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, ...
Read More
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
Abbas Saidi; Zahra Hajibrat; Ahmad Mosuapour Gorji; Rahim Ahmadvand
Abstract
Potato is one of the most important sources in the supply of food and industrial raw materials not only in Iran but also in the world which its yield is affected by various pathogens. Among these pathogens, PVY, PVX and nematode are the main factors of yield reduction. The molecular mechanism underlying ...
Read More
Potato is one of the most important sources in the supply of food and industrial raw materials not only in Iran but also in the world which its yield is affected by various pathogens. Among these pathogens, PVY, PVX and nematode are the main factors of yield reduction. The molecular mechanism underlying disease resistance in potato remains largely unknown. In this study, analysis of gene expression profiles from the GEO data of three pathogen infections in potato was performed and morphological traits under four stresses were investigated. For this purpose, 501 common genes with different expression (DEGs) were studied in two experiments. Functional enrichment analysis showed that DEGs are more involved in nitrogen and primary metabolic cycle, GTP binding and GTPase binding, which are continuously up-regulated after inoculation with different pathogens. Based on the analysis of morphological traits under four stresses, PVY and PVX/PVY interaction left a significant difference with other stresses (PVX and nematode) on these traits. Potato microarray data extracted from GEO database were used for weighted gene co-expression network analysis (WGCNA). Based on the results of the network, 2 groups (modules) of genes were obtained whose expression profiles were highly correlated with each other in response to the above-mentioned four stresses. The results of this experiment provide valuable insight into the pathways and genes affected by PVY, PVX, PVX/PVY and potato nematode viruses, which may facilitate to identify genes resistant to many diseases in potato.
Bioinformatics
Abbas Saidi; Zohreh Hajibarat; Mohammar Reza Ghaffari; Mehrshad Zeinalabedini
Abstract
Nitrogen is one of the most important components of biomolecules, amino acids, nucleotides, proteins, chlorophyll, and many plant hormones, which are essential and necessary for plant growth and development. In the condition of nitrogen deficiency very different responses such as yield reduction, leaf ...
Read More
Nitrogen is one of the most important components of biomolecules, amino acids, nucleotides, proteins, chlorophyll, and many plant hormones, which are essential and necessary for plant growth and development. In the condition of nitrogen deficiency very different responses such as yield reduction, leaf chlorosis, plant growth and root structure formation appears in phenotypes of plants. In the last decade, to increase the amount of biomass and as a result the yield of plants, a wide use of nitrogen has attracted the attention of researchers. In this study, the expression analysis of seven nitrate transporter genes (NRT2) was investigated in Arabidopsis in response to nitrogen deficiency stress at 4 and 7 days after this stress. The expression analysis of NRT2.3 and NRT2.4 genes showed increased expression at 7 days after applying nitrogen deficiency stress. But all the genes did not show a significant increase in expression at 4 days after N stress application. NRT2.4 gene showed a significant increase in 4 and 7 days after applying nitrogen stress compared to other genes. Overall, our results showed that increased nitrate transporter gene expression in leaves contributes to nitrogen uptake for plant growth and nitrogen accumulation in response to long-term low nitrogen stress. These findings can lead to a better understanding of the mechanism of low nitrogen tolerance and therefore the increase of other cultivars with nitrogen deficiency stresses.
Bioinformatics
Abbas Saidi; Zohreh Hajibarat
Abstract
Calmodulin is a regulated protein of calcium and is a small intracellular protein that binds to calcium ions and mediates many of its intracellular actions. Calmodulin-binding transcription factors (CAMTAs) are recognized as one of the stress-responsive proteins. In this study, CAMTA genes were selected ...
Read More
Calmodulin is a regulated protein of calcium and is a small intracellular protein that binds to calcium ions and mediates many of its intracellular actions. Calmodulin-binding transcription factors (CAMTAs) are recognized as one of the stress-responsive proteins. In this study, CAMTA genes were selected in maize. In this study, CAMTA family genes in maize were selected and chromosomal distribution, gene structure, domain patterns, and phylogenetic tree of CAMTA genes in maize were analyzed to further evaluate. To identify expression levels in different plant tissues, CAMTA gene expression analysis in response to heat stress and germination was studied. ZmCAMTA1 and ZmCAMTA2 genes were expressed in heat stress. Gene structure was similar in most proteins in each group, confirming the phylogenetic classification of CAMTA. Prediction of cis-elements in the promoter region of genes showed that bZIP and AP2 / ERF had the highest cis-elements in the promoter region of ZmCAMTA genes. In leaf tissue, ZmCAMTA1 gene was up-regulated expression in response to heat stress. ZmCAMTA2 gene was up-regulated in stem tissue in response to heat stress. The ZmCAMTA2 gene in response to increased expression germination showed that this study could be considered as a useful resource for future comparative studies of ZmCAMTA in different plant species and provide useful information for finding candidate genes in response to stress.
Biotic and Abiotic stress
Zahra Hajibarat; Abbas Saidi; Ahmad Mosuapour Gorji; Mehrshad Zeinalabedini; Mohammad reza Ghaffari; Rahim Ahmadvand
Abstract
Potato virus Y (PVY) and Potato virus X (PVX) are the most important potato-infecting agent causing yield loss and tuber quality reduction. In this study, an experiment was conducted in Karaj, Iran, to investigate the effects of mentioned viruses on the yield and resistance level of 33 potato genotypes. ...
Read More
Potato virus Y (PVY) and Potato virus X (PVX) are the most important potato-infecting agent causing yield loss and tuber quality reduction. In this study, an experiment was conducted in Karaj, Iran, to investigate the effects of mentioned viruses on the yield and resistance level of 33 potato genotypes. The experiment was performed based on randomized complete design in factorial format under two levels viruses with three replications. The results revealed that the viral infection had a significant impact on mean yield, seed yield (tuber size 35-55), ware yield (tuber size > 55 mm), and non-marketable yield (tuber size< 35). Based on cluster analysis for PVY, cluster VII was considered maximum resistant genotypes to PVY in terms mean absorption and yield, while cluster VI was identified susceptible genotypes in to PVY. According to cluster analysis of PVX virus, cluster I was considered highest resistant genotypes in terms mean absorption and yield and cluster III were maximum susceptible genotypes to PVX infection. Results of this study showed that genotype G23 with a mean-absorption of 0.01 and 0.032 for PVY and PVX, respectively, and mean yield of 4.1 kg/m2 was considered as a highly resistant genotype to both viruses. The concurrent selection of genotypes for high yield and resistant to both viruses (PVX and PVY) can facilitate potato breeding programs.
Bioinformatics
Mohsen Hosseini; Abbas Saidi
Abstract
Intracellular polyamine contents are regulated not only by biosynthesis and transport but also by catabolism through FAD dependent polyamine oxidases (PAOs). The results of various studies on PAO proteins in developmental processes and response to environmental stresses confirm the importance of this ...
Read More
Intracellular polyamine contents are regulated not only by biosynthesis and transport but also by catabolism through FAD dependent polyamine oxidases (PAOs). The results of various studies on PAO proteins in developmental processes and response to environmental stresses confirm the importance of this protein in plant life; however, there is no comprehensive study of phylogenetic and structural relationships of plant PAOs. In the present study, to better understand phylogenetic and structural relationships of PAO proteins, bioinformatics analyses were performed on 58 PAO protein sequences of 15 different plant species. Multiple clusters with gene duplications were identified in both dicot and monocot-species. According to the conserved motifs obtained by MEME and MAST tools, four motifs were similar in most plant species. As there is no structural information available on PAOs, structural analyses were carried out on PAOs from Oryza sativa and Arabidopsis thaliana as representative of monocot and dicot plants, respectively. Secondary structure analysis revealed that alpha helix dominated among secondary structure elements followed by random coils, extended strand and beta turns for all sequences. Tertiary structures were predicted with SWISS-MODEL server. The best templates with high similarity that their structure determined by experimental methods were selected. To our knowledge, this is the first report of phylogenetic and structural relationships of plant PAOs. Our results may provide a theoretical basis for future studies of functional and structural details of plants PAOs.
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 ...
Read More
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.
Molecular Plant Breeding
Zohreh Hajibarat; Abbas Saidi; Reza Talebi; Zahra Hajibarat
Volume 4, Issue 6 , October 2014, , Pages 85-94
Abstract
Identification of genetic diversity and classification of genetic resources (germplasm) are of important and essential activities in breeding and management of plant genetic resources. In order to study of genetic diversity of chickpea genotypes, 38 pair’s primers of SSR were used on 18 landrace and ...
Read More
Identification of genetic diversity and classification of genetic resources (germplasm) are of important and essential activities in breeding and management of plant genetic resources. In order to study of genetic diversity of chickpea genotypes, 38 pair’s primers of SSR were used on 18 landrace and 30 improved varieties. After genomic DNA extraction and PCR reaction, primers produced 117 polymorphic bands and the mean of polymorphic band per primer was 3.5. The highest value of polymorphic information content (PIC) belonged to TAA170 primer (0.77) and the lowest value of PIC belonged to Cstms5 primer (0.08). Mean of PIC for all primers was 0.48. Calculated Jacard similarity coefficient ranged from 0.47 to 0.94 among genotypes. In order to assess genetic relationships, cluster analysis was performed by method NJ with Splitstree (ver 4.13.1) software. Results of this study revealed that SSR molecular markers has a valuable potential for evaluation and discrimination of chickpea genotypes.
