Research Paper
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.
Research Paper
Medicinal plant Biotechnology
Faeze Aibabaei; Forough Sanjarian; Nima Ahmadi
Abstract
In the current study, the effects of three levels of methyl jasmonate concentration were studied on the hairy root cultures of Origanum vulgare. For this purpose, A. rhizogenes strain A13 was used to create stable hairy root lines from shoot explants. In this regard, two co-cultivation media (MS and ...
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In the current study, the effects of three levels of methyl jasmonate concentration were studied on the hairy root cultures of Origanum vulgare. For this purpose, A. rhizogenes strain A13 was used to create stable hairy root lines from shoot explants. In this regard, two co-cultivation media (MS and modified MS), two inoculation times (5 and 10 min) as well two concentrations of acetosyringone (0 and 100 µM) were attentively studied. Propagated hairy roots were treated with different concentrations of methyl jasmonate (0.1, 0.2, and 0.5 µM). Sampling after 24 and 96 h of methyl jasmonate application, the activities of antioxidant enzymes were evaluated. Moreover, the gene expression level of OvDXR and OvTPS2, two important genes involved in the MEP pathway, were studied using real-time PCR technique. The highest transformation rate was observed in the explants cultured modified MS which were incubated in the bacterial suspension with acetosyringone for 10 minutes. The biomass of hairy root cultures was significantly decreased by methyl jasmonate compared to control samples. In addition, the results indicated that the concentration of methyl jasmonate, harvesting time, and their interactions significantly affected the activity of catalase, peroxidase, and SOD enzymes. The expression of OvDXR significantly increased after 24 h of treatment by 0.2 µM methyl jasmonate, while in the same sample, the expression of OvTPS2 decreased noticeably. The expression of OvDXR and OvTPS2 genes was significantly increased by 0.5 µM methyl jasmonate after 96 h. The application of methyl jasmonate as an efficient elicitor in hairy root culture system of O. vulgare is suggested for the production of valuable metabolites.
Research Paper
Bioinformatics
Aboozar Soorni; Parnian Karimzadeh; Samira Dehghani
Abstract
Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed ...
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Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed to investigate the transcriptomes of T. daenensis, T. vulgaris, T. lancifolius, T. persicus, T. pubescens to identify key genes in the biosynthesis of monoterpenoids, chloroplast genes sequence and evaluation of similarities and differences among these species. For this purpose, total RNAs extracted from vegetative growth were sent to Macrogene of Korea for sequencing with theIllumina HiSeq 2500 platform. After assembling the sequences using various tools, the best results was selected and transcripts were documented in different databases. Then, according to the documented results, key genes responsible in the synthesis of terpenoids and chloroplast gene sequence were identified, and then phylogenetic relationships among species was investigated. According to the evaluation indicators, the best assembly was a product of Binpacker tools. Based on the results, the sequence of 10 genes involved in the synthesis of terpenoids was obtained. Interestingly, among the identified TPSs, most of the contigs were classified into the TPSb and TPSa classes of terpenoids. The sequence of 73 chloroplast genes was extracted from the transcriptome data and finally the phylogenetic relationship was evaluated according to 400, 70 bp of cpDNA. The study of phylogenetic relationships showed a close genetic relationship between T. daenensi and T.vulgaris which can introduce T. daenensis as an appropriate replacement for T. vulgaris in different purpose, especially in pharmacological applications. The results show that Z. multiflora can most probably be as one of the ancestors of Thymus, which is significantly different from Thymus species in terms of its genetic structure, especially the key genes of the terpene biosynthesis pathway.
Research Paper
Molecular Plant Breeding
Nasrin Akbari; Reza Darvishzadeh
Abstract
With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability ...
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With expensing the amount of data, speed and accuracy in breeding evaluations are very important. The multivariate statistical methods, such as GGE Biplot that reduce the data volume and computational complexity, help in this direction. The use of GGE is useful for introducing genotypes with high stability and performance. Therefore, in order to introduce a stable genotype with high adaptation to drought stress, 100 oilseed sunflower genotypes were evaluated in a 10×10 simple lattice design under normal and limited irrigation conditions during two successive years (2013-2014). The results of composite variance analysis revealed a significant difference among genotypes in terms of the evaluated agromorphological traits. Based on graphical evaluation of genotype × environment interaction using GGE Biplot in metan program under R, genotypes 57 (SDR19), 41 (F1250/03), 8 (254-ENSAT), 24 (8ASB2) and 26 (H049+FSB) were introduced as the best genotypes in terms of stability and performance. The genotype 8 (254-ENSAT) had the highest performance among all genotypes in all environments. Meanwhile, genotypes 26 (H049+FSB) had the highest performance in Y1D (First year-limited irrigation) and Y1N (First year-normal irrigation) environments, and genotypes 57 (SDR19), 41 (F1250/03) and 24 (8ASB2) had the highest performance in Y2D (Second year -limited irrigation) and Y2N (Second year -normal irrigation) environments. Based on the results, genotype with code number of 8 with high and stable performance can be used in all environments as a parent in the development of high-yielding and stress-tolerant hybrids. The results show that GGE Biplot is a useful statistical method to achieve practical and accurate results.
Research Paper
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.
Research Paper
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.
