Research Paper
Bioinformatics
Zahra Hajibarat; Abbas Saidi; Zohreh Hajibarat
Abstract
Flower initiation is an important factor influencing plant yield. Environmental factors significantly affect flowering initiation. Bioinformatic analysis was performed on MADS-box transcription factors which are considered as important components in the flower formation. Brachpodium is a new experimental ...
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Flower initiation is an important factor influencing plant yield. Environmental factors significantly affect flowering initiation. Bioinformatic analysis was performed on MADS-box transcription factors which are considered as important components in the flower formation. Brachpodium is a new experimental model which used to understand the genetic, cellular mechanism and molecular biology of plants. In this study, 43 sequences of Brachypodium MADS-box genes were analyzed using phylogeny relationships, conserved motifs, chromosomal location, detection of transcription factor binding sites, and amino acid composition. The aim of this study was to better identify molecular mechanisms related to flowering. In this study, results showed that MADS-box genes distribute on all Brachypodium chromosomes, while gene clusters were located on all chromosomes except chromosome five. Analysis of the amino acid composition revealed that lucine, serine, and glutamate, with the highest amount, and tryptophan, with the least amount, elicit appreciable flowering. Based on the phylogeny analysis the genes were divided to four clusters. Tajima test indicated the presence of balancing selection in MADS-box sequences and as a result polymorphism is conserved in the sequences. Thus, the total diversity in MADS-box genes were high. Overall, our results provided useful information for the survey of flowering response genes, thereby detection of molecular mechanism and intergenic relationships facilitate flowering pathway.
Research Paper
Bioinformatics
Parviz Heidari; Thomas Nussbaumer
Abstract
Next-generation sequencing (NGS) techniques such as RNA-Seq can provide expression information per gene and can be used to construct co-expression networks. These networks can produce valuable information to understand plant responses when facing environmental changes. In this study, a complete profile ...
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Next-generation sequencing (NGS) techniques such as RNA-Seq can provide expression information per gene and can be used to construct co-expression networks. These networks can produce valuable information to understand plant responses when facing environmental changes. In this study, a complete profile of tomato gene expressions under low temperature treatment was analyzed by “Weighted Gene Co-expression Network Analysis”. The clustering results allowed to group 20,267 genes into eight modules. The results of Gene ontology (GO) term analysis highlighted different functions between co-expression groups in terms of biological process and molecular function. Accordingly, the first module overrepresented to heat shock proteins (HSPs). Protein kinases and proteins involved in post-translational modification were in the second and third modules, respectively. The promoter of genes in fifth module was screened according to the different expression patterns in the tomato genotypes. The cis-elements such as ACGTG and TTGAC were observed in promoter site of all genes. The transcription factor families of AP2 / ERF and ZF-HD have the highest binding status in promoter of genes of the fifth module. The results present the key cis-regulatory elements that effect on co-expressed genes network and involve in anti-oxidant process under cold stress.
Research Paper
Biotic and Abiotic stress
Ahmad Ali Shoushi Dezfuli1 Shoushi Dezfuli; Ahmad Kalantar ahmadi
Abstract
Salinity is one the major problems for production and increasing the area under cultivation around the world and Iran. Understanding of defense mechanisms and genes involved could improve tolerance to different stresses in crops by using some methods such as genetic manipulation. Regulation in the gene ...
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Salinity is one the major problems for production and increasing the area under cultivation around the world and Iran. Understanding of defense mechanisms and genes involved could improve tolerance to different stresses in crops by using some methods such as genetic manipulation. Regulation in the gene transcription phase is one the most methods to control stress in plants. Transcription factors thought binding with transcription elements in DNA promoters regulate genes expression which plays a key role in tolerance to salinity stress in plants. An experiment was conducted to evaluate four genes expression of transcription factors of MYB (MYB14 and MYB112) and WRKY (WRKY53 and WRKY70) in leaf and root tissue of Yazdi genotype (tolerant genotype to salinity) and Diabloverde (sensitive genotype to salinity) under salinity stress. The selection of these genes was based on the statistical analysis of the microarray data that was related to a study on the effect of salinity stress on Medicago truncatula. Short-term salinity stress caused a significant variation in the expression of these genes in leaf and root tissues of Yazdi and Diabloverde genotypes. Real-Time PCR analysis revealed that higher expression of transcription factors (MYB112 and MYB14) associated with more tolerance to salinity stress. This finding could be assisted plant breeders to apply these transcriptional factors to choose tolerant genotypes to salinity in alfalfa.
Research Paper
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. ...
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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.
Research Paper
Molecular Plant Breeding
Maliheh Shahraki; Abbasali Emamjomeh; Baratali Fakheri; Bahman Fazeli-Nasab
Abstract
To evaluate genetic diversity between Sistan common wheat cultivars, it was used 10 SSRs primers associated to stem, leaf and yellow rusts resistance genes. The lowest (3) and highest (7) allele number were generated by 12C, SCS719 and Xgdm116 primers and Xgwm443 primer, respectively (4.55 allele per ...
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To evaluate genetic diversity between Sistan common wheat cultivars, it was used 10 SSRs primers associated to stem, leaf and yellow rusts resistance genes. The lowest (3) and highest (7) allele number were generated by 12C, SCS719 and Xgdm116 primers and Xgwm443 primer, respectively (4.55 allele per each primer). The highest genetic diversity (0.39) and MI (2.29) was related to Xgdm116 and Xgwm533 primers, respectively; also, the lowest genetic diversity (0.1) and MI (0.33) was related to Xcfd36 primer. Xgdm36 primer showed the highest Ne, Shannon diversity and Nei diversity (1.45, 0.63 and 0.44, respectively); on the other hand, Xcfd36 primer the lowest Ne, Shannon diversity and Nei diversity (1.18, 0.19 and 0.11, respectively). The highest polymorphic bands between wheat cultivars were related to Arg. Arg and Aflak showed the least diversity for resistance to yellow rust and leaf rust, respectively. Also, Arg had the highest diversity for three types of rusts. The Xgdm116, Xwmc810 and SCS719 primers had more effect on identification of wheat cultivars. Finally, Arg cultivar can be recommended as a donor parent in wheat breeding programs for rust resistance. To gain the highest heterosis, it can be suggested hybridization between Arg and Hirmand cultivars.
Research Paper
Biotic and Abiotic stress
Seyyed Hamidreza Hashemi-Petroudi; Hamidreza Ghorbani; Markus Kuhlmann
Abstract
Bioinformatic analysis plays an important role in the study of genes and the prediction of their function in response to stresses. Halophyte Aeluropus littoralis, a valuable genetic resource for identifying genes involved in plant tolerance to abiotic stresses. In this study, Phosphoglycerate Dehydrogenase ...
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Bioinformatic analysis plays an important role in the study of genes and the prediction of their function in response to stresses. Halophyte Aeluropus littoralis, a valuable genetic resource for identifying genes involved in plant tolerance to abiotic stresses. In this study, Phosphoglycerate Dehydrogenase (PGDH) gene as the first important enzyme in the synthesis of serine, was Isolated based on EST sequence from plant Aeluropus littoralis in salinity using by the RLM-RACE method. By overlapping the 3’ and EST sequences, a 1506 bp fragment including the ORF region (1268 nucleotides) and 3’UTR region (238 nucleotides) were obtained. The phylogenetic analysis of AlPGDH was done with other ortholog genes in different plants and its homologs were identified. Based on phylogram, the high degree of homology was observed between AlPGDH gene and other homologous genes from monocot cereals such as sorghum, foxtail millet and rice. The AtPGDH co-expression network analysis showed the important role of the PGDH gene in biosynthetic pathways, including amino acid synthesis, secondary metabolites synthesis and the pathway of glycine, serine and threonine metabolism, and its expression analysis indicated that the expression was increased in different stresses. The Phenotyping of the Arabidopsis knockout mutants for PGDH gene in NaCl and PEG stress condition indicated that the growth characteristics were significantly reduced in compared to the control plant, which could be confirmed the role of this gene in the response to salt and drought stress. The findings of this study reveal the functional characteristics of AlPGDH gene, phenotypic changes in AtPGDH mutant plants in exposure to salt and drought stress, and its possible role in increasing plant tolerance to stress.
