula and P. vulgaris. All studied MTPs were classified into three major cation diffusion facilitator (CDFs) groups; Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. In silico subcellular location results revealed that these proteins have the maximum activity in the vacuole in all three plants, and a small number are located in the cell wall and nucleus. According to gene structure and protein motifs of studied MTPs, they are highly conserved but their expression measurement showed that each one of them have different levels of expression during growth stage. It confirms their importance for plants during growth and development.
Medicinal plant Biotechnology
Mona Faraji Heriss; Mohammad Reza Vaezi Kakhki; Nasrin Mollania; Mohammad Armin
Abstract
Abiotic stress and callus formation can increase total phenolic content and antioxidant activity. The aim of this study was to increase the amount of total phenol and antioxidant activity in Securigera securidaca L. and its calli by ultrasonic stress in vitro conditions. The plants were grown in the ...
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Abiotic stress and callus formation can increase total phenolic content and antioxidant activity. The aim of this study was to increase the amount of total phenol and antioxidant activity in Securigera securidaca L. and its calli by ultrasonic stress in vitro conditions. The plants were grown in the greenhouse. Callus formation was performed with MS culture medium containing α-naphthalene acetic acid (2.2 mg/L) and 6-Benzylaminopurine (8.8 mg/L). Ultrasonic stress was applied to the main plants for 10, 20 and 30 minutes in 15 days in vitro conditions; in addition, the ultrasonic stress was applied to the calli for 10 minutes at the same time. The samples were collected on the first, fifth, tenth and fifteenth days. The samples were then dried in an oven, then their ethanolic extract was prepared. Total phenol content and antioxidant activity tests were performed by Folin-Ciocalteu and Wu methods respectively on the leaves of the main plant and its calli. The results showed that the amount of total phenol in the 30 minutes on the first day of ultrasonic treatment is higher than the control. In all treatments, antioxidant activity was reduced compared to the control sample. The highest amount of phenol was observed in calli in ultrasonic stress treatment on the 15th day. Antioxidant activity was reduced in calli under ultrasonic stress compared to the control sample. Therefore, it can be concluded that ultrasonic stress in the samples of this experiment increased the amount of phenolic but did not affect the antioxidant activity. Callus formation and ultrasonic stress also increase total phenol content simultaneously.
Tissue culture and Micropropagation
Zeinab Chaghakaboodi; Mahdi Kakaei; Alireza Zebarjadi; danial kahrizi
Abstract
Rapeseed (Brassica napus) is recognized as one of the most important oilseed crops worldwide and its development of cultivation has received attention due to the importance of importing oil. The current study aimed to investigate the effect of drought stress on some Rapeseed genotypes under tissue culture ...
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Rapeseed (Brassica napus) is recognized as one of the most important oilseed crops worldwide and its development of cultivation has received attention due to the importance of importing oil. The current study aimed to investigate the effect of drought stress on some Rapeseed genotypes under tissue culture and field conditions and to identify stable genotypes in the field. The possible responses of 14 different canola genotypes to Callus induction resulting from Hypocotyl cultivation and evaluation their drought tolerance were studied using Polyethylene Glycol 6000 (PEG 6000) at five different levels, including zero (as control), 10%, 20%, 30%, and 40% PEG concentrations based on a completely randomized design (CRD) with three replications. Measured traits included relative growth rate, growth rate, relative water content, and proline content of the Callus. Furthermore, in the field sector, the genotypes were investigated in four environments (two consecutive years in 2016-2018 under rainfed and irrigated conditions) based on randomized complete block design with three replications. According to the Callus culture results, the assessed traits, except the Proline content of Callus, decreased with increasing stress level. In laboratory conditions, genotype number seven (Dante) was introduced as the superior genotype. The results of Additive Main effects and Multiplicative Interaction (AMMI) analysis showed the significance of both additive effects of genotype and environment and the multiplicative effect of genotype × environment interaction. The results of cumulative additive effects (decomposition of variance) and multiplicative interaction effects (decomposition into principal components) showed that the first two components explained 53.02 and 33.65% of the variance of the interaction effect for oil yield. Dante and SLM-046 genotypes were introduced as stable genotypes.
Biotic and Abiotic stress
Arezoo Asl alizade; Mahmoud Toorchi; Ali Bandehhagh
Abstract
Salinity is one of the most important environmental stresses that disrupt the natural growth of plants. Plant use different mechanisms to cope with stress conditions, such as salinity, in which changes in protein expression is the most important one at molecular level. Changes in protein expression depends ...
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Salinity is one of the most important environmental stresses that disrupt the natural growth of plants. Plant use different mechanisms to cope with stress conditions, such as salinity, in which changes in protein expression is the most important one at molecular level. Changes in protein expression depends on their physicochemical changes such as half- life, stability index, iso-electric point, molecular weight, extinction coefficient etc. Furtermore, identification of motifs, patterns and protein domains make it possible to predict changes in the conformation, structure and proteins functions. In this research was selected a number of changed protein in expression under salinity stress in wheat based on the previous proteomic studies for further was selected bioinformatic analysis. Study Physicochemical properties of proteins by ProtParam software, identification of domains by InterProScan and CDD, identification patters for prediction of post translational modification by ScanProsite, similarity by Blast, alignment of similar proteins for identification of conserved block was performed by T-Coffee. Out of the 25 proteins associated with salinity stress, 20 proteins have a half-life more than 20 hours. The molecular weight of these proteins was varied between 13 to 117 kDa and 15 protein showed instability index of less than 40 and therefore classified as stable proteins. Investigation of proteins using TMHMM and Protscale softwares, it was found that Aquaporins, Plasma membrane intrinsic proteins, Plasma membrane ATPase and Rust resistance kinase Lr10 are highly hydrophobic proteins, whose major structure located inside the membranes. Out of 25 proteins, 8 proteins were selected and analyzed for identification of patterns, domains, structure and function. α-tubulin as a monomer participates with -tubulin to make α-tubulin dimer. Tubulin create a major part of microtubules that are essential for cell growth and division. This protein consisted of one pattern, Tubulin subunits alpha, beta and gamma signature domain namly PLN00221. For the Triosphosphate isomerase protein, a domain called TIM, which is involved in the catalytic mechanism and for the Calmodulin protein a domain called PTZ00184 was identified which is a calcium binding domain. For the Putative glycine decarbixylase subunit a domain called PRK01202 has been identified that has carboxylase activity. For Cu/Zn superoxide dismutase protein the domain called as SOD is involved in the absorption of superoxide. For Fructose-bisphosphate aldolase protein, the catalytic converter domain was identified as PLV02455 and for Hsp 70- Hsp 90 organizing protein, STI1 domain was identified with ATPase property. For the 2- Cys peroxiredoxin BAS 1 protein, for the PRX-Typ 2 cys domain that plays an important role in regulating oxidation- cell reduction.
Biotic and Abiotic stress
Alireza Tarang
Abstract
Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression ...
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Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression of transcription factor genes DREB2A and ZFP252 at vegetative and reproductive stages were investigated in TH1 line (drought sensitive) and Neda (drought tolerant). Drought stress was induced by stopping irrigation at tillering and heading stages. Investigation of morphological traits showed tiller and panicle numbers as production indices were significantly higher in Neda cultivar than TH1 line. Real Time PCR Neda genotype showed a significant increase (3.217 expression ratio) in expression of transcript level of ZFP252 at vegetative stage under drought stress. This indicates the importance of this drought stress responsive gene in acquisition of drought tolerance in this genotype at this stage. Investigation of expression level changes in TH1 line showed significant increase in DREB2A and ZFP252 genes expression under drought stress at the vegetative stage. Gene expression analysis in this study suggesting that tolerant and sensitive plants may be using genetic regulations and different mechanisms to be exposed to stress conditions. Deciphering of these molecular mechanisms will aid to better understand stress tolerance and to select strategies for improving crop productivity facing climate change.
Molecular Genetics and Genetic Engineering
Seyede mehri Javadi; Zahra-Sadat Shobbar; Asa Ebrahimi; Maryam Shahbazi
Abstract
Drought is the most important environmental stress that reduces crop yield. Therefore, research toward developing tolerant varieties is of great importance. In this study, microarray data analysis was used for identification of drought stress responsive genes and relevant hub genes in the reproductive ...
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Drought is the most important environmental stress that reduces crop yield. Therefore, research toward developing tolerant varieties is of great importance. In this study, microarray data analysis was used for identification of drought stress responsive genes and relevant hub genes in the reproductive stage of barley, and then their promoter analysis was performed. To achieve the goal, all the differentially expressed genes (DEGs) at drought conditions with fold changes ≥+2.5 and ≤-2.5 were identified between two microarray data-series in barley using FlexArray software. Bioinformatics analysis indicated that 559 genes were drought responsive at reproductive stage. The hub genes were distinguished using three Cyto-Hubba computational algorithms by Cytoscape software. Based on the hub analysis results, 10 unique (non-redundant) genes were identified as the most effective genes in response to drought stress. According to the gene ontology analysis of DEGs and hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) at drought tolerance mechanism. Amongst the hubs, several TFs such as HvCBF6, HvDRF1.3, LFL1, VP1, ABI5 and WRKY71 genes (belonged to AP2, WRKY and bZIP families) were observed. Promoter analysis was also revealed that some TF families including AP2, AT-hook family, bHLH, NAC, bZIP and MYB had binding site in 85% of promoters of the drought responsive genes and the hub genes in barley. Studying these transcription factors can help in better identification of drought tolerance mechanism in barley.
Mojgan shahivand; Reza Mir drikvand; masod gomarian; Kamran Samiei
Abstract
The Real-time PCR is a very powerful technique for the analysis of gene expression in various organisms. However, normalizing gene expression data and obtaining reliable results largely depends on the selection of stable reference genes. In this study, the expression stability of six general reference ...
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The Real-time PCR is a very powerful technique for the analysis of gene expression in various organisms. However, normalizing gene expression data and obtaining reliable results largely depends on the selection of stable reference genes. In this study, the expression stability of six general reference genes (EF-1α, 18S rRNA, ACTIN, β-Tubulin, HSP and GAPDH) was investigated in green and red cultivars of sweet basil under five abiotic stresses (cold, drought, heat, salt and light). The stability of these reference genes was analyzed using BestKeeper and NormFinder softwares. Results showed that all reference genes had different expression levels in both green and red cultivars of sweet basil. There was no significant difference in expression between green and red cultivars. The highest and lowest expression levels were calculated for β-Tubulin and 18S rRNA reference genes, respectively. The results of BestKeeper software identified HSP and ACTIN genes as stable reference genes, respectively. The NormFinder software identified β-Tubulin genes as stable reference gene. Final ranking of the results of BestKeeper and NormFinder softwares identified ACTIN gene as the most stable reference gene for the gene expression studies in green and red cultivars of sweet basil using real-time PCR.
Genetic Engineering and Gene Transformation
Mohamad Amin Neycee; Motahhareh Mohsenpour; Hassan Rahnama
Abstract
Safflower with low oleic acid content is one of the native plants of Iran. Generally,, high oleic acid oils have more oxidative stability than the oils with high linoleic acids . Genome editing technology enable us to obtain oilseeds with high oleic acid. In this research, two guide RNA sequences ...
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Safflower with low oleic acid content is one of the native plants of Iran. Generally,, high oleic acid oils have more oxidative stability than the oils with high linoleic acids . Genome editing technology enable us to obtain oilseeds with high oleic acid. In this research, two guide RNA sequences were designed to target of Fatty Acid Desaturase 2 (FAD2-1) gene, which were located within the coding region and at a distance of 640 base pairs from each other. The guide sequences along with the codon optimized Cas9 gene were cloned in the T-DNA region of the Agrobacterium construct and transferred to the safflower by the In-planta method. The resulting seeds were cultivated and the plants were screened to track changes in the fatty acid profile of the seeds. The results showed that the amount of oleic acid in the seeds of one of the lines reached 53.14% on average. This line had four amino acid changes (L66F, N204D, S236A and I238V) at the same time. This is while the amount of oleic acid in the control plant was measured as 11.62% on average. The results showed that in the segregating generation, the change in fatty acid profile occurred in the line with homozygous amino acid change, and the heterozygous plants have the same oil profile as the control plants. Also, the results of this research can indicate the possibility of increasing the amount of oleic acid in oilseeds by changing the FAD2 enzyme sequence and without gene knockout.
Biotic and Abiotic stress
Ali Maleki; Leila Zarei; Sohbat Bahraminejad; Kianoosh Cheghamirza; Leila Akbari; Fardin Fatahi
Abstract
Germination is one of the most important stages of crop plant growth and proper germination in a wide range of environmental conditions is necessary for plant establishment. In this research, 20 varieties of Iranian barley and 24 varieties of European barley were used in three salinity levels (100, 200 ...
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Germination is one of the most important stages of crop plant growth and proper germination in a wide range of environmental conditions is necessary for plant establishment. In this research, 20 varieties of Iranian barley and 24 varieties of European barley were used in three salinity levels (100, 200 and 300 mM sodium chloride) and a control level (distilled water) in order to investigate the tolerance of salinity stress in the germination stage, as a factorial test based on a completely randomized design with three replications in the mushroom cultivation chamber with controllable temperature and light and sterile conditions in the Nosoud agricultural service center by a protein marker in the biotechnology laboratory of the agriculture and natural resources of Razi university. The results of analysis of variance of traits related to germination showed that the effect of salinity, cultivar and salinity × cultivar were significant for all traits. By increasing the salinity level from 0 to 300 mM, all traits and indices decreased except the average germination time. The germination percentage had a positive and significant correlation with the total seedling length, shoot length, seed germination index, average germination rate and germination rate index. Stepwise regression analysis of different traits with protein markers showed that there were 13 bands associated with different traits. The most significant correlation with traits was related to the 60 kDa marker which was related four indices of seed germ, average germination speed, shoot length and cleoptile length. After the validation studies and confirmation of the results, the identified markers can be used in marker-assisted selection for related traits.
Biotic and Abiotic stress
Khosro Mafakheri; Mostafa Valizadeh; Seyed Abolghasem Mohammadi
Abstract
Abiotic stresses, especially water deficit stress in plants, cause oxidative stress and as a result, they produce reactive oxygen species (ROS) and cause serious damage to the DNA, protein and internal structure of plants. Plants have enzymatic and non-enzymatic defense mechanisms and systems to deal ...
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Abiotic stresses, especially water deficit stress in plants, cause oxidative stress and as a result, they produce reactive oxygen species (ROS) and cause serious damage to the DNA, protein and internal structure of plants. Plants have enzymatic and non-enzymatic defense mechanisms and systems to deal with these stresses. Currently due to climate changes, Water deficit stress is one of the problems of agricultural production. Given the importance of molecular studies and molecular and enzymatic responses of plants under abiotic stress conditions, therefore, relative expression of catalase and DREB-2 genes were studied by RT-PCR and catalase enzymatic activity were studied in SC706 and SC260 genotypes. The experiment was performed as a split plot based on a randomized complete block design with three replications and three irrigation conditions of (normal irrigation, intermediate stress and severe water deficit stress) under field condition. Results of relative expression analysis of genes showed a significant difference between the treatments so that by increasing the intensity of water stress compared to normal irrigation, the amount of enzyme activity and relative expression of the studied genes were increased. Under severe and intermediate water deficit stress, compared to normal irrigation, DREB-2 gene showed the highest increase with 690 and 211% respectively. In this study, based on the activity of catalase enzyme and the expression of CAT genes, DREB2 of SC706 genotype had higher performance than SC260, more appropriate physiological-molecular behavior and more expression of genes, which indicates more tolerance of SC706 genotype than SC260. The stress conditions applied in this study are the results that can be used in molecular breeding programs of maize.
Bioinformatics
Solmaz Azizi; Nasser Zare
Abstract
Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in the apoptotic (programmed cell death) pathway and biotic and abiotic stress responses in plants. In the present study, we identified 95 LOX homologous genes from four Fabaceae species (Cicer arietinum, Glycine max, Phaseolus vulgaris, ...
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Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in the apoptotic (programmed cell death) pathway and biotic and abiotic stress responses in plants. In the present study, we identified 95 LOX homologous genes from four Fabaceae species (Cicer arietinum, Glycine max, Phaseolus vulgaris, Medicago truncatula), which could be divided into 9-LOX, 13-LOX type I, and type II subgroups according to their phylogenetic relationships with Arabidopsis, rice, barley, and foxtail millet. LOX genes are distributed unevenly across the chromosomes, and their coding enzyme is active in the cytoplasm and chloroplast. These genes are intron rich, have six to nine introns, and are conserved in gene structure and intron phase. All identified genes have the conserved lipoxygenase and PLAT/LH2 domains. Several cis-acting elements related to hormones and stresses, such as ERE, MYB, and MYC in the LOXs promoters, indicated the role of these genes in plant development and responses to environmental stresses. In addition, different miRNA molecules were identified that regulate the post-transcriptional expression of LOXs genes through cleavage or inhibition of translation. Transcriptome data-based gene expression analysis showed that Glycine max LOXs expression pattern differed under abiotic stress conditions, and GmLOX4, GmLOX21, GmLOX25, GmLOX5, GmLOX22, GmLOX24, GmLOX14, GmLOX16, GmLOX7, and GmLOX26 were highly expressed in response to salt, drought, cold and heat stresses, indicating that they can improve the tolerance of Glycine max to abiotic stress. This study provides valuable information for a better understanding of the function of LOX genes and further exploration of the LOX gene family in Fabaceae.
Biotic and Abiotic stress
Zohreh Hajibarat; Abbas Saidi; MohammadReza Ghaffari; Mehrshad Zeinalabedini
Abstract
Plants use a variety of strategies to cope with abiotic stress, depending on the species and the growth of the plant. Abiotic stresses such as drought is the most important stress that affects yield of agricultural products. In addition, drought stress is one of the main limiting factors in plant growth, ...
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Plants use a variety of strategies to cope with abiotic stress, depending on the species and the growth of the plant. Abiotic stresses such as drought is the most important stress that affects yield of agricultural products. In addition, drought stress is one of the main limiting factors in plant growth, it can also inhibit respiration, photosynthesis, and thus affects the growth and physiological metabolism of plants. Plants activate several mechanisms such as morphological and structural changes as well as the expression of drought-resistant genes, the synthesis of hormones and osmotic regulators to reduce drought stress. Drought accelerates grain leaf senescence, altering the expression of thousands of genes and ultimately affecting grain protein content and grain yield. However, the genotypic variability exists for drought induced disruption and tolerance in barley. In this review, the approaches can help for improving barley genotypes in response to drought stress through breeding and physiological traits, genetic engineering, and marker-assisted selection (MAS). We detected genes and proteins involved in response to drought-tolerance using proteomics, transcriptomics and metabolomics approaches. Also, the introduced Quatitatives Traits Loci (QTLs) related to yield and Stay green and physiological traits found in this study can be used for MAS in barley improvement for drought tolerance in the future. In particular, comparative studies of genetically diverse germplasm exposed to adverse conditions such as drought provide valuable insights into plant responses to stress and create information on biochemical pathways involved in adaptation to environmental limitations. Proper evaluation of omics data can help the biomarker discovery.
Plant Disease and Biotechnology
Behzad Naeimi Nezamabad; Fakhtak Taliei; Abbas Biabani; Hossein Sabouri; Masume Kheirgu
Abstract
Fungal leaf diseases are the most destructive factors to wheat (Triticum aestivum L.) yield. Therefore, identification of resistance sources to important fungal diseases is a great importance to increase wheat yield. In order to identify informative CBDP and SCoT markers for leaf rust, powdery mildew ...
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Fungal leaf diseases are the most destructive factors to wheat (Triticum aestivum L.) yield. Therefore, identification of resistance sources to important fungal diseases is a great importance to increase wheat yield. In order to identify informative CBDP and SCoT markers for leaf rust, powdery mildew and septoria leaf blotch disease, 63 wheat genotypes were planted through the augment design in agricultural research station of Araghimahaleh (Gorgan) during 2018-19. Clustering based on UPGMA, put the genotypes into 3 groups with 24, 17 and 22 individuals. Among the studied genotypes, genotypes No. 49 and 60 showed highest resistance to all three diseases. Association analysis showed that from 16 CBDP and SCoT primers, 99 bands produced in total, which 43 bands were polymorph. The maximum percent of polymorphism belonged to SCoT primers and the minimum polymorphism belonged to CBDP. SCoT11-2, CBDP 10-2 was shown significant correlation with all three diseases. SCoT21-3 was also significantly (P
Bioinformatics
Hadis Boroun; Amir Siahpoosh; Seyyed Mohsen Sohrabi; Mohammad Reza Nikbakht; Javad Ghasemian Yadegari; Mohsen Mohammadi; Seyed Sajad Sohrabi
Abstract
Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin ...
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Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin gene family members were identified and characterized from onion (Allium cepa L.) using bioinformatics and experimental methods. All snakin protein sequences were retrieved from NCBI database. The snakin consensus sequence was obtained from alignment of retrieved sequences. Then, the consensus sequence was aligned against the onion transcriptome using tBLASTn tool. The resulting sequences were analyzed to determine the full-ORF, and to prediction of functional domains, signal peptides, subcellular localization, physicochemical properties, amino acid frequency and anti-microbial activity. The complete coding sequence of snakin genes were amplified by PCR. Finally, the presence of seven snakin genes, with an average ORF length of 332 bp, were confirmed in onion. The high similarity of the onion snakin genes with homologous snakin genes belonging to other plant species in terms of nucleotide and protein sequences as well as structural was revealed by bioinformatics analysis. The results also showed that all identified onion snakins had the potential antimicrobial activity. Due to the potential antimicrobial activity of identified peptides, by producing these peptides in different expression systems, they can be used as new antimicrobial agents against human, animal and plant pathogens.
Mahdieh Shojaee; Razieh Sarabadani
Abstract
Immune system disorders have been recognized as a cause of the autism spectrum disorder (ASD). TNFα and IL-6 are significant markers of the ASD. Increased levels of these cytokines in the brain and blood of the ASD-engaged patients not only affect the immune system disorders but also contribute to many ...
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Immune system disorders have been recognized as a cause of the autism spectrum disorder (ASD). TNFα and IL-6 are significant markers of the ASD. Increased levels of these cytokines in the brain and blood of the ASD-engaged patients not only affect the immune system disorders but also contribute to many common behavioral abnormalities exhibited by such patients. In this research, we investigated the effect of the broccoli extract and its sulforaphane content on two immune system factors, namely TNFα and IL-6. For this purpose, with its effectiveness confirmed via gas chromatography – mass spectroscopy (GC-MS) and MTT assay, the broccoli extract was subjected to immune system induction to maximize the activity of the immune system factors. The cells were treated with the broccoli extract at three different dosages, namely 1, 1.5 and 2 mg of the cell per milliliter of the broccoli extract, enzyme-linked immunosorbent assays (ELISA) were performed for three treatment times, namely 1, 2, and 3 days. A comparison between the stimulated immune system cells without treatment against those treated with the 2 mg of broccoli extract for 3 days clearly demonstrated the effectiveness of the broccoli extract for attenuating the activity of the TNFα and IL-6 factors. It was also observed that higher concentrations of the extract and longer treatment time were more effective in reducing these two factors. In general, the results of the present experiment suggest the effect of broccoli extract on reducing the inflammation of the immune system caused by these two factors.
