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 ...
Read More
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.
Molecular Plant Breeding
Somayeh Ebrahimi; Ahmad Ismaili; Seyed Sajad Sohrabi; Hasan Torabi Podeh
Abstract
Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock ...
Read More
Abiotic stresses, including drought in plants, lead to physiological and biochemical changes that are controlled by regulating gene expression. Transcription factors are considered as the most key molecular elements for regulating genes in response to biotic or abiotic stresses. The role of Heat shock transcription factors (HSFs) in the molecular mechanism of response to various abiotic stresses has been confirmed; therefore, this study used the analysis of RNA sequencing data to identify, classify and evaluate changes in HSF expression in lentil under water-deficit stress, and finally, the expression of some transcripts were examined using qRT-PCR. From the total assembled transcripts of lentil, 35 transcripts belonging to three HSF classes were identified. Also, according to the results, the expression of 14.28% of the identified transcripts, which often belonged to class A, is altered in lentil under water-deficit stress. The expression of 14.28% of the identified transcripts, most of which belonged to class A, is altered in lentil under water-deficit stress. In general, the results show that changes in the expression of some transcripts of one HSF gene take precedence over those of other transcripts of that gene in response to drought stress; therefore, it is of particular importance to study alternative splicing in response to this environmental factor in lentil. The HSF genes identified in this study can be used in future experiments to understand better the molecular mechanism of water-deficit stress tolerance in lentil.
Molecular Plant Breeding
Sajjad Zare; Farhad Nazarian-Firouzabadi; Ahmad Ismaili; Hassan Pakniyat
Abstract
Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought ...
Read More
Study of stress tolerance in barley can help for a better understanding of the genetic basis of drought stress tolerance mechanisms and lead to improve the genetic properties associated with drought tolerance through modern molecular genetic techniques. To this end, microRNAs associated with drought stress in barley leaf and root ESTs were analyzed in Nimruz and spantaneum barley genotypes. Bioinformatics databases were mined for relevant EST libraries and bioinformatics services were used for pre-processing and identify genes with different expressions among libraries. The expression profile of candidate genes was studied, by using Real time-PCR in a factorial-split plot design, including Nimruz as tolerant and Spontaneum as a drought sensitive in pots with three replications. Sampling time was also considered at 0, 24 and 72 hours after drought stress as sub factor. Results of this study led to identification of three highly-expressed miRNAs (ath-miR414, os-miR2102-5p and osa-miR414). The expression analysis showed that miR414 and miR2102 expression was significantly (P< 0.05) increased in both genotypes in response to drought stress. After 72h in Nimruz and Spontaneum, the expression of miR414 reached 2.61 and 2-fold and the expression of miR2102 was 2.4 and 2.8-fold of that of control (Spontaneum at control condition at 0 times), respectively.
Molecular Genetics and Genetic Engineering
Hadi Karimbeigi; Farhad Nazarian Firouzabadi; Saber Golkari; Ahmad Ismaili; Masoud Alirezaei
Abstract
Histamine, an important biogenic amine, is produced by many organisms and play a diverse role in living organisms. Many micro-organisms synthesis and stored histamine in food, especially in canned food products, posing health threat to human. Diamine oxidase or histaminase catalysis histamine in healthy ...
Read More
Histamine, an important biogenic amine, is produced by many organisms and play a diverse role in living organisms. Many micro-organisms synthesis and stored histamine in food, especially in canned food products, posing health threat to human. Diamine oxidase or histaminase catalysis histamine in healthy individuals and reduces its harmful side effects. In this study, a full-length cDNA encoding an amine oxidase was isolated from a chickpea (Cicer arietinum) landrace (grit), deposited in Genbank database (KU058599) and cloned in a binary expression vector. The cloned cDNA had an ORF with 2013 bp length encoding a protein with 670 amino acids and a molecular mass of 75.7 KDa. Multiple sequence alignments analysis showed that the active site and important amino acids are highly conserved in E.coli, pea and grit histaminases. Bioinformatics analysis revealed differences in 4 amino acids between grit histaminase and that of GenBank deposited Cicer arietinum amine oxidase (CAA08855). Phylogenetic analysis grouped grit histaminase (KU058599) with plant, especially legume histaminases with 99% bootstrapping.
Biotic and Abiotic stress
Seyedeh Zahra Hosseini; Ahmad Ismaili; Farhad Nazarian Firouzabadi; Hossein Fallahi; Abdolhossein Rezaeinejad
Abstract
Lentil (Lens culinaris) is one of the important grain legumes in feeding (as protein-reach food) and industry (such as biopolymer industry) and the problem of lower yield of this plant in Iran rather than average global yield is affected by exposure of plant to environmental stresses especially drought. ...
Read More
Lentil (Lens culinaris) is one of the important grain legumes in feeding (as protein-reach food) and industry (such as biopolymer industry) and the problem of lower yield of this plant in Iran rather than average global yield is affected by exposure of plant to environmental stresses especially drought. Identification of molecular markers that closely linked to drought resistant genes help to implementation of breeding programs aimed at the production of drought tolerant plants. The gol of this study was identification of EST-SSR markers which closely linked to the genes involved in drought resistance and use of these information in identification of drought resistant genotypes in breeding programs. PEG was used for stress treatment, and after conduction of treatments, leaf samples were collected. Total RNA was extracted and cDNA libraries were sequenced. Results showed that 10546 (16%) of uni-genes contained at least one EST-SSR and about 27.5% of these sequences were annotated. Among different SSR motif-classes, tri-nucleotide repeats (46.03%) were the most abundant followed by mono-nucleotide repeats (37.25%) and di-nucleotide repeats (15.18%). The results of the functional annotation of these sequences, showed that the highest number of EST-SSRs were belonged to subgroups of binding (872), catalytic activity (806), metabolic processes (755), and cell components (651), respectively.The results showed that genes associated with these markers, involved in important biological functions and are an appropriate tool for study the genes involved in tolerance to stresses including drought stress.
Molecular Plant Breeding
Seyed Sajad Sohrabi; Ahmad Ismaili; Farhad N azarian Firouz-Abadi; Hossein Fallahi
Volume 8, Issue 22 , September 2018, , Pages 1-14
Abstract
Development and improvement of lentil breeding programs to deal with adverse environmental factors in comparison to other legumes has more challenges due to poor pool of genetic resources. EST-SSR (EST-Simple Sequence Repeats) markers are one of the most commonly used molecular markers in many plant ...
Read More
Development and improvement of lentil breeding programs to deal with adverse environmental factors in comparison to other legumes has more challenges due to poor pool of genetic resources. EST-SSR (EST-Simple Sequence Repeats) markers are one of the most commonly used molecular markers in many plant breeding programs due to polymorphism in genes coding regions. Hence, in the present study, for the development of EST-SSR markers, assembly process of RNA sequences of lentil under cold stress and normal condition was used. In order to apply cold stress, lentil plants treated at 4 °C condition. Total RNA was extracted from plant samples and was sequenced. 8905 microsatellite locations in 7211 unigene derived from lentil RNA sequences data was identified that 1293 unigene of them contained more than one SSR marker location. The most abundant type of EST-SSR marker was found to be of single nucleotide type. In this study, A/T, AG/CT and AAG/CTT motifs had the highest frequency among the one, two and three nucleotide motifs, respectively. The results of blast of unigene containing SSR showed that 80% of the unigenes had a similar record in the non-redundant protein database. The functional annotation of the unigenes showed that unigene containing SSR marker are subordinate to the critical stress-responsive terms such as binding, cell, cell parts and metabolic. Also, according to the results of this study, it can be stated that most of the identified EST-SSR markers were found in genes that play an important role in responding to cold stress, and UTR regions is often possible position. Hence, more analysis of these areas in candidate gene transcripts in response to cold stress is more important.
Plant Disease and Biotechnology
Azam Badr Hadad; Farhad Nazarian Firouzabadi; Ahmad Ismaili; Hedayat Bagheri
Volume 7, Issue 19 , November 2017, , Pages 1-13
Abstract
Antimicrobial peptides are ancient and conserved molecules which are found in defense mechanisms of almost all living organisms from bacteria to animal and plant species. Identification and introduction of novel antimicrobial peptides, is a cost-effective way to improve crop plants resistance to pathogens ...
Read More
Antimicrobial peptides are ancient and conserved molecules which are found in defense mechanisms of almost all living organisms from bacteria to animal and plant species. Identification and introduction of novel antimicrobial peptides, is a cost-effective way to improve crop plants resistance to pathogens by using recombinant DNA technology. Therefore, an expression construct containing omiganan antimicrobial encoding gene from the cytoplasmic granules of bovine neutrophils, was cloned and transferred to the tobacco leaf disk using Agrobacterium tumefaciens mediated-transformation. The presence of the antimicrobial peptide encoding gene in the genome of transgenic plants was confirmed by PCR analysis. Six putative transgenic lines and a non-transgenic control plant were selected for further molecular analysis. Total protein was extract from transgenic and non-transgenic control plants and used for antimicrobial activity assay against some human; E. coli, Salmonella, Staphylococcus, Bacillus, and plant: Xanthomonas and Pseudomonas pathogens by disc diffusion method. Results of this experiment showed that total protein extract from transgenic lines, as compared to non-transgenic plant, was significantly (P
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) ...
Read More
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.
