Research Paper
Molecular Plant Breeding
Zeinab Shahabzadeh; Reza Darvishzadeh; Reza Mohammadi; Morad Jafari; Hadi Alipour
Abstract
Study of genetic diversity and association analysis of agronomic traits with ISSR and EST-SSR markers in tall fescue (Festuca arundinacea)
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Study of genetic diversity and association analysis of agronomic traits with ISSR and EST-SSR markers in tall fescue (Festuca arundinacea)
Research Paper
Bioinformatics
Behnaz Karami Lake; Mohammad Sohani; Amin Abedi
Abstract
The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. In the present study, using related database, 14 CaCA genes were identified in the maize genome and classified according to their structural ...
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The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. In the present study, using related database, 14 CaCA genes were identified in the maize genome and classified according to their structural organization and evolutionary association with the identified CAX, CCX and MHX proteins. Most of the ZmCaCA proteins had two Na_Ca_ex domains. All of the identified genes had at least one functional motif and gene structure of each CaCA subgroup is highly conserved. In the prediction of reactive miRNAs relative to CaCA genes in maize, 33 different miRNA variants were identified that regulate the expression of 13 CaCA genes through cleavage or inhibition of translation. In addition, several cis-acting regulatory elements in ZmCaCA genes were found to be related to hormones stress responses. The variable expression of most ZmCaCA genes at different stages of development indicates their distinct role in development. Expression of these genes in abiotic stresses (cold, salt, and drought) indicates their role in stress response. The greatest high expression and down regulation of gene expression is related to CAX genes. The results of this study provide basic data about phylogeny and putative function of these genes for future studies on the role of CaCA genes in maize.
Research Paper
Molecular Plant Breeding
Maryam Shirani-Bidabadi; Farhad Nazarian-Firouzabadi; Karim Sorkheh; Ahmad Ismaili
Abstract
Potato is the fourth most valuable plant for human nutrition. In addition to carbohydrates, potato tuber contains important vitamins and micronutrients for human health. During developmental stages of Potato; morphological, physiological and molecular changes occur. From the genetic point of view, studying ...
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Potato is the fourth most valuable plant for human nutrition. In addition to carbohydrates, potato tuber contains important vitamins and micronutrients for human health. During developmental stages of Potato; morphological, physiological and molecular changes occur. From the genetic point of view, studying these events is crucial for breeding potatoes with nutritional values and a higher yield. The next-generation sequencing methods generate abundant and useful genetic data for molecular breeding of crop plants. In this study, two different potato tuber developmental stages (S1 and S2) were chosen and sampled. Following RNA extraction and cDNA synthesis, Illumina RNA sequencing was performed in two replications for each stage. Bioinformatics analysis, gene ontology, and gene set enrichment analysis were performed. Finally, out of 1829 differential expression genes, 1186 genes were identified and valided by bioinformatics resources. The result of gene ontology comparison showed that 393, 483 and 669 genes were involved in biological processes, cellular components, and molecular functions, respectively. Most genes were present in the phenylpropanoid biosynthesis, biosynthesis of secondary metabolites and metabolic pathways. Peroxidase and membrane transporters coding genes were the most important genes at the beginning of tuber onset to tuberization. These results suggested that development in potato tuber activates metabolic pathways, which not only promotes growth and development but also activates the pathways involved in stress responses and synthesis of different compounds. Ten key genes were identified involved in starch biosynthesis, most of which showed a significant up-regulation, suggesting that the starch biosynthesis pathway starts from the onset of stolon development to tuber maturation.
Research Paper
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.
Research Paper
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.
Research Paper
Biotic and Abiotic stress
Mehraneh Taslimi; Atefeh Sabouri; Amin Abedi
Abstract
Drought is one of the most important limiting factors for economic produce crops especially rice in the world. In order to identify related markers to yield and agronomic traits under drought stress condition, 40 recombinant inbred lines F9 (RILs) derived from IR28 and Shah-Pasand varieties evaluated ...
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Drought is one of the most important limiting factors for economic produce crops especially rice in the world. In order to identify related markers to yield and agronomic traits under drought stress condition, 40 recombinant inbred lines F9 (RILs) derived from IR28 and Shah-Pasand varieties evaluated at Rice Research Institute of Iran (Rasht) in the spring and summer 2018, as randomized block design with three replications. In this regard, 110 SSR and EST-SSR markers were assessed on parents of population and identified 41 markers had proper polymorphism between two parents. According to the regression analysis results, 24 and 22 significant markers identified under normal and drought stress conditions respectively. The maximum adjusted (R2) under normal and drought stress conditions were assigned to RM3496 linked to days to flowering (24.8%) and RMES6-1 linked to panicle exsertion (28.1%), respectively. Two markers RM211 and RM6697 had the most number of significant relationship with different traits including panicle length, flag leaf length, number of filled grains per panicle, the total number of grain per panicle, and weight of filled grain per panicle under non-stress and drought stress conditions respectively. According to the bioinformatics searches, the maximum gene expression pattern under drought stress condition was related to gene with accession code LOC_Os01g43370. The identified informative markers and the detected genes by bioinformatics approaches after validation can be utilized in marker assisted-selection (MAS) or gene transfer approaches for improving rice yield and tolerance to drought stress.
